doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
METAGENOMIC AND FUNCTIONAL ANALYSIS OF HINDGUT MICROBIOTA OF A WOOD FEEDING HIGHER TERMITE
TABLE OF CONTENTS MATERIALS AND METHODS 2 • Glycoside hydrolase catalytic domains and carbohydrate binding modules used in searches that are not represented by Pfam HMMs 5 SUPPLEMENTARY TABLES • Table S1. Non-parametric diversity estimators 8 • Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies 8 • Table S3. Summary of numbers glycosyl hydrolases (GHs) and carbon-binding modules (CBMs) discovered in the P3 luminal microbiota 9 • Table S4. Summary of glycosyl hydrolases, their binning information, and activity screening results 13 • Table S5. Comparison of abundance of glycosyl hydrolases in different single organism genomes and metagenome datasets 17 • Table S6. Comparison of abundance of glycosyl hydrolases in different single organism genomes (continued) 20 • Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 23 • Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families 24 • Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. 25 • Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. 29 • Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. 30 SUPPLEMENTARY FIGURES • Fig. S1. Phylogenetic identification of termite host species 38 • Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota 39 • Fig. S3. Phylogenetic diversity of P3 luminal microbiota within the phylum Spirocheates 40 • Fig. S4. Phylogenetic diversity of P3 luminal microbiota within the phylum Fibrobacteres 41 • Fig. S5. Phylogenetic diversity of P3 luminal microbiota within the phylum Bacteroidetes 42 • Fig. S6. Phylogenetic diversity of P3 luminal microbiota within the phylum Chlorobi 43 • Fig. S7. Phylogenetic diversity of P3 luminal microbiota within the phylum Acidobacteria 44 • Fig. S8. Phylogenetic diversity of P3 luminal microbiota within the phylum Cyanobacteria 45 • Fig. S9. Phylogenetic diversity of P3 luminal microbiota within the phylum Firmicutes 46 • Fig. S10. Phylogenetic analysis of the glycoside hydrolase family 5 (GH5) diversity encoded by the P3 luminal microbiota 47 • Fig. S11. Phylogenetic analysis of the glycoside hydrolase family 9 (GH9) diversity encoded by the P3 luminal microbiota 48 • Fig. S12. Phylogenetic analysis of the glycoside hydrolase family 10 (GH10) diversity encoded by the P3 luminal microbiota 49 • Fig. S13. Phylogenetic analysis of the glycoside hydrolase family 11 (GH11) diversity encoded by the P3 luminal microbiota 50 • Fig. S14. Phylogenetic analysis of overrepresented conserved hypothetical gene family TOG1 (TIGR02145) encoded by the P3 luminal 51 microbiota • Fig. S15. Phylogenetic diversity of iron-only hydrogenases encoded by the P3 luminal microbiota 52 • Fig. S16. Domain composition of iron-only hydrogenase families found in the P3 luminal microbiota 53 • Fig. S17. Three-dimensional structure of a family 2 iron-only hydrogenase 54 • Fig. S18. Predicted hydrogen diffusion channels in a family 2 iron-only hydrogenase 55 • Fig. S19. Recovery of genes or partial genes encoding proteins relevant to the Wood-Ljungdahl pathway of CO2-reductive homoacetogenesis 56 • Fig. S20. Phylogeny of the only two putative formate dehydrogenases identified in the P3 luminal microbiota metagenomic dataset 57 • Fig. S21. Metagenomic formyl-tetrahydrofolate synthetases, markers of CO2-reductive homoacetogenic metabolism, affiliate with known 58 homoacetogenic Spirochetaetes, not Firmicutes. • Fig. S22. Phylogeny of carbon monoxide dehydrogenase catalytic Subunits (CooS) recovered during Nasutitermes P3 Metagenomic analysis. 59 • Fig. S23. Abundance distribution of “Signal Transduction Mechanism COG” genes and functional domains among metagenomic datasets and 60 representative single bacterial genomes.
www.nature.com/nature 1 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
GLYRDAVGAEWIGKKGIRALLTDSIEVGASNWTPRMVEEFRARRGYDPVPFLPALTGAVVGSAA GLYCOSIDE HYDROLASE CATALYTIC DOMAINS AND RSDAFLHDFRQTLADLLADAHYGTIAKVAHEQGLIVYGEALENGRPVLGDDLAMRAHADVPMA CARBOHYDRATE BINDING MODULES NOT ALWTYNRGSAPRPTLIGDMKGAASVAHIYGQNIVSAESMTAAFSPWAFAPADLKRVIDLEFVSG VNRPIVHTSVHQPVDDKLPGLSLAIFGQYFNRHDSWAEMARPWVDYMARTGFLLQQGRDHADI REPRESENTED BY PFAMS. For several CAZy GH and AWFHGEDMPVTALFEHGEPAGLPRRHGYDFVNADILAKVLKVEGGELVAPGGARYRALYLGGS SRVMTLPTLRRIAQLAEQGATVIGTAPERSPALQDDPTAFRALVARLWNGAPVTPVGQGRVIAET CBM families, no Pfam HMM is available. In these cases, DVEKALAGIGIGPDFSFAGAGPDADLRFLHRKLADGDLYFIRNGLFRPEKIEARFRVTGRQPELWR representative sequences were selected from the CAZy website, ATDGAVQPLS
and the sequence region corresponding to the family of interest >GH104==142853476 [Aeromonas salmonicida subsp. salmonicida A449] NCHPQMAAFLDLLAFAEGTKGLGDDGYNKLVNPAGLFTDYRTHPNVKVQVNPHLVSTAAGRY was determined. These sequence regions were then used in QFLSKHWSHYRDQLGLLDFGPESQDTWAIQLIRERKALADVVDGRIAQAVPKCANIWASLPGAG BLAST searches against the termite gut community YGQREHKLADLLAKFIEFGGVLA
metagenome to identify potential sequences belonging to these >GH104==12514804 [Escherichia coli O157:H7 EDL933] -6 NLNPQRKAFLDMLAWSEGTDNGRQPTRNHGYDVIVGGELFTDYSDHPRKLVTLHPKLKSTAAG CAZy GH and CBM families. An e-value cutoff of 10 was RYQLLSRWWDAYRKQLGLKDFSPKSQDAVALQQIKERGALPMIDRGDIRQAIDRCSNIWASLPG used in these searches. The following are the partial sequences AGYGQFEHKADSLIAKFKEAGGTVR
representing such GH and CBM families: >GH103==89952579 putative lytic murein transglycosylase [Saccharophagus degradans 2-40] MFSTLKKVFSTTALAAVITASPLALADYSEHPEAKAFIAKMVNEYGLSEKEVVRILKDANKQQSI LDAIARPAEKTKPWFEYRNIFLGESRITQGVEFWAENADTLAKASKEFGVPEQIIVAIIGVETRYGR >GH110==29610934 [Streptomyces avermitilis MA-4680] HAGSYRVIDALTTLGFDYPPRSTFFAKELENFLLLTTEQKQNPLALKGSYAGAMGYGQFMPSSYR MAHGCSGGAMSRFVFLGVALALLGGATSPAAAAPRVTPVVVDVDDYGADPTGRTDSTPAVAA AYAVDFDGDKKADIWNNPKDAIGSVANYFRAHKWQTGEPVMVRARIAEGYDESILDSRSRPSLT ALRHAKSVDRPVRIVFSKGTYQLYPERAETRELYMSNTVGADQRYRDKKIGLLVEDMHDVTVD ATEVAAKGFTPVDVEIPGDTKVMPIAYDGEKGKEYWLGYDNFYVITRYNRSHMYARAVWELSE GGGAKLVHHGLQTAFASIRSTDVTFQNFSFDYAAPEVIDATVATTGVTDGHAYRVLKIPAGSPYR EILYRHNS VNGTHITWLGETSPATGQPYWSGVDGLQYTQIHDPEAQRTWRGDNPLFNDVAAVTDLGGRRIRI DYTTAARPADAGLVYQMRLIERTEPGAFIWESKNVTMRSMNAYYLQSFGVVGQFSENISIDKVN >GH103==MLTB_ECOLI - Escherichia coli FAPDPRSGRSTASFADFVQMSGVKGKVSITRSLFDGPHDDPINIHGTYLEVVGKPGPSTLTLAYKH MFKRRYVTLLPLFVLLAACSSKPKPTETDTTTGTPSGGFLLEPQHNVMQMGGDFANNPNAQQFI PQTAGFPQFAPGDEVEFATKRTMTPLADAHAQVTAVDGPSGMDHTKPLTTMTVTFDRPVPAGV DKMVNKHGFDRQQLQEILSQAKRLDSVLRLMDNQAPTTSVKPPSGPNGAWLRYRKKFITPDNV ETGGTVVENITATPSVVISGNVFRNVPTRGILVTTRKPVLITGNRFDGMSMASIYVSADAYQWYE QNGVVFWNQYEDALNRAWQVYGVPPEIIVGIIGVETRWGRVMGKTRILDALATLSFNYPRRAEY SGPVADLTIRGNSFTRPSGPVIFVEPTNQVIDPATPVHHNISVEHNSFDIGDVTVVNAKSVGGFAFT FSGELETFLLMARDEQDDPLNLKGSFAGAMGYGQFMPSSYKQYAVDFSGDGHINLWDPVDAIGS GNTVRRLDGADHPPYTSPLFVFHGSSGIRIARNHYDKGLNTSVVTD VANYFKAHGWVKGDQVAVMANGQAPGLPNGFKTKYSISQLAAAGLTPQQPLGNHQQASLLRL DVGTGYQYWYGLPNFYTITRYNHSTHYAMAVWQLGQAVALARVQ >GH109==6137031 [Streptomyces coelicolor A3(2)] VRVAVIGLGNRGGGMITGWAAVPGCTVTAVCDIRADRAERAADRLESKGNPRPAEYGGSADSY >GH101==O86617_STRCO - Streptomyces coelicolor ARMLRRDDIDLVYIATPWEFHYEHGRAALLSGRHAVVELPVATELRQLWDLVDTSERTRRHLLL GRARVRRHGAVVAALGLTAGLLSAAALPAGAAPPRPAAAAAPAGAPTPVELSRGGLTVTVAKE SENCNYGRNELAMLKAAHDGLFGDLTNGHGGYLHDLRELLFSDTYYTDSWRRLWHTRSTASFY FPQVISYRLGRRGLDGRATALDGFTVNGESHRATTTVKAKGSRAVYTSTFEDLPGLTITSSITVTK PMHGLAPIAAAMDVNRGDRMTTLRATTTAPKGLADYRARFVPRDHPSWKETYINGDLVTCMIE ETTVVFAVEKISGEAAPGVRTLAIPGQSLVSVDSAEPGANLARTKISTDSTTTADRFVPVTGDTAP TAKGRTVRAEHDVSSPRPYSRINTLAGSRGIVEDYAGSAPTGARIYVEPDHGGHTWRDFETYRKE DKGPVGTPYAFVGNAQLSAGIITNATEDSPQDDNTDWNTRLQSRIVDEGEGRRRAELSAGTYTY YDHWLWQKVGDDAANNGGHGGMDYVLQWRTVQLMRAGLVPDIDVYDSAAWCSPVPLSVTSL HPEGATDPRVDTYELPRATVVLAADANRDGTVDWQDGAIAHREHMRRPLGADRVPERVVQRIP ARGGRPVEIPDFTRGAWRERRPGLDSAPTD FNFASQATNPFLKTLDNTKRISMATDDLGQWVLEKGYASEGHDSAHPDYGGNENVRAGGWKD LNRLTRTGAGYNADFAVHVNATEAYAQARTFTEDMVAGQADGWDWLNQAYHIDQRKDLGTG >GH109==124053159 [Elizabethkingia meningoseptica] AVLDRFKQLRKEAPGIRTVYIDAYYSSGWLADGLAAGLREMGFEVATEWAYKFEGTSVWSHW VRIAFIAVGLRGQTHVENMARRDDVEVVAFADPDPYMVGRAQEILKKNGRKPAKVFGNGNYDY AADKNYGGATNKGINSDIVRFIANADRDVWNVDPLLGGASVVEFEGWTGQDDWNAFYRNIWT KNMLKDKNIDAVFVSSPWEWHHEHGVAAMKAGKIVGMEVCGALTMDECWDYVKVSEQTGVP DNLPTKFLQHFQVLDWDRGRSARLTGGVDVKSVDGERRISMDGTEVLKGDTYLLPWQNAGKD LMALENVCYRRDIMAGLNMVRKDMFGELIHGTGGYQHDLRPVLFNSGINGKNGDGVEFGDKAF DGTSSPRDADKMYFYSASGGEHTFELTGQFAGTEDFTLYELTDQGRAEKARVTAHEGRVTLTAE SEAKWRTNHYKNRNGELYPTHGLGPLHTMMDINRGNRLLRLSSFASKARGLHKYVVDKGGESH KGQPYVLVPNGGRAPHRDAHYGEFTGLSDPGFNGGDLDAWNASGGAEIVRAGNGDNVVRLGE PNAKVEWKQGDIVTTQIQCNNGETIVLTHDTSLQRPYNLGFKVQGTEGLWEDFGWGDAAQGFIY DASGIAQRVRGLTPGERYTLGADVGIGPGERRETTLRVRGGKDSEARTFDITPARNRMASDEKRD FEKIMNHSHRWDGSEKWMKEYDHPMWKKHEQKAVGAGHGGMDYFLDNTFIECIKRNEAFPLD TYSQRASVSFTAPRDGSVTVELGAVAGGAPVVLDDVRVMVDTTAPLPRSQDGTVVAHDDFEGN VYDLATWYSITPLSEKSIAENGAVQEIPDFTNGKWKTVKNTFAINDDY RPGWGPFVKGDAGGVTDPRTSISDLHAPYSQKEWKNTYSPYDTGALKGRAVDDVLAGRHSLKS HAENTGLVHRTTPATVPFEEGHRYRVSFSYQTNVEGQWAWVTGADRVADGTTTSRDITRDVLA >GH107==115530293 [Flavobacteriaceae bacterium SW5] PALDTAAYSREFVAGCGDTWVGLRRLGSARGTDLVLDDFTVTDLGEADTGAACAAVTAPSGAE MKKTLPTKKSNLWFLMACLIITFHKVEAQVPDPNQGLRAEWMRGALGMLWLPERTFNGNIEGIR LSPGVPGEYVTAFTNHESAGAENVGIALQGLPEGWKAEVKEKDGNLFERVQPGATVRTTWLLTP IDDFLTQIKDIRTVDYVQLPLTSPNIFSPTHVAPHPIIESLWQGDTDANGDPINLVAPRESVDDPLLS PAGTAGTSATWQVTAAYAHEGATRTVSTGARAAVTDEPVLAPAST WLKALRAAGLRTEIYVNSYNLLARIPEDTQADYPDVSARWMEWCDTNTEAQAFINSQTYHEGN GRRKYMFCYAEFILKEYAQRYGDLIDAWCFDSADNVMEDECGDDPASEDVNDQRIYQAFADAC >GH101==Q8XMJ5_CLOPE - Clostridium perfringens HAGNPNAAIAFNNSVGDREGNPFTSATLFDDYTFGHPFGGAGNMVVPEALYTYNHDLVVFMQT GQVAVSNLPDVRGKVGLTGWFGNKNVTLDNLVVEELGGIMAPEVGPLEEQSIESDSMKVVLDN NNGYAFRDDTRTWNDNVVAHFFPKQSTTSWNAGNTPCLTDEQFVEWTSTGIVNGGGITWGTPL RFPTVIRYEWKGTEDVLSGASVDDLEAQYMVEINGEKRIPKVTSEFANNEGIYTLNFEDIGMTITL VRTNLENAPVLTLQPYALNQFELTDTYLKEFQSPGKPNWSRQYTILPAIYPGQPYSHNLVEGVDF KMTVNENKLRMEVTDIQEGDVKLQTLNFPNHSLASVSSLNNGKTASVLTTGDWNNINEEFTDVA WDPEGVGITGLTASGTLPAWLTISQTATGTWTLSGTPPVSEASNYTFELMAQDSDGVTNREVKLE KAKPGVKGKTYAFINDDKFAVTINNNTIEGGNRVVLTTENDTLPDNTNYKKVGISNGTWTYKEIL VISHPAGFTNPGDGTPVWFSNPMVLAKATALKDYGSLLKLGVDFYDFEGDVLTITKTSGPDWLV QDTTDQGSKLYQGEKPWSEVIIARDENEDGQVDWQDGAIQYRKNMKIPVGGEEIKNQMSYIDFN LTQNSDDTWRLSGMPTAADAGENSFTFNVSDGILSSDTEIKITVDHVAGFTNLGNGAPVWSSPIL IGYTQNPFLRSLDTIKKLSNYTDGFGQLVLHKGYQGEGHDDSHPDYGGHIGMRQGGKEDFNTLIE NLTDGKGSFAYNYTLQLGTDYYDFEGDALTITKTSGPDWLTIQQTDANSWKLSGTPINSDAGENS QGKEYNAKIGVHINATEYTMDAFEYPTELVNENAPGWGWLDQAYYVNQRGDITSGELFRRLDM FTFNLSDDTNSTTAEILINVIATIISDGNVEIKATANTTYGINTVASMYSAVQTAPDGLATYRISIDV LMEDAPELGWIYVDVYTGNGWNAHQLGEKINDYGIMIATEMNGPLEQHVPWTHWGGDPAYPN TPPTDKGIYSGSSGGITTTTSWGIGDGTDAIQNTIFRGSDNEWTESINNIKMVDFNANGGSLTTDN KGNASKIMRFMKNDTQDSFLADPLVKGNKHLLSGGWGTRHDIEGAYGTEVFYNQVLPTKYLQH VTMFFKSISIGNSQSVNDFVSLKVGGVISNPGRSANQYETIDLTLATSVSNIANFAIGTGNDSDTNK FQITKMSENEVLFENGVKAVRENSNINYYRNDRLVATTPENSIGNTGIGDTQLFLPWNPVDEANS WSVEGITVFVDFAGTLSVTNPIQDDVDSFKLYPNPAKDRIFINKQPVTVQIFDVTGKLVKVDFKGK EKIYHWNPLGTTSEWTLPEGWTSNDKVYLYELSDLGRTLVKEVPVVDGKVNLEVKQDTPYIVTK NELDISTLKQGLYILKIQTAEGNMLFEKFIKK EKVEEKRIEDWGYGSEIADPGFDSQTFDKWNKESTAENTDHITIENESVQKRLGNDVLKISGNEG ADAKISQSISGLEEGVTYSVSAWVKNDNNREVTLGVNVGGKDFTNVITSGGKVRQGEGVKYIDD >GH106==116228189 [Solibacter usitatus Ellin6076] TFVRMEVEFTVPKGVNSADVYLKASEGDADSVVLVDDFRIWDHPGHTNRDGYVFYEDFENVDE ALLAGLALGADPANITELQRGFQHPPDEARIMVRWWWFGPAVTKPELEREMRLMKQGGIGGFE GISPFYLSPGRGHSNRSHLAEKDISIDANQRMNWVLDGRFSLKSNQQPKEIGEMLTTDVSSFKLEP VQPTYALELDNAEKGIKNLPYMSPEFLEALRFTGEKAKELGLRMDLTLGSGWPFGGPHIPVELAS NKTYEFGFLYSLENAAPGYSVNIKNRDGEKIVSIPLEATGSNYAQDIFTKTKSVTHEFTTGDFAGD PRLRVARAAVTAGAAAINVPELQPSEKLIAAFLGNQELEAAGSQSFRLPPSAAGQVTFFISSHTRQ YYITLEKGDGFKEVILDNIYVKEIDKSIESPELAHVNLNTVEHDLEVGQSVPFAINALMNNGANVN TVKRPAVGAEGWVLNHYDRAAIEQHFKSVGEPMLNALAKTPPAAIFSDSLEVYNSDWTGDFLA LEEAEVEYKVSKPEVLTIENGMMTGASEGFTDVQVNITVNGNKVSSNTVRVKVGNPEVEEEEVI QFAKRRGYDLKPYLPALAGDIGEKTGAIRNDWGQTLSELAEENYLKPLTAWAHQHNTKFRSQTY VNPVRNFKVTDKTKKNVTVSWEEPEKTYGLEGYVLYKDGKKVKEIGADKTEFTFKGLNRHTIY GIPPVTLSSYSLVDLPEGEGTQWRHFSSTRWATSASHLYNRPVTSSETWTWLHSPVFRATPLDMK NFKIAAKYSNGELSTKESITVRTAR AEADLHFLQGVNQLVAHGWPYSPPSVGEPGWRFYAAAVFNEHNPWWIVMPDIATYMQRVSWM LRQGKPVNDVAVYLPTHDAFAGFTLGRDSVNQAMEGILGPKLVPTILDAGYGFDFIDDGAIAAG >GH99==119765938 [Shewanella amazonensis SB2B] GVPHKILIVPGAERIPLATYQKIEEYRRDGGKVFFTKRLPSLAPGLREEGDTAKIRELSAKHVVTG FYYGWYGNPQQDGQWQHWNHRVLPYGDIPLEGRLDFPGADDIGANFYPSLGSYSSHDPEIIEQH DDGLAGALHDALPADFTAPPEIGVVHRKLAYADVYFLANTSNHAVKGAAKFRASGMPAAWWD LEMMRQAGIGVVSVSWLGADDFAARSIDFFMDKAAEKGLQINFHIEPNYRSAEEFHAIIAELMRK PVTGKSSKADLNLELAPYESRVLVFSRAGGAVMGQAMSLPEVDISSDWTITFPGEQPVKMATLRP FGTHPALYRYRGKPLYYVYDSYKMPVSEWQKLLLPGGELSLRTPELDGQFIGLWVNQGEEAFFL WTDEENRKFYSGTATYERKVTATPAMAAAHVFLNFGEGTVADPASERRAPSGMRAWLESPVRE DTGFDGFYTYFASEGFVWGSTSTNWPYLAGWASRHGKLFIPSVGPGYADDRIRPWNGANFKARE AAQVFVNGKPAGAVWKAPYEVDVTGLLQAGENSIRVVVANLALNVLAKGPLPDYKELTAKYG QGRYYDRMFSQALNTKPDIVTITSFNEWHEGTQIEPAVVKQLPDYRYLDYGDLPEDYYLQRTLD EKFQAQDMQSVRALPGGMMGPVKLVS WSRKLSAIPVNS
>GH106==45219920 [Sphingomonas paucimobilis] ALLACAASFAVPSWADELADGFHNPPQSARPRVWWHWMNGNVTKDGISKDLDWMQRVGIGG >GH99==29341178 [Bacteroides thetaiotaomicron VPI-5482] VQNFDANLSTPQIVPERLIYMTEQWKDAFRHAVREADARGLEFAIAVSPGWSETGGPWVKPEDA FYYNWYGNPSVDGEMKHWMHPIALAPGHSGDVGAISGLNDDIACNFYPELGTYSSNDPEIIRKHI MKKLVWAEADLRGGQRLKGALPAPPSITGPFQSAQFHEALPGGAEMQTLPAFYRDARVLAYSLV RMHIKANVGVLSVTWWGESDYGNQSVSLLLDEAAKVGAKVCFHIEPFNGRSPQTVRENIQYIVD PKALPRPAVSEGDGSPVDAAPLLDGDLETVARIGKGDAARPGTMVLDYGKPVTVRSASLFVPHA TYGDHPAFYRTHGKPLFFIYDSYLIKPAEWAKLFAAGGEISVRNTKYDGLFIGLTLKESELPDIETA RPPFGDPDYRPALEVEQDGGWRRIGAFPLTEVATTISFAPVTGRRFRLVLAPNDAPRAPGLGEGAP CMDGFYTYFAATGFTNASTPANWKSMQQWAKAHNKLFIPSVGPGYIDTRIRPWNGSTTRDREN GAITMDVFARPQSDTLAIGDFRLLAEARIDRFEAKAGFALVSDYNALAEKSAADLPAIDPAKVVD LTDRLRPDGTLDWTAPAGSDWRIVRMGYSLTGKTNHPATPEATGLEVDKYDPAAVRRYLETYL
SUPPLEMENTARY INFORMATION Warnecke et al: Page 2 www.nature.com/nature 2 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
GKYYDDMYKAAIESGASYISITSFNEWHEGTQIEPAVSKKCDAFEYLDYKPLADDYYLIRTAYW >GH94==Q8VP44_CLOTM-N - Clostridium thermocellum VDEFRKARSAS MKFGFFDDANKEYVITVPRTPYPWINYLGTENFFSLISNTAGGYCFYRDARLRRITRYRYNNVPID MGGRYFYIYDNGDFWSPGWSPVKRELESYECRHGLGYTKIAGKRNGIKAEVTFFVPLNYNGEVQ >GH97==89951605 a-glucosidase-like protein [Saccharophagus degradans 2-40] KLILKNEGQDKKKITLFSFIEFCLWNAYDDMTNFQRNFSTGEVEIEGSVIYHKTEYRERRNHYAFY MHNNSQQIPQRTAHLPPVTPKWRSALRLPVIALALCSLSTISANALAKTFELTSPNEQLKIEVHTG SVNAKISGFDSDRDSFIGLYNGFDAPQAVVNGKSNNSVADGWAPIASHSIEIELNPGEQKEYVFIIG KQTTFEVHLNNKQVLAPSSIDLMLMSGEKLASNITVKQEKRYAVSNTLTPAVSHKSSKIAENYNA YVE LNLAFSNNFGIDFRAYNDGFAYRFTGERAGEIIIKNEHLALNFTQNATTLFPEEETFISHFERLYLPE TVANISPKRFASLPTYIKSNDVNVVVTEADLYDYPGLFLFGTNKNGFTAGFPNAVAKTTPKAGSE >GH94==Q9X2G3_THEMA-N - Thermotoga maritima DRNQEFEYENYIAKTSGTRTFPWRVAIITKEDTDLVASQLVYLLSSENKIGDTSWIKPGRIAWDW MRFGYFDDVNREYVITTPQTPYPWINYLGTEDFFSIISHMAGGYCFYKDARLRRITRFRYNNVPTD YNANNLFDVDFKAGLNTQTYKYYIDFAEKYGLEYVILDEGWTKTTTNTKESNPDIDVKELIAYG AGGRYFYIREENGDFWTPTWMPVRKDLSFFEARHGLGYTKITGERNGLRATITYFVPRHFTGEVH KKKNVAIILWTLWEPLDKDYENILALYAQWGAAGIKVDFMQRADQYMVNYYEKIAKAAAKNK YLVLENKAEKPRKIKLFSFIEFCLWNALDDMTNFQRNYSTGEVEIEGSVIYHKTEYRERRNHYAF LLVDYHGGFKPAGLRRAYPNVMTYEGVKGNENNKWSADITPEHNVTLPYIRMVAGPMDYTPGA YSVNQPIDGFDTDRESFIGLYSGFEAPQAVVEGKPRNSVASGWAPIASHYLEIELAPSEKKELIFIL LRNKQLANHNVNHFRPEAIGTRAHQLAMYAVFESALQMLCESPSTYLREPLITEYIAKFPSVWDE GYVE TRVLKGEVANYILLARRKGDTWYIGAMTDMTARTLTLNLSFLDGGKYSLHGVADGLNVEQYAE DYQFIHQTVTAKDSLQLNLAAGGGWSAVITPAK >GH94==89950565- [Saccharophagus degradans 2-40] MKFGHFDDKAREYVITDPKTPYPWINYLGNEDFFSLVSNTGGGYSFYKDAKFRRLTRYRYNNVP >GH97==P71094_BACTN - Bacteroides thetaiotaomicron VDNGGKYFYINDSGDVWSPGWKPVKAELDAYSCAHGLSYTRITGERNGIQAEVLSFIPLGTWAEI MKKRKILSLIAFLCISFIANAQQKLTSPDNNLVMTFQVDSKGAPTYELTYKNKVVIKPSTLGLELK QKVSLKNTSGATKKFKLFSFAEWCLWNAEDDMTNFQRNFSTGEVEVEDSVIYHKTEFKERRNHY KEDNTRTDFDWVDRRDLTKLDSKTNLYDGFEVKDTQTATFDETWQPVWGEEKEIRNHYNELAV AFYSVNAPIQGFDTDRDKWKGLYNDFDKPDAVFEGEPRNSEAHGWSPIASHYLEVELAPGESKD TLYQPMNDRSIVIRFRLFNDGLGFRYEFPQQKSLNYFVIKEEHSQFGMNGDHIAFWIPGDYDTQE LIFVLGYIE YDYTISRLSEIRGLMKEAITPNSSQTPFSQTGVQTALMMKTDDGLYINLHEAALVDYSCMHLNLD DKNMVFESWLTPDAKGDKGYMQTPCNTPWRTIIVSDDARNILASRITLNLNEPCKIADAASWVK >GH94==89950153-N [Saccharophagus degradans 2-40] PVKYIGVWWDMITGKGSWAYTDELTSVKLGETDYSKTKPNGKHSANTANVKRYIDFAAAHGFD MLKAINNGERYQLTSPTAMPQSASFLWNKKMMIQVNCRGYAVAQFMQPEPAKYAYAPNLEAK AVLVEGWNEGWEDWFGNSKDYVFDFVTPYPDFDVKEIHRYAARKGIKMMMHHETSASVRNYE TFMQPEQPYYAHHPGRFFYIKDEETGEIFSAPYEPVRSQLNNFSFNAGKSDISWHIAALGIEVELCL RHMDKAYQFMADNGYNSVKSGYVGNIIPRGEHHYGQWMNNHYLYAVKKAADYKIMVNAHEA SLPVDDVVELWELKIKNGGAQPRKLSIYPYFPVGYMSWMNQSGDYSQTAGGIIASCVTPYQKVA TRPTGICRTYPNLIGNESARGTEYESFGGNKVYHTTILPFTRLVGGPMDYTPGIFETHCNKMNPAN DYFKNKDFKDKTFFLHETAPAAWEVNQKNFEGEGGLHNPNAIQQETLGCGNALYETPTAVLQY NSQVRSTIARQLALYVTMYSPLQMAADIPENYERFMDAFQFIKDVALDWDETNYLEAEPGEYITI RRELAAQEQQTFRFIFGPA ARKAKDTDDWYVGCTAGENGHTSKLVFDFLTPGKQYIATVYADAKDADWKENPQAYTIKKGIL TNKSKLNLHAANGGGYAISIKEVK >GH93==Q9K438_STRCO - Streptomyces coelicolor MRNPSPTLRRSPALLGVLALLTALLSLWSQPASAAPVGQVLASPDLAAHPQGDNSYPRAVRLDH >GH96==121309479 [marine bacterium JAMB-A33] DGSAGQTMLATYAKREQGATNTLPVHRSTDGGRTWSAAPISTITSHTPGWDIEAPVLYEVPRTAN AIPSPIYNPDDHFVAEIQGPQTDVTYLKKPVEIPANKKVLKSDVWYTYPQNRELEGYDNFGATGA GLNQGDLLAAGTAWQAGDYTTQRVEVFKSTDHGQSWQYLSDCTRTSGLPDTIGHGIWEPWFLL FWGHPPEHDFYDDTVIMDWAVDAVYAFQAEGYEYTARGEFDWGYGWFTEYTTNPQPHYVRTL APDNTLACFISDERPANSPTNNQVIGHYTSTDGGRTWSGTLTQDVAFPADNLARPGMSIVVPLPD DDRNVRMTFMGYLSHDGYNNNWLSNHSPAFVPFMKSQVDQILKANPDKLMFDTQTNSTRSTD GRFMMAYEMCRDATDADHACEVYTKTSPDGLNWAPADDPGTLVRTADGRELLHTPYLAWVPG MRDFGGDFSPYAMENFRVWLSKKYSTGELAALGINDINSFDYGDFLRAQGVTHTSWSNAGDTLS GGPDGTLLMSGQRVVSGPTGNKTVLSESGTVVFANTHLGTGEWTEIEAPVRTDPTGGYNPGEPS GNIPLQEDYIYFNRDVWNQKFAEVLDYIRQQQPDIEIGASTHLFESRGYVFNENLTFLSGELNLGA CPGYSSPIVPRADGTSFLYLTATWLGTGNQCQVRFGTGGLGGP RTTISELPTNILVHLKGAQAVDKTLVYFPYPWEFDELRLQDAPRFGRGWVAQAYAYGGLFSIPAN VWVGGEVWTWSPGADNYRDIYLFVRAQADLLDDYTSYSKVGLVHAMYSSMKAGFIDGGNQIQ >GH91==72132980 [Bacillus sp. snu-7] SSTKLLTEGNINFDLLVFGDEGYPVVPRPEDFDKFDHIFFDGDEQYLTAEQQALLDQQGDKVRHI YDVTTWRIKAHPEVTAQSDIGAVINDIIADIKQRQTSPDARPGAAIIIPPGDYDLHTQVVVDVSYLT GQRGTVSGIEITVSISGTESNETVSAVSRIHETDAAAPYVVHLVNRPFAGGVTPTLNNVEVAIPQSY IAGFGHGFFSRSILDNSNPTGWQNLQPGASHIRVLTSPSAPQAFLVKRAGDPRLSGIVFRDFCLDG FPEVVTGATLHLPDGTSTSLTLSTNADGDVVLPVNNLEVWGILELAH VGFTPGKNSYHNGKTGIEVASDNDSFHITGMGFVYLEHALIVRGADALRVNDNMIAECGNCVEL TGAGQATIVSGNHMGAGPDGVTLLAENHEGLLVTGNNLFPRGRSLIEFTGCNRCSVTSNRLQGFY >GH96==Q9LAP7_9ALTE - Alteromonas agarilytica PGMLRLLNGCKENLITANHIRRTNEGYPPFIGRGNGLDDLYGVVHIAGDNNLISDNLFAYNVPPA AVKQPRVYNPNEHIVAEIQGPATGLQYLKTPVEIPLANKVLKSDVWYTYPQNRNLVVDGDTPYA NIAPAGAQPTQILIAGGDANVVALNHVVSDVASQHVVLDASTTHSKVLDSGTASQITSYSSDTAIR DFGATGAFWGHPPEHDFYDDTVIMDWAVNVVDDFQSEGFEYTARGEFDWGYGWFTEFTTNPQP PTP HYVQTLDGRNVRMTFMGYLSHDGYNNNWLSNHSPAFVPFMKSQVDQILKANPDKLMFDTQTN STRSTDMRTFGGDFSPYAMENFRVWLLKKYSNAQLVSMGINDITSFDYGAYLRAQGITHTDWSN >GH91==1110443 [Arthrobacter globiformis] AGDTISGNIPMMEDFIYFNRDVWNQKFAEVLEYIRQQRPNIEIGASTHLFESRGYIFNENITFLSGE YDVTTWSGATISPYVDIGAVINQIIADIKANQTSQAARPGAVIYIPPGHYDLLTRVVVDVSFLQIKG LNLGARTSISELPTNILVHLKGAQAVDKTLAYFPYPWEFDELRIQNAPRFGRGWVAQAYAYGGL SGHGFLSEAIRDESSTGSWVETQPGASHIRVKNTDGNREAFLVSRSGDPNVVGRLNSIEFKGFCLD FSIPANVWVGGEVFTWSPGADNYRDIYQFVRAQANLLDGYTSYAKAGYVHAMFSSMKAGFIDG GVTDSKPYSPGNSKIGISVQSDNDSFHVEGMGFVYLEHAIIVKGADAPNITNNFIAECGSCIELTGA GNQVQSSVKILTEDNINFDMLVFGDAGYPVVPRQADFDKFEYIFYDGDLNYLTAEQQAVLDAQG SQVAKITNNFLISAWAGYSIYAENAEGPLITGNSLLWAANITLSDCNRVSISSNKLLSNFPSMVALL SKVKHIGQRGTIAGLQINVSINGSVSNETVSAVSRIHETDSTAPYVVHLINRPFAGGVTPILNNVEV GNCSENLIAANHFRRVSGDGTSTRFDDLFGLVHIEGNNNTVTGNMFSFNVPASSISPSGATPTIILV AIPASYFPQGVTSAKLHLPDGSSSTVAVSTNANGDTVVSVSNLEVWGILELAH KSGDSNYLATNNIVSNVSAMVVLDGSTTATRIIYSAKNSQLNAYTTSYTLVPTP
>GH95==71915747 [Thermobifida fusca YX] >GH90==TSPE_BPP22 - Bacteriophage P22 MTYSTPTQGTATRLPAASWEEALITGNGRQGVLAHSMQTQIRLTLSHERLFWPREEPLPAPHTAP MTDITANVVVSNPRPIFTESRSFKAVANGKIYIGQIDTDPVNPANQIPVYIENEDGSHVQITQPLIIN ALDELRSLIRAGRPRAAAEHVTELARTEHPGYAHTRWIDPLTGAGTLTFIPDAPAWGPIHRTCDY AAGKIVYNGQLVKIVTVQGHSMAIYDANGSQVDYIANVLKYDPDQYSIEADKKFKYSVKLSDYP TTGVVREELPNGIRHDVFASRADNVIVIRLSADHELAGTLQLAPLPGEPPTPADTRLTSTPHTLTLH TLQDAASAAVDGLLIDRDYNFYGGETVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFME TAFARTWPTTLTGYTLTCRIIAPGGHLRPLEPGRLHLSGARHVLLLVRTTVTSETTPAPGDPDLAR STTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITS LTPDFDTLLRRHTAHHTPLITRSRIRLSPRQPHPDPLPGEALLAQGPTPHLMERLVEAGRYATVCAI TLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGR GELPPTLQGVWSGTYSPPWSSGYTFDGNLASAVAALHPLGTPELMLPVFDLVDTLLDDFTHNAQ TSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPV RLYGCRGILVPPHASTHGRHNHFGPEWCLTLWTAGAAWLARLYWDHYSYTRDPGFLRERALPF WDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNI LHHAAAFYEDFLTDDGFVPSYSPENTPADSDSQACANATMDLAAVRDLVRNLLRAHRILDLPGA TVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQGLTIDAPN RRWAELGARLPRYRIAPTGELAEWATPAGPLDQTDRHTHRHASHLFPFWYEGDPAFADPTLRAA STVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGAGS AVRAIRARLAWWRSAASDEMAFGLVQLGLAAANLGLATEAATTLELMATRYWRPTLVSTHNR GSAYTQLTAISGSTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVK RALFNTDICGGFPAVVAAMLLRSREGRCDLLPALPPAWPEGEARGLCGRGGVLVDHLEWTPTR KPNGELVRLTLATL MRARLRARHTTRVRIGLPDGATRVVTLDPDQAVDVTAPLTLHQ >GH90==56128763 [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150] >GH95==34451973 - [Bifidobacterium bifidum] MTDITANVVVSNPRPIFTESRSFKAVANGKIYIGQIDTDPVNPANQIPVYIENEDGSHVQIAQPLIIN VKATSTADGTVKTLTEGNGEDNYTIDTSAFDSASIGVYPVTVKYNKDPEIAASFNAYVIASVEDG AAGKIVYNGQLVKIVTVQGHSMAIYDANGSQVDYIANVLKYDPDQYSIEADKKFKYSVKLSDYP GDGDTSKDDWLWYKQPASQTDATATAGGNYGNPDNNRWQQTTLPFGNGKIGGTVWGEVSRER TLQDAASAAVDGLLIDVDYHFYNGEKVDFGGKVLTIECKAKFIGDGNLIFTKLGKGSRIAGVFME VTFNEETLWTGGPGSSTSYNGGNNETKGQNGATLRALNKQLANGAETVNPGNLTGGENAAEQG STTTPWVIKPWTDDNQWLTDAAAVVATLKQSKTDGYQPTVSDYVKFPGIETLLPPNAKGQNITS NYLNWGDIYLDYGFNDTTVTEYRRDLNLSKGKADVTFKHDGVTYTREYFASNPDNVMVARLTA TLEIRECIGVEVHRASGLMAGFLFRGCHFCKMVDANNPSGGKDGIITFENLSGDWGKGNYVIGGR SKAGKLNFNVSMPTNTNYSKTGETTTVKGDTLTVKGALGNNGLLYNSQIKVVLDNGEGTLSEGS TSYGSVSSAQFLRNNGGFERDGGVIGFTSYRAGESGVKTWQGTVGSTTSRNYNLQFRDSVVIYPV DGASLKVSDAKAVTLYIAAATDYKQKYPSYRTGETAAEVNTRVAKVVQDAANKGYTAVKKAH WDGFDLGADTDMNPELDRPGDYPITQYPLHQLPLNHLIDNLLVRGALGVGFGMDGKGMYVSNI IDDHSAIYDRVKIDLGQSGHSSDGAVATDALLKAYQRGSATTAQKRELETLVYKYGRYLTIGSSR TVEDCAGSGAYLLTHESVFTNIAIIDTNTKDFQANQIYISGACRVNGLRLIGIRSTDGQGLTIDAPN ENSQLPSNLQGIWSVTAGDNAHGNTPWGSDFHMNVNLQMNYWPTYSANMGELAEPLIEYVEGL STVSGITGMVDPSRINVANLAEEGLGNIRANSFGYDSAAIKLRIHKLSKTLDSGALYSHINGGPGS VKPGRVTAKVYAGAETTNPETTPIGEGEGYMAHTENTAYGWTAPGQSFSWGWSPAAVPWILQN GSAWTQLTAISGNTPDAVSLKVNHKDCRGAEIPFVPDIASDDFIKDSSCFLPYWENNSTSLKALVK VYEAYEYSGDPALLDRVYALLKEESHFYVNYMLHKAGSSSGDRLTTGVAYSPEQGPLGTDGNT KPNGELVRLTLATL YESSLVWQMLNDAIEAAKAKGDPDGLVGNTTDCSADNWAKNDSGNFTDANANRSWSCAKSLL KPIEVGDSGQIKEWYFEGALGKKKDGSTISGYQADNQHRHMSHLLGLFPGDLITIDNSEYMDAA >GH87==Q93R89_9ACTO - Streptomyces sp. J-13-3 KTSLRYRCFKGNVLQSNTGWAIGQRINSWARTGDGNTTYQLVELQLKNAMYANLFDYHAPFQI DTAASYTLDLIEAEETGSAATLPSGYVSAADLGVTPGGQDVTAALNNALNTAKNQGKGLFLPAG DGNFGNTSGVDEMLLQSNSTFTDTAGKKYVNYTNILPALPDAWAGGSVSGLVARGNFTVGTTW TYKISDHINLSGVKLRGAGVWHTVLRGTGLKGGLFGQGGTSTIENLMIDGENTVRDDAGGQAAI KNGKATEVRLTSNKGKQAAVKITAGGAQNYEVKNGDTAVNAKVVTNADG EGDFGTGSVIKNVWIQHTKVGLWISGPTTGLKAGDLRIRNTYADGVNLHGAVRDTVISNSSIRGT GDDALAMWSDGAAVTNSAFRNNTVQLPSLANGAAVYGGNGNSVENNLISDTVVAAAGITVSTR >GH94==1336047-N [Clostridium stercorarium] FGEPFSGTTTVSGNLLRRTGSMEVNWNTKLGALWVYADQHDITQPVVLRNNTVEDSTYSGLLIS MKFGYFDDVNREYVITTPATPYPWINYLGCQDFFSLISNTSGGYCFYRDARLRRITRYRYNNVPID WEKQVSDLRVDGLTIDRTGANGIEGNAGGKGTFSNTKITGTAEAPLNMTGGFTIQRGSGNSGW SGGRYFYIYDSGDYWTPGWMPVKRELDRYECRHGLGYTRITGERNGVEVSQLAFVPLNYNGEV NQVVITNKSGSEKEIALFSFVEFCLWNAMDDMTNFQRNFSTGEVEVEGSAIYHKTEYRERRNHY >GH87==110743487 [Bacillus circulans] AFFWVNSPIDGFDTDRESFLGLYNGFDSPKNVAAGKPTNSIASGWSPIASHYIKMSLKPGEKRSYI ADSLEYGVDFLEIEAVPAAIARPANSVSVTDFGAVANDGQDDLAAFEAAVNAAVTSGKILYIPAG FVLGYVE TFHLGNMWKIGSVANKINNITIMGAGIWHTNIQFTNPNQASGGISFRVTGQLDFSHIYMNSNLRSR YGEQAVYKGFMDNFGTNSKVHNVWVEHFECGFWVGDYAHTPAIIANGLVIENSRIRNNLADGV NFAQGTSNSTVRNSSIRNNGDDGLAVWTSNVNGAPAGVNNTFSYNTIENNWRAAGIAFFGGSGH
SUPPLEMENTARY INFORMATION Warnecke et al: Page 3 www.nature.com/nature 3 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
KATHNLIVDTVGGSAIRMNTVFPGYHFQNNTGIVFSDTTIINSGTSRDLYNGERGAIDLEASNDPIK NSIDLSTRFSPFLDQAKSVLSANNPARDNLTYNIVDGTVNGWAVNDVSKNADLDFLYSEIWYLSD NVTFTNIDIINTQRSAIQFGYGGGFENIVFNNININGAGKDGVLTSRFSSPHPGAAIYTYTGNGSATF SYNQLKNYIEQLRANGGNKAVVLAAYMNYADNAGTRY NNLTTNDIAHPNLYFIQNGFNLTIQ >GH64==E13B_CELCE - Cellulosimicrobium cellulans (Arthrobacter luteus) >GH86==89951900 [Saccharophagus degradans 2-40] MPHDRKNSSRRAWAALCAAVLAVSGALVGVAAPASAVPATIPLTITNDSGRGPIYLYVLGERDG TCANTPALEFANEQGCSSSQVANTHVVNVSVNANFKRSVNGVFDFGRRRHMTAHTAIHEPDWV VAGWADAGGTFHPWPGGVGPVPVPAPDASIAGPGPGQSVTIRLPKLSGRVYYSYGQKMTFQIVL GHTDKLNYLFNTLDVYMGRDNGSATWKFNDTTEDPNKPNWPNMDYMVERGKGLREAHDQNP DGRLVQPAVQNDSDPNRNILFNWTEYTLNDGGLWINSTQVDHWSAPYQVGVQRADGQVLSTG LFKRFSAEKQLLIAGTNPHALYPTLSWFPNAFTWSGWQPKNIETSAAWVGQYMEHYFANASNG MLKPNGYEAFYTALEGAGWGGLVQRAPDGSRLRALNPSHGIDVGKISSASIDSYVTEVWNSYRT YVGEQLPEYWEVVNEPDMKMKTGQFMVTNQEAIWEYHNLVAQEIRDHLGAEAPPIGGMTWGQ RDMVVTPFSHEPGTQFRGRVDGDWFRFRSGSGQEVAAFKKPDASSVYGCHKDLQAPNDHVVGP HDFYRRDGISRFADDSYDQWITNDDQVLQAEARAFYRNAMATTVDDTRDQDWYQWDVMWKG IARTLCAALVRTTALTNPNQPDANSAGFYQDARTNVYAKLAHQQMANGKAYAFAFDDVGAHE FMDAAGDNMDFYSVHIYDWPGENVGDTTVVRRGGHTSAMLEMMEWYDVKRNGFNNRKPIVL SLVHDGNPQAAYIKLDPFTGTATPLGNGGSTEQPGTPGGLP SEYGSVNGAWDNRAHEERYDIASIKAFNGMLMQFLERPDYVIKSLPFTPAKPLWGYLPGGCGYD DAVACTTRYHYAMLIEDELNSGNWEWSSYIKFYELWADIDGTRVDSKSSDVDVQVDSYVKGNE >GH58==115513819 [Escherichia coli APECO1] LFVILNNLEAADTTVNLDVSGIASVQNVELRNMHFDIQETHLDRHHMSAAPKTVTLAADATVVL MTVSTEVDHNEYTGNGVTTSFPYTFRIFRKSDLVVQVSDLNGNVTELVLDTGYTVTGAGTYSGG RYTLASSVAVNNTVVEKKYF SVVLPSPLATGWRITIDRVLDVVQETDLRNQGKFFPEVHEDAFDYLTMLIQQCFGWFRRALMKPS LLAKYYDAKQNKISNLADPSFEQDAVNNRSMRNYVDAAIAGVVGGFGWFIQYGSGAVYRTFQD >GH86==AGAR_ALTAT - Alteromonas atlantica KMRDAISPKDFGAVGDGINDDSTAISACLEASSPGYKIDGLGLTFKVSTLPDVSRFKNARFLFERIP MLKVIPWLLVTSSLVAIPTYIHATTEVVVNLNVKHSVEGKSEFERKNHIKLHSTLNDNDWQGEED GQPLFYASEDFIQGELFKITDTPWYNAWTQDKTFVYDNVIYAPFMAGDRHGVNNLHVAWVRSG KLKYMMEELDVYFGRDNGGTVWNFNQAIEDPANIGYADPQNIIARGQAQRETNWGQNKSALHQ DDGKTWTTPEWLTDLHENYPTVNYHCMSMGVVRNRLFAVIETRTVSGNKLQVAELWDRPMSR YDGRGDLMIGGQPRAHYLGNTSPCCGGSAWQAKGGDAVGDFLGQYVNEFFRSAGDPVTKGHL SLRVYGGITKAANQQVAYIRITDHGLFAGDFVNFSNSGVTGVTGNMTVTTVIDKNTFTVTTQNTQ APVYFEVLNEPLYQVTDAPHELGLEQPIPPIDIFTFHNDVADAFRQHNTHIKIGGFTVAFPIFEQREF DVDQNNEGRYWSFGTSFHSSPWRKTSLGTIPSFVDGSTPVTEIHSFATISDNSFAVGYHNGDIGPR ARWEERMKLFIDTSGSHMDVYSTHFYDLEDDNRFKGSRLEATLDMIDQYSLLALGETKPHVISEY ELGILYFSDAFGSPGSFVRRRIPAEYEANASEPCVKYYDGILYLTTRGTLSTQPGSSLHRSSDLGTS GGRNRPMENAPWSALRDWWFLKTASPMLMQFLSRPDSVLTSIPFVPIKALWGTAADGTPYNWR WNSLRFPNNVHHSNLPFAKVGDELIIFGSERAFGEWEGGEPDNRYAGNYPRTFMTRVNVNEWSL LLRQQKEAPNETGENWVFTEMVKFYQLWSDVKGTRVDTFSTNSDFLIDSYVQNDKAYVLISNLT DNVEWVNVTDQIYQGGIVNSAVGVGSVCIKDNWLYYIFGGEDFLNPWSIGDNNRKYPYVHDGH EQAEKIVVHKYGAPASSQPTTRIKHLYLKGAAPRLMKQVMRQISKKSRLLLKRLW PADLYCFRVKIKQEEFVSRDFVYGATPNRTLPTFMSTSGVRTVPVPVDFTDDVAVQSLTVHAGTS GQVRAEVKLEGNYAIIAKKVPSDDVTAQRLIVSGGETTSSADGAMITLHGSGSSTPRRAVYNALE >GH82==Q9F5I8_9ALTE - Alteromonas sp. ATCC 43554 HLFENGDVKPYLDNVNALGGPGNRFSTVYLGSNPVVTSDGTLKTEPVSPDEALLDAWGDVRYIA MRLYFRKLWLTNLFLGGALASSAAIGAVSPKTYKDADFYVAPTQQDVNYDLVDDFGANGNDTS YKWLNAVAIKGEEGARIHHGVIAQQLRDVLISHGLMEEESTTCRYAFLCYDDYPAVYDDVITGQ DDSNALQRAINAISRKPNGGTLLIPNGTYHFLGIQMKSNVHIRVESDVIIKPTWNGDGKNHRLFEV REMPLTDNDGSIIVDEDDNPVMVMEDIIERVEITPAGSRWGVRPDLLFYIEAAWQRREMDKIKERI GVNNIVRNFSFQGLGNGFLVDFKDSRDKNLAVFKLGDVRNYKISNFTIDDNKTIFASILVDVTERN QSLEER GRLHWSRNGIIERIKQNNALFGYGLIQTYGADNILFRNLHSEGGIALRMETDNLLMKNYKQGGIR NIFADNIRCSKGLAAVMFGPHFMKNGDVQVTNVSSVSCGSAVRSDSGFVELFSPTDEVHTRQSW >GH55==Q8NIP1_ASPOR - Aspergillus oryzae KQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFGTVKVFDVTARF MLFLAHVLLLLGLPAGMVGAVPLGQETDITTNLAARAASEYWVGTIKRQGAVAFGNGTDYQVY GYNADLKQDQLDYFSTSNPMCKRVCLPTKEQWSKQGQIYIGPSLAAVIDTTPETSKYDYDVKTF RNVKDFGAKGDGSTDDTAAINQAISSGNRCGKGCDSSTVTPALVYFPPGTYVVSKPIVQYYYTQI NVKRINFPVNSHKTIDTNTESSRVCNYYGMSECSSSRWER VGDAVNLPVIKAAAGFAGMAVIDADPYEDDGSNWYTNQNNFFRAIRNLVIDLTAMPQGSGAGIH WQVGQATSLQNIRFEMIKGGGDANKQQGIFMDNGSGGFMSDLTFNGGNYGMFLGNQQFTTRNL >GH80==Q9S589_9SPHI - Sphingobacterium multivorum TFNDCNTAIFMNWNWAWTFKSLSINNCQVGLNMSNAPQNQTVGSVLILDSQLTNTPTGVVSAFT MHSRSPSVRRIGVQAALTVLALVCGASAAVAAGKPKAAAQTNGQPSVYVQDGWVYTNTFTAT ENSIPIGGGVLILDNVDFSGSKVAVAGITGNTILAGGSVVTNWVQGNGYLPGSAKQKREASVKVT GQPLVTATKAAAAAGVIPVGDSRVYGNVFDKGRKLTVNQWQAVLSMDAYPENGTTNYQDPEP TQTVTETVEVCTADYTDSPSAPTALPSSLGESRTAGLLPTLPLPNIPLLSGLLSGSQSSATQPAGVL WRYCEVDYEASEGISDYRGNTFGPVGVTTVGDFPDYFKNAYAPYVLGKTGATNTDMKNWGVQ SSEVPEPTATPSTPEEAEPSTEVQSTPQPSAPAQSQPETPVESTVAAPLIPSQPSPTVQGSSSVVTGP VTGIAAADMKADDTRLDPYPNLARSNSKKRAALTKICQALQSDFDNRQAQYVMSHYAHIDSDK ASSSVAHATNQCSVKTVTKTRLQTALPTHAKPSSLLNGGKVYERSKPLYTSYDASSFVSVKSAGA LLPVLDALKKLGFTSFGQYNLVGLAFQVQVNTGSIGSISAFSSVKSAGNCGSMSNETCFATYLTD KGDGSTDDTAAIQKILNSAKEDQIVYFDHGAYIITDTIKVPKNVKITGEVWPVLMAYGQKFGDEK QYIRWLKSSSLGDDAGNCWRASMALDIYKQDPTMGNVSVVTSIINSKYPNNSGKCPTSGVKWSK NPIPMLQVGEVGETGSVEITDIALQTKGPAPGAILMQWNLAESSQGAAGMWDTHFRIGGSAGTEL NMAWN QSDKCAKTPKQTTTPNKECIAAFMLMHITEKASAYIENSWFWVADHELDLPDHNQINVYNGRGV YIESQGPVWLYGTASEHNQLYNQLYNYQVTNAKNVFMGLIQTETPYYQANPNALTPFTPQTNW >GH74==Q9WYE1_THEMA - Thermotoga maritima NDPDFSYCKTDGCRKAWGLRVQNTSDMYVYGAGLYSFFENYGQTCLATESCQENMVEVDCSD WKSVEINGGGFVPGIIFHPASPGLLYARTDVGGLYRWDEETKRWKQLFDFLRRDQSDYMGVLSV VHIYGLSTKASTNMITSNSGAGLVPQDENRSNFCSTIALFQQS ALDPSDPKRIYAMTGKYTQDWAGYGAILISEDYGETWTIVNLDKYGIKVGGNEDGRNAGERLQV DPNFSSVLFMGTTKYGLWKSEDFGKNWKKVDSFPSTSVTFVLFDEKSGEKGSPTPRIFVGCSEPK >GH55==116227509 [Solibacter usitatus Ellin6076] GIFVTEDGGTTWNVLPNLPNDLIPLRGKIHDGILYVTLSNALGPNGATRGAVMKYVIADQKWYD MHPLTRCLLLATLLAAASSTALSESVMTTRPDDPKAVTLSAAEFGVRGDGQADDSAAIQAAIDK VTPMKGDFGYCGIDVQENVVIVSTLDRWYPHDEIFISLNGGETWRPLLEKANFDINKAPWIKDLN AENHVREGILFVPPGRYRLTRTVYVWPGVRVFGYGATRPVFVLAGNTPGFQKGVGVMVMFTGA PHWISDVKIDPFDMNRAIFTTGYGVWVTYELKKSFEGMGKPVKWIFENRGLEETVVLQLVPPIGE RPANPPRAGFRIPFPPVGSVPPNSAIADANPGTFYSAMSNIDFEIGDANPAAIAIRFHAAQHAYLSH RPLLSAIADWGGFRHESLDTPPSSMYKPLKWTSLGIAFAYQNSKFVARVHTYTYPFLSYSEDGGI MDFHTGSGLAALTQVGNEAEDLHFYGGRYGILTDKPSPAWQFTLIDSLFEGQREAAIREHEAGLT NWREIETVPEGITDGGRLSLAVSNDGKTLVWSPANHEVIVSSDKGKSWKKAISVPVPEFNYFPAS LIRDTFRDVPAAIDIDPHYSDQLWVKDCRFEKISRAAVIISNEKSPLTEIGFENAVLKDAPVFALFR DPVNPSKFYIFDWKNGDFLISKDGGKSFMKGAKLPSFDNWWVSLYSFPVLAPDREGDIWLALQW ESGKQVAGKGPVYCVGNFNFGLIVSGTATTGAIGMLYDALPLRSLPEALRPAIPALPPTGDWVNV NGLYRSKDGGITFERLGNVDIAYVIGFGAPKPGTDYPAIYLNGMVNGVYGIFMSTDEGKTWMRI HTLGVAGDGAADDTAAIQKAIDGHRVLYFPTGHYLVRDTLTLKPDTVMIGLHPTLTRFDLADGT NNDKHQFGWIHYMIGDMNEFGRIFLGTEGRGIIVG PGYQGVGGPRAMILAPAGGRNLISGFGVFTGGINPRAVGVLWSAGAESLIDDVRLLGGHGSGPNP YNANHSADPDPRKRWDGQYPSLWVTHGGGGTFANIWTPSTFAQAGFYVSDTTTPGHVYQLSSE >GH74==71915745 [Thermobifida fusca YX] HHVRTEIKFDHAENWDLHAPQTEEESGESAECLSLELNWSKNITIANYHAYRVARSRAPFPAAVR WRNVEIVGGGFVPGIVFNQSEPDLIYARTDIGGAYRWDPATERWIPLLDHVGWDDWGHSGVVSI LYRSADIHFRNVHVNAESGFAFCDQEGCGTFLRASKFPYENSIQDLTHHREVREREFAVLDIPGEA ATDPVDPDRVYAAVGTYTNDWDPNNGAIKRSTDRGETWETTELPFKLGGNMPGRGMGERLAID AASAPASKLKKLEDGFYSISGAAVDSAGKLYFVDHHEQRIYGWSSTEGLTVERDQPLDAVNLAF PNDNSVLYLGAPSGHGLWKSTDYGKTWQKVTSFPNPGNYVADPSDVGGYLGDNQGVVWVVFD DRTGNLLVLSSAGPGGTVYSFRPGSPGDQITELAPHDTKPRPGARAILPVNYWNNGEFANQLDFE PTSSSPGHVTKDIYVGVADKQNTVYRSTDGGQTWERIPGQPTGFLAQKGVFDHVNGLLYIATSDT TMTYTTPAEMFRRDVATPRAHQYVSTDGSVFLPAVRVVQQGPPDYTGWRFSHTLDTHAFTSAAP GGPYDGSDGEVWRYDTTTGTWTDITPADPDGFEYGFSGLTIDRQNPDTIMVVSQILWWPDIQIWR GERVYVSNESEDITYGALVGADGTLTDLRPFAQRGGESVAVDPNGNVYVANGEIFVYNPAGVQI STDRGETWSRIWEFSGYPDRTLRYNHDISAAPWLDFNRQDNPPEVSPKLGWMTQAFEIDPFNSDR ARIEVPERPLDIVFGGAGRRTLFVLTHHALFAYFL MLYGTGATIYGSDNLTNWDEGKKIDIKVRAQGIEETAVQDLIAPPGDTELVSALGDIGGFVHDDI TVVPDAMFDSPFHGNTRSIDFAELNPSVMARVGEAVDGEVDSHIGISTSGGSHWWAGQEPSGVT >GH55==116224917 [Solibacter usitatus Ellin6076] GAGTVAVNADGSRIVWSPDGTGVHYSTTLGSSWTPSQGVPAGARVEADRVNPDKFYAFANGTF MLKRILAGLIAAAVLPAASYYTLRLEDSKAVYLTPGDGAADASDTIQQAIDKVQAAAGEGIVFVP YTSTDGGATFTKSSAAGLPTKGNIRFAAVPGHEGDIWLAGGETNSTYGMWRSTDSGATFTRITAV EGRYRLTKTVYIPAAIRLIGYGATRPVFVLGPNTPGYQDPANEKYMIFFSGRGRGEAGAGTFYSG DEGDVVGFGKPAPGRSYPAVYTSSKINGVRGIFRSDDAGTTWVRINDDQHQWAWTGAAITGDP MSNIDLEVLAGNAGAVGVRGKYAQHCILAHMDFRIGSGLAGVHETGNVMEDVSFHGGQYGIWT DVYGRVYIGTNGRGVIVG GTPSPGWQLTLVDARFEGQREAAIREKAAGLTLVRPHFRSVPTAISIDAGSHEELWVKDARFEDIS GPAVIVSLEENPRTQINIENAVCRRVPVFASLRDSGRQFTAPGEVYAVPVFSHGLRFADIGAAPITS >GH74==37651953 [Clostridium thermocellum] SVFEIEKLTAMPAPVKSDLPDLPSRDSWVNIRSLGAKGDGSSDDTEVFRKAVAAHRAIYLPQGKY WDNVVIGGGGGFMPGIVFNETEKDLIYARADIGGAYRWDPSTETWIPLLDHFQMDEYSYYGVES VISDTIALRPDTVLIGLHPSATQLVLRDSTAAFQGVGAPKPMIEAPQRGSNIVIGLGLYTNGINPRA IATDPVDPNRVYIVAGMYTNDWLPNMGAILRSTDRGETWEKTILPFKMGGNMPGRSMGERLAID VAAKWMAGAGSLMNDVRFLGGHGTSKLEGGRDNPYNNAHSADPDLNRRWDGQYPSLWVTDG PNDNRILYLGTRCGNGLWRSTDYGVTWSKVESFPNPGTYIYDPNFDYTKDIIGVVWVVFDKSSST GGGTFFDIWTPSTFAQSGMLVSNTATEGRIYQMSSEHHVRYEVQLHNVSNWKVYALQTEEERGE PGNPTKTIYVGVADKNESIYRSTDGGVTWKAVPGQPKGLLPHHGVLASNGMLYITYGDTCGPYD GGFALPLEIQSSSNITVANFHIYRVISSFQPFPYAVKVLNSRDIRFRNIHCYSNSKVSFDSAIYDQTH GNGKGQVWKFNTRTGEWIDITPIPYSSSDNRFCFAGLAVDRQNPDIIMVTSMNAWWPDEYIFRST DSALRQREFAWLTLSGAAPAARTRPASTVLDAAAKVEKLAGGFYNISGGAASPAGDFYFVDAH DGGATWKNIWEWGMYPERILHYEIDISAAPWLDWGTEKQLPEINPKLGWMIGDIEIDPFNSDRM WQRIYRWSGQLSTVRDNPLDPVNLAFDKAGNLMVVSYAGAGMVYSFKPGSPESEITLLTPQPAA MYVTGATIYGCDNLTDWDRGGKVKIEVKATGIEECAVLDLVSPPEGAPLVSAVGDLVGFVHDDL PRPGMIPVLPVSDWRMNPQTLAQPHRQYVSPDGSTFIPAGQDFVSGAMSWGVKSSALLRGFGLA KVGPKKMHVPSYSSGTGIDYAELVPNFMALVAKADLYDVKKISFSYDGGRNWFQPPNEAPNSV AAAQGKPVYLTSESEVTTWQASLTPAGGMTDFKVFANQGGESVAVDEKGNVYVAAGQIFVYDP GGGSVAVAADAKSVIWTPENASPAVTTDNGNSWKVCTNLGMGAVVASDRVNGKKFYAFYNGK AGRLIETIDVPERPLQLVFGGADGKTLFVPARTSLYAVRTKFAGRRAQ FYISTDGGLTFTDTKAPQLPKSVNKIKAVPGKEGHVWLAAREGGLWRSTDGGYTFEKLSNVDTA HVVGFGKAAPGQDYMAIYITGKIDNVLGFFRSDDAGKTWVRINDDEHGYGAVDTAITGDPRVY >GH54==Q8NK89_ASPKA - Aspergillus kawachi GRVYIATNGRGIVYG PCDIYEAGDTPCVAAHSTTRALYSSFSGALYQLQRGSDDTTTTISPLTAGGIADASAQDTFCANTT CLITIIYDQSGNGNHLTQAPPGGFDGPDTDGYDNLASAIGAPVTLNGQKAYGVFMSPGTGYRNNE >GH66==CTA1_BACCI - Bacillus circulans ATGTATGDEAEGMYAVLDGTHYNDACCFDYGNAETSSTDTGAGHMEAIYLGNSTTWGYGAGD MVRFMYALRKRRLSLLLAMSLLVMCVASVVSPPPQALASGSGGIERVFTDKARYNPGDAVSIRV GPWIMVDMENNLFSGADEGYNSGDPSISYRFVTAAVKGGADKWAIRGANAASGSLSTYYSGAR QAKNGTGSSWSGAARLEIFHLENSVYTSSQSLSLTNGQSTTLTFTWTAPSTDFRGYFVRIDAGTLG PDYSGYNPMSKEGAIILGIGGDNSNGAQGTFYEGVMTSGYPSDDTENSVQENIVAAKYVVGSLVS QGATAIDVSSDFTKYPRYGYISEFESGETALESKAKVDQLAQDYHINAWQFYDWMWRHDKMIK GPSFTSGEV RTGGSIDSTWLDLFNREISWSTLQNQIDAVHDVNGKAMAYAMIYASRENYSPLGISPTWGIYEDS SHTNQFDVDFGDGSTYLYMSDPQNPNWQNYIHAEYIDSINTAGFDGIHVDQMGQRSNVYDYNG
SUPPLEMENTARY INFORMATION Warnecke et al: Page 4 www.nature.com/nature 4 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
>GH54==116224401 [Solibacter usitatus Ellin6076] PCDIYAAAGDPCVAAHSTTRALYAGYNGPLYQVLRQSDGKTLDIGVVQPAASPLQDAGGYANA >GH36==RAFA_ECOLI - Escherichia coli AAQDAFCANTYCWVSIIFDQSPKHNDVIHAPRGGFSGPSMGGFNNLPVADMAPITIMGHKAYGV LGLFSSPGLEGHRNGLDASPVFYTVDVEHTENTLRLTSEDSVAGLRLVSELVMTPSGILKVRHAL FITPGMGLRQNDAKGTAVDDQAEGQYWVINGHHYNSGCCFDYGNAEIDSRDDDNGTMETTYY TNLREGDWQINRFAITLPVAERAEEVMAFHGRWTREFQPHRVRLTHDAFVLENRRGRTSHEHFP GNATSWYHGNPAGPWIMTDQENNLVGCVNPDGTKLCASLPNITWRFVTAMAKGEPHHWTSMG ALIVGTPGFSEQQGEVWAVHLGWSGNHRMRCEAKTDGRRYVQAEALWMPGEKALRKNETLYT GDAQHGALKVMFDGPRVDVTYDPMRKQGAILLGNGGDNSVGSQGTFYEGAMTAADTFPSDAT PWLYACHSADGLNGMSQQYHRFLRDEIIRFPEQKLRPVHLNTWEGIYFNHNPDYIMQMAERAAA DQLVQANVVAARYDLPRLSLAPASATAAPPGLQTFSPGSSQNTTLTFTNTTGAPVVGVQLSLSVP LGVERFIIDDGWFKGRNDDRAALGDWYTDEQKYPNGLMPVINHVKSLGMEFGIWVEPEMINPDS RQWTSVVTGASTTSATIAGPVAPGASVSATFKVTSGPVAFNGDLVGNARFTNQATGAKQFETTS DLFRLHPDWILSMPGYSQPTGRYQYVLNLNIPEAFDYIYKRFLWLLGEHPVDYVKWDMNRELVQ EKVRNVSPVKINEFRITDGSPTNSTNSFIELYNAGARDVDISNWTLTQHPAQQAIFSAVKIPARTKL AGHEGRAAADAQTRQFYRLLDLLRERFPHVEFESCASGGGRIDFEVLKRTHRFWASDNNDALER TPGGFYLLGLANSGLAVPARAGDKTIHVRSTAGMNVGDTISIESGSGAETHKIVNVGTAAGAGTT CTIQRGMSYFFPPEVMGAHIGHRRCHATFRQHSIAFRGLTALFGHMGLELDPVAADAKESDGYR LWQPLPDGPVIKLPAGSTNVPVTSVAGFAAGEKIAIGYGAVYPAVARTIEQYEVATVTAVGKPGT RYALLYKEWRQLIHTGVLWRVDMPDSSIQVQGVVSPDQSQALFMISQLAMPDYTLPGILRFPGL QAFLGVDAAAGATNIKVTSVANISAGDRIRLDIESVGHGIETVAVTKVGTQSSRTALSADAHAGA AAEVRYRLRVIDHPEIQLVGEGGHT TNIKVRNANGFTVGDKLTVGTPANHETVTITAVADGVDFTPALAKAHLNREFVVAQGTGLDLAA P >GH36==O33835_THEMA - Thermotoga maritima MEIFGKTFREGRFVLKEKNFTVEFAVEKIHLGWKISGRVKGSPGRLEVLRTKAPEKVLVNNWQS >GH54==91690082 [Burkholderia xenovorans LB400] WGPCRVVDAFSFKPPEIDPNWRYTASVVPDVLERNLQSDYFVAEEGKVYGFLSSKIAHPFFAVED PCDAAATANTPCSAAHSVTRLLTRNYRGPLFQVQRASDNAKQDIYPYTSSTLPHGADRSLIGSAN GELVAYLEYFDVEFDDFVPLEPLVVLEDPNTPLLLEKYAELVGMENNARVPKHTPTGWCSWYH VKSANTFCNNTTCSVTYIYDQIDLVAPLKGGAFGNVPATLTLNPDGTESLTVPNSGSRPQKTTTVP YFLDLTWEETLKNLKLAKNFPFEVFQIDDAYEKDIGDWLVTRGDFPSVEEMAKVIAENGFIPGIW VLNGFATITLPGTSGALAVQLSQPPTALTAQSPTLQLSIGNDLPALSGTPAKLGFVPLQGAQIPALG TAPFSVSETSDVFNEHPDWVVKENGEPKMAYRNWNKKIYALDLSKDEVLNWLFDLFSSLRKMG TLAGQAYRNRFGTVNQSIGDSDIAEYMVAGAHYSQSSTCCGTYGNMENSANPGTYAHGEIEGE YRYFKIDFLFAGAVPGERKKNITPIQAFRKGIETIRKAVGEDSFILGCGSPLLPAVGCVDGMRIGPD MFALAFSNGNAAVFGYCDGNSNQPPNVKDPVCNARDTNWPGVDAEAGVYLYGPPQPAREKFV TAPFWGEHIEDNGAPAARWALRNAITRYFMHDRFWLNDPDCLILREEKTDLTQKEKELYSYTCG TVLSKYSPVTASNIFAVKGGSASQSVLTALYDQAPPEAYNFGNDAGHAFNGQWQGGLSLGEGG VLDNMIIESDDLSLVRDHGKKVLKETLELLGGRPRVQNIMSEDLRYEIVSSGTLSGNVKIVVDLNS DGSAAPIQFFEGAVITKATSDTTDNAIQASIASFYGPPADKAVAACYANNLINSPLSLATPDIWSQQ REYHLEKEGKSSLKKRVVKREDGRNFYFYEEGERE NGGTAVPATDISGVNRGAATVTSTNGSSVSNVREIIRVQGGQSYSFTDYVLATSNATVFPGGSIQT DDPSGTEFAWVLNTNTGAVVRGTWGAGQPTALSAVRSGNWWKVTMTLTAPAGSNNASVFIDPP >GH23==Q9HXN1_PSEAE - Pseudomonas aeruginosa TSNAAGARSQQASYLSATHYCPSLAIVASSGT VITRNSPATYFQDRNGETGFEYELAKRFAERLGVELKIETADNLDDLYAQLSREGGPALAAAGLT PGREDDASVRYSHTYLDVTPQIIYRNGQQRPTRPEDLVGKRIMVLKGSSHAEQLAELKKQYPELK >GH51==ABFA_BACST - Geobacillus stearothermophilus YEESDAVEVVDLLRMVDVGDIDLTLVDSNELAMNQVYFPNVRVAFDFGEARGLAWALPGGDD MATKKATMIIEKDFKIAEIDKRIYGSFIEHLGRAVYGGIYEPGHPQADENGFRQDVIELVKELQVPI DSLMNEVNAFLDQAKKEGLLQRLKDRYYGHVDVLGYVGAYTFAQHLQQRLPRYESHFKQSGK IRYPGGNFVSGYNWEDGVGPKEQRPRRLDLAWKSVETNEIGLNEFMDWAKMVGAEVNMAVNL QLDTDWRLLAAIGYQESLWQPGATSKTGVRGLMMLTNRTAQAMGVSNRLDPKQSIQGGSKYFV GTRGIDAARNLVEYCNHPSGSYYSDLRIAHGYKEPHKIKTWCLGNEMDGPWQIGHKTAVEYGRI QIRSELPESIKEPDRSWFALAAYNIGGAHLEDARKMAEKEGLNPNKWLDVKKMLPRLAQKQWY ACEAAKVMKWVDPTIELVVCGSSNRNMPTFAEWEATVLDHTYDHVDYISLHQYYGNRDNDTA AKTRYGYARGGETVHFVQNVRRYYDILTWVTQPQMEGSQIAESGLHLPGVNKTRPEEDSGDEKL NYLALSLEMDDFIRSVVAIADYVKAKKRSKKTIHLSF >GH23==SLT_ECOLI - Escherichia coli >GH51==125715257 [Clostridium thermocellum ATCC 27405] VVEQMMPGLKDYPLYPYLEYRQITDDLMNQPAVTVTNFVRANPTLPPARTLQSRFVNELARRED MKKARMTVDKDYKIAEIDKRIYGSFVEHLGRAVYDGLYQPGNSKSDEDGFRKDVIELVKELNVP WRGLLAFSPEKPGTTEAQCNYYYAKWNTGQSEEAWQGAKELWLTGKSQPNACDKLFSVWRAS IIRYPGGNFVSNYFWEDGVGPVEDRPRRLDLAWKSIEPNQVGINEFAKWCKKVNAEIMMAVNLG GKQDPLAYLERIRLAMKAGNTGLVTVLAGQMPADYQTIASAIISLANNPNTVLTFARTTGATDFT TRGISDACNLLEYCNHPGGSKYSDMRIKHGVKEPHNIKVWCLGNEMDGPWQVGHKTMDEYGRI RQMAAVAFASVARQDAENARLMIPSLAQAQQLNEDQIQELRDIVAWRLMGNDVTDEQAKWRD AEETARAMKMIDPSIELVACGSSSKDMPTFPQWEATVLDYAYDYVDYISLHQYYGNKENDTADF DAIMRSQSTSLIERRVRMALGTGDRRGLNTWLARLPMEAKEKDEWRYWQADLLLERGREAEAK LAKSDDLDDFIRSVIATCDYIKAKKRSKKDIYLSF EILHQLMQQRGFYPMVAAQRIGEEYELKIDKAPQNVDSALTQGPEMARVRELMYWNLDNTARS EWANLVKSKSKTEQAQLARYAFNNQWWDLSVQATIAGKLWDHLEERFPLAYNDLFKRYTSGK >GH50==AGAA_VIBS7 - Vibrio sp. (strain JT0107) EIPQSYAMAIARQESAWNPKVKSPVGASGLMQIMPGTATHTVKMFSIPGYSSPGQLLDPETNINIG SEVSTEQATDGNQSIKASFDAAFKPMVVWNWASWNWGAEDVMSVDVVNPNDTDVTFAIKLIDS TSYLQYVYQQFGNNRIFSSAAYNAGPGRVRTWLGNSAGRIDAVAFVESIPFSETRGYVKNVLAY DILPDWVDESQTSLDYFTVSANTTQTFSFNLNGGNEFQTHGENFSKDKVIGVQFMLSENDPQVLY DAYYRYFMGDKPTLMSATEWG FDNIMVDGETVTPPPSDGAVNTQTAPVATLAQIEDFETIPDYLRPDGGVNVSTTTEIVTKGAAAM AAEFTAGWNGLVFAGTWNWAELGEHTAVAVDVSNNSDSNIWLYSRIEDVNSQGETATRGVLV >CBM8==GUN6_DICDI - Dictyostelium discoideum KAGESKTIYTSLNDNPSLLTQDERVSALGLRDIPADPMSAQNGWGDFVALDKSQITAIRYFIGELA PSSGESLSIYKSGLKNDFQDWSWGEHSLTDTTNVESGETNSISFTPKAYGAVFLGCFECIDTDTYN SGETSQTLVFDNMRVIKDLNHESAYAEMTDAMGQNNLVTYAGKVASKEELAKLSDPEMAALGE NIEFDINGGSSGAQLLRITVVKNSKSVGSKLITDLNGGTPIEANSWTKIKASFIDDFKVSGKVDGIW LTNRNMYGGNPDSSPATDCVLATPASFNACKDADGNWQLVDPAGNAFFSTGVDNIRLQDTYTM IQDIKGDTQSTVYISNIIATA TGVSSDAESESALRQSMFTEIPSDYVNENYGPVHSGPVSQGQAVSFYANNLITRHASEDVWRDIT VKRMKDWGFNTLGNWTDPALYANGDVPYVANGWSTSGADRLPVKQIGSGYWGPLPDPWDAN >CBM8==108462586 polysaccharide deacetylase domain protein [Myxococcus xanthus DK 1622] FATNAATMAAEIKAQVEGNEEYLVGIFVDNEMSWGNVTDVEGSRYAQTLAVFNTDGTDATTSP PDLTAGLFVYTDALQNGFANWSWADHSLDETGVVHAGSAAIRFEPDTWNGLLFHHHGLDLAQY AKNSFIWFLENQRYTGGIADLNAAWGTDYASWDATSPAQELAYVAGMEADMQFLAWQFAFQY QSIRVWVHGGTAGGQAVRLVLHDGTQMLGTTRLDTALGAPIAPGVWQQVTIPLSSIGATTGTLR FNTVNTALKAELPNHLYLGSRFADWGRTPDVVSAAAAVVDVMSYNIYKDSIAAADWDADALSQ DIYFQDDSGTDQPALYLDDVVLLPQ IEAIDKPVIIGEFHFGALDSGSFAEGVVNATSQQDRADKMVSFYESVNAHKNFVGAHWFQYIDSP LTGRAWDGENYNVGFVSNTDTPYTLMTDAAREFNCGMYGTDCSSLSNATEAASRAGELY >CBM23==Q9XCV5_CELFI - Cellulomonas fimi VAAAPAQPVVHIASPADGARVASAPTTVRVRVGGTDVQSVTVEVAQGGTVVDTLDLAYDGAL >GH50==Q9RKF0_STRCO - Streptomyces coelicolor WWTAPWSPTSAQLDNSTYTVTATATTAAGTLDVTNEVVLGPRPTFPAGVVDDFEGYGDDTALR MTVHKRACTTPPPRASRSFRVRWPVLIAAACAGLVLATTSPPAVAAGAHDLGDETMLYDFQDGL AEYVTYGANTISLETGSVGGGAKALRLDYDFATQTYTGVGKQLSGDWSDFNELAIWVDPDGSN VPAEVGPYQAKTTIVGRGDKKLRVDFQARKNYYSSFSVRPEPVWNWSAEESESLGIAMELTNPS NRMVLQLNAGGVAYEAYPSLAGDEPQLVTIPFVDWRPAPWDTAHADRRMSDDDLRALTSFNVY DRSVQLTIDLESSTGVATRSVNVPAGGGGTYYFDVDSPALHRDTGLRADPSWLADKDVTSAVW VNSAEGGAASGSLVVDDIAAH MWGSKETDTSRISQLNFYVAGLLHDRSVIVDDIRVVRDAPADPDYLKGLVDAFGQNNKVDYKG KVSRTSEILRQRAAEAKDLRRHPVPEDRSRYGGWLNGPRLEATGNFRVEKYQGRWTLVDPDGY >CBM24==Q9P563_NEUCR- - Neurospora crassa LFFSTGIDNARMFDSPTTTGYDFDHDAIQELPPPSLTAGGPEDLNRVQKSALPTRTKMSETRADLF CVEGTAAAGFDELCAFTCKYGYCPVGACLCTKMGPGNKLPGPETPGFGTVGFPAKGRTASYGGL SKLPKYRTRAGEGFGYAPDTLAGPVAQGETYSFYKANVARKYPGSNYMERWRDNTVDRMLSW CSFACNYGYGCPNAYC GFTSFGNWTDPEMYDNDRIPYFAHGWIKGDFKTVSTGQDYWGPMPDPFDPAFSDAAARTARAV ADEVADSPLAIGVFMDNELSWGNAGSFSTRYGVVIDTMSRDAAESPTKSAFSDELEEKYGTIDAL >CBM24==Q9P563_NEUCR-2 - Neurospora crassa NAAWQTTVPSWEALRSGSADLGSDETAKESDYSALMTLYATQYFKTVDAELDKVMPDHLYAG CTSGVGEGGLGGLCSFSCNFGFCPIHSCTCTSTGALHVPPGASDTITGKADPSVDERTYGPLCEFA SRFASWGRTPEVVEAASKYVDIMSYNEYREGLHPSEWAFLEELDKPSLIGEFHMGTTTTGQPHPG CSRGYCPEGAC LVSAGTQAERARMYAEYMEQLIDNPYMVGGHWFQYADSPVTGRALDGENYNIGFVSVTDRPYP EIVAAARDVNQRLYDRRYGNLATAEGHYTGRRSAE >CBM24==Q8WZM7_TRIHA Alpha-1,3-glucanase - Trichoderma harzianum CVAGTVADGESGNYIGLCQFSCNYGYCPPGPCKCTAFGAPISPPASNGRNGCPLPGEGDGYLGLC >GH44==MANB_CALSA - Caldocellum saccharolyticum SFSCNHNYCPPTACQYC PSVVEITINTNAGRTQISPYIYGANQDIEGVVHSARRLGGNRLTGYNWENNFSNAGNDWYHSSDD YLCWSMGISGEDAKVPAAVVSKFHEYSLKNNAYSAVTLQMAGYVSKDNYGTVSENETAPSNR >CBM26==Q9KFR4_BACHD - Bacillus halodurans WAEVKFKKDAPLSLNPDLNDNFVYMDEFINYLINKYGMASSPTGIKGYILDNEPDLWASTHPRIH YYKTGWTHPHIHYSLNQGAWTTLPGVPLTKSEYEGYVKVTIEAEEGSQLRAAFNNGSGQWDNN PNKVTCKELIEKSVELAKVIKTLDPSAEVFGYASYGFMGYYSLQDAPDWNQVKGEHRWFISWYL QGRDYDFSSGVHTLADGRILSGT EQMKKASDSFGKRLLDVLDLHWYPEARGGNIRVCFDGENDTSKEVVIARMQAPRTLWDPTYKT SVKGQITAGENSWINQWFSDYLPIIPNVKADIEKYYPGTKLAISEFDYGGRNHISGGIALADVLGIF >CBM26==Q97GW3_CLOAB Hypothetical protein CAC2252 - Clostridium acetobutylicum GKYGVNFAARWGDSGSYAAAAYNIYLNYDGKGSKYGNTNVSANTSDVENMPVYASINGQDDS FKDPNGWSAPNIYYYDPAGKLTGPGWPGVKMNSDGNGWYSYTIQNWTSAKVLFDDGTNQIPGV ELHIILINRNYDQKLQVKINITSTPKYTKAEIYGFDSNSPEYKKMGNIDNIESNVFTLEVPKFNGVS NQPGIDVTG HSITLDFNVSIKIIQNEVIKFIRNLVFMRALV >CBM26==AMY_BACSU Alpha-amylase precursor - Bacillus subtilis >GH44==P71140_CLOTM - Clostridium thermocellum YQNPNHWSQVNAYIYKHDGSRVIELTGSWPGKPMTKNADGIYTLTLPADTDTTNAKVIFNNGSA AKVVDIRIDTSAERKPISPYIYGSNQELDATVTAKRFGGNRTTGYNWENNFSNAGSDWLHYSDTY QVPGQNQPGFDYVLNGLYNDSGLSGS LLEDGGVPKGEWSTPASVVTTFHDKALSKNVPYTLITLQAAGYVSADGNGPVSQEETAPSSRWK EVKFEKGAPFSLTPDTEDDYVYMDEFVNYLVNKYGNASTPTGIKGYSIDNEPALWSHTHPRIHPD >CBM27==P77847_CALSA-1 - Caldocellum saccharolyticum NVTAKELIEKSVALSKAVKKVDPYAEIFGPALYGFAAYETLQSAPDWGTEGEGYRWFIDYYLDK VESSVNPVVLDFEDGTVMSFGEAWGDSLKCIKKVSVSQDLQRPGNKYALRLDVEFNPNNGWDQ MKKASDEEGKRLLDVLDVHWYPEARGGGERICFGADPRNIETNKARLQAPRTLWDPTYIEDSWI GDLGTWFGGVVEGQFDFTGYKSVEFEMFIPYDEFSKSQGGFPYKVVINDGWKELGSEFNITANA GQWKKDFLPILPNLLDSIEKYYPGTKLAITEYDYGGGNHITGGIAQADVLGIFGKYGVYLATFWG GKKVKINGKDYTVIHKAFAIPEDFRTKKRAQLVFQFAGQNSNYKGPIYLDNVRIRPEDASN DASNNYTEAGINLYTNYDGKGGKFGDTSVKCETSDIEVSSAYASIVGEDDSKLHIILLNKNYDQPT TFNFSIDSSKNYTIGNVWAFDRGSSNITQRTPIVNIKDNTFTYTVPALTACHIVLEAAEPVVYGDLN NDSKVNAVDIMMLKRYILGIIDNINLTAADI
SUPPLEMENTARY INFORMATION Warnecke et al: Page 5 www.nature.com/nature 5 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
>CBM27==P77847_CALSA-2 - Caldocellum saccharolyticum >CBM38==O52973_BACCI-3 - Bacillus circulans YPEQGKSFVYNFEIDTMGFYKYSGDGFNKKTKSLEYSQDLKRSGNNGALKVNASLAGTAFDEM NIIPAEIANRGFETGNLDGWTVEGDAFHVTDEAHAAKEGNFYALSSTEGQGSITSNTFTLQGAGII NIAIKLTDKDDKKFDFSKYSTLEYTLYIPNPDKISGKLMVASAIDNPWQIIKDFTAINYKDKNAIQK NFTVLDILNPEGAYVALYDASSNTVIKITGNIGANEQISWKVQEHYNKKLYVKVVDQSGDAGIAV INGKDYAVIKCSDNLYNVNTKANVLVLRIAGSYVKYTGPIYIDNVKLVAGKKVA DGF
>CBM38==O52973_BACCI-4 - Bacillus circulans >CBM27==Q9X0V4_THEMA - Thermotoga maritima NEQAGGDSLTGTLRSQNFVLGGNGRIDFLMSGGRDIDRLYVALVRASDGKELFKETATNYEEYQ VNEARYVLAEEVDFSSPEEVKNWWNSGTWQAEFGSPDIEWNGEVGNGALQLNVKLPGKSDWE RKIWDASDYIGEELYIKVVDQSTGGFGHLNVDDF EVRVARKFERLSECEILEYDIYIPNVEGLKGRLRPYAVLNPGWVKIGLDMNNANVESAEIITFGGK EYRRFHVRIEFDRTAGVKELHIGVVGDHLRYDGPIFIDNVRLYKRTGGM >CBM39==BGBP_PLOIN - Plodia interpunctella >CBM29==Q9C171_PIREQ-1 - Piromyces equi YVVPSAKLEAIYPKGLRVSIPDDGFSLFAFHGKLNEEMDGLEAGHWARDITKPKEGRWTFRDRN RKVSATYSVVYETGKKLNSGFDNWGWDSKMSFKDNSLVLTADPDEYGAISLKNLNSNYYGKGG VKLKLGDKIYFWTYVIKDGLGYRQDNGEWTVTEFVNEDGTPADT CIYLQVKTETEGLVKVQGVRGYDETEAFNVGSFRSSSDFTEYKFEVDDEYQFDRIIVQDGPASNIP IYMRYIIYSTGSCDDFNPPVDTTKVPVTT >CBM39==BGBP_BOMMO - Bombyx mori YEAPPATLEAIHPKGLRVSVPDEGFSLFAFHGKLNEEMEGLEAGHWSRDITKPKNGRWIFRDRNA >CBM29==Q9C171_PIREQ-2 - Piromyces equi ALKIGDKIYFWTFVIKDGLGYRQDNGEWTVEGFVDEAGNPVNT SNVRATYTVIFKNASGLPNGYDNWGWGCTLSYYGGAMIINPQEGKYGAVSLKRNSGSFRGGSLR FDMKNEGKVKILVENSEADEKFEVETISPSDEYVTYILDVDFDLPFDRIDFQDAPGNGDRIWIKNL >CBM41==PULA_KLEAE - Klebsiella aerogenes VHSTGSADDFVDPIN LVDIAGITSSTPADYATKNLYLWNNETCDALSAPVADWNDVSTTPTGSDKYGPYWVIPLTKESGS INVIVRDGTNKLIDSGRVSFSDFTDRTVSVIAGNSAVYDSRADAFR >CBM30==P71140_CLOTM - Clostridium thermocellum KLLDVQIFKDSPVVGWSGSGMGELETIGDTLPVDTTVTYNGLPTLRLNVQTTVQSGWWISLLTLR >CBM41==145409304 [Caldicellulosiruptor saccharolyticus DSM 8903] GWNTHDLSQYVENGYLEFDIKGKEGGEDFVIGFRDKVYERVYGLEIDVTTVISNYVTVTTDWQH KTTLIIHYYRYNEDYQGWNLWIWPVEPVGTEGKAYEFTSKDDFGVKAVVELPGKVTKVGIIVRK VKIPLRDLMKINNGFDPSSVTCLVFSKRYADPFTVWFSDIKITSEDNEKSAPAIKVNQLGFIPEAEK GNWEAKDVAVDRFISGINGTKEVWLIEGEEQIYTSQPQKTP YAL >CBM41==89949809 [Saccharophagus degradans 2-40] >CBM30==P77865_FIBSU-1 - Fibrobacter succinogenes PNQAILFFNKADGDYEGYRLHNWNSETCNAYAEGSLAASWSNGLVHSGVDPVYGAYWLLDLV KRPHLAVYKFFDEQYRPGGYDYSYGGTSKGVTITKSGGYKSKAALNIKLDPKEYSGASICLYNEF EGHDDCGHFIIHVGTDDAGKEMGGGDWIMPLAQDDPKFTRMNFTFSGVGSVFEFPVPSLGPQKV FDLNKYMLDSKVEFMIKGKNGGESVKVGLLDEEVSDGKKTQVVLPMNKYIEGGAVTTDWKKV AIAGAAAHWLDIDTLVWNLDTTDVADVKLHYSATAGITVDDDSNVSGSTADLTFATLSEELQQL SIPLVDFPDRGLYWDNTRKSEFPSRIDWDKIAEIRFSIDKSAASEFEVWVDNIEIVKGNKKAAPKK VPHMASWPAFGNMLTASD QMVYWDENNDIID >CBM41==PULA_THEMA - Thermotoga maritima >CBM30==P77865_FIBSU-2 - Fibrobacter succinogenes ETTIVVHYHRYDGKYDGWNLWIWPVEPVSQEGKAYQFTGEDDFGKVAVVKLPMDLTKVGIIVR KAKTLATFYDNQVKGFSYSYGGLTAQREAQSKTPGNKNVLAMYIDNNDWSGVTYSLGEGKFID LNEWQAKDVAKDRFIEIKDGKAEVWILQGVEEIFYEKPDTSP LSKVRDKGGLYFWIKGKLGGEKLYVGILDNQGNDIKSQTKVGLNDWIKVSKDWQLAKIPLKRFT DKGKAWDANKSAEVAKDIKWDKIQEIRFSVGKGENAGEPGKPAPVTVFVDQITFTSNIDWVDPD >CBM42==Q8NK89_ASPKA - Aspergillus kawachi LKWDSFKSNAPDYVI LVSGPSFTSGEVVSLRVTTPGYTTRYIAHTDTTVNTQVVDDDSSTTLKEEASWTVVTGLANSQCF SFESVDTPGSYIRHYNFELLLNANDGTKQFHEDATFCPQAALNGEGTSLRSWSYPTRYFRHYENV >CBM30==Q9AQF4_CLOCL - Clostridium cellulovorans LYAASNGGVQTFDSKTSFNNDVSFEIETAFAS KLMDLEVFKSASITGWSGSAGGELEVASDSNLPIDTSATYNGLPSLRLNVTKASAQWWSSLLTLR GWCTQDLTQYLANGYLEFNVKGKVGGEDFQIGLQDQTHERAAGDSVTSVKSIKNYVNISTNWQ >CBM42==125712765 [Clostridium thermocellum ATCC 27405] HVKIPLKDIMGPSTGFDPTTARCINIVKGSSEIFTAWINDLKITSTDNEKSYAPIKVNQDGYLPSSEK FATSVCYSTNPITKAKFQSYNYPNMYIRHANFDARIDENVTPEMDSQWELVPGLANSGDGYVSIQ YAL SVNYPGYYLRHSNYDLSLEKNDGTSLFAESATFKIVPGLADPSYISFQSYNFPTRYIRHYNYLLRL DEIVTELDRQDATFKIIS >CBM31==Q8RS40_9BURK - Alcaligenes sp. XY-234 GTEPPENCQDDFNFNYVSDQEIEVYHVDKGWSAGWNYVCLNDYCLPGNKSNGAFRKTFNAVLG >CBM43==Q94G86_OLEEU Beta-1,3-glucanase-like protein - Olea europaea QDYKLTFKVEDRYGQGQQILDRNITFTTQVCN SWCVPKPGVSDDQLTGNINYACGQGIDCGPIQPGGACFEPNTVKAHAAYVMNLYYQSAGRNSW NCDFSQTATLTNTNPSYGACNF >CBM35==Q840C0_9GAMM - Cellvibrio japonicus MAVPEGNSWTYTAASASITAPAQLVGNVGELQGAGSAVIWNVDVPVTGEYRINLTWSSPYSSKV >CBM44==P71140_CLOTM - Clostridium thermocellum NTLVMDGTALSYAFAEATVPVTYVQTKTLSAGNHSFGVRVGSSDWGYMNVHSLKLELLGGLTI TEKAFKGERGLKWTVTSEGEGTAELKLDGGTIVVPGTTMTFRIWIPSGAPIAAIQPYIMPHTPDWS RSPAN EVLWNSTWKGYTMVKTDDWNEITLTLPEDVDPTWPQQMGIQVQTIDEGEFTIYVDAIDW
>CBM35==Q9F1T9_CLOTM - Clostridium thermocellum >CBM45==Q9CAR6_ARATH - Arabidopsis thaliana MENKTSIKVFLALMLAVLMPVVSCINVSNAVLSDGDKYEFEDGIHKGAQIYTDYVGQNEYGEVF LHHSYLRHNSKVNRGNRSFIPISLNLRSHFTSNKLLHSIGKSVGVSSMNKSPVAIRATSSDTAVVET DLTGSTCSFIAQKGTSTSVNVEVDKEGLYEIFICYVQPYDKNKKVQYLNVNGVNQGEISFPFTLK AQS WREISAGIVKLNAGINNIELESYWGYTYFDYLIVKPAD >CBM45==3287270 R1 [Solanum tuberosum] >CBM36==Q9RC94_9BACI - Bacillus sp. 41M-1 LTSTVLEHKSRISPPCVGGNSLFQQQVISKSPLSTEFRGNRLKVQKKKIPMEKKRAFSSSPHAVLTT EAESMTKGGPYTSNITSPFNGVALYANGDNVSFNHSFTKANSSFSLRGASNNSNMARVDLRIGGQ DTSSELAEKFSL NRGTFYFGDQYPAVYTINNINHGIGNQLVELIVTADDGTWDAYLDYLE >CBM46==Q9KF82_BACHD-1 - Bacillus halodurans >CBM36==P77853_DICTH - Dictyoglomus thermophilum RSSVAESNFIYLKQGDRIADATVSLQLHGNELTGLRANGQRLTPGQDYELNGERLTVKAHVLSAI ECENMSLSGPYVSRITNPFNGIALYANGDTARATVNFPASRNYNFRLRGCGNNNNLARVDLRIDG ASSGTLGTNGMVTAEFNRGADWHFRVNT RTVGTFYYQGTYPWEAPIDNVYVSAGSHTVEITVTADNGTWDVYADYLV >CBM46==GUNB_PAELA-1 - Paenibacillus lautus >CBM36==XYND_PAEPO-1 - Paenibacillus polymyxa RSSTASSDLIHVKQGTAVKDTSVQLNLNGNTLTSLSVNGTTLKSGTDYTLNSSRLTFKASQLTKLT EAETIAWQAGVTTEPTQASGGPISNLNVTNIHNGDWIAVGKADFGSAGAKTFKANVATNVGGNI SLGKLGVNATIVTKFNRGADWKFNVVL EVRLDSETGPLVGSLKVPSTGGMQTWREVETTINNATGVHNIYLVFTGSGSGNLLNLDAWQ >CBM46==Q9KF82_BACHD-2 - Bacillus halodurans >CBM36==XYND_PAEPO-2 - Paenibacillus polymyxa PVLQSTQGHVSNFSIPASFNGNSLATMEAVYVDGGNAGPQDWTSFKEFGYAFSPSYDANEMKLT EAENMKIGGTYAGKISAPFDGVALYANADYVSYSQYFANSTHNISVRGASSNAGTAKVDLVIGG EAFFREVRDGEVRLTFHFWSGETVNYTIIKNGNQVTGIAA VTVGSFNFTGKTPTVQTLSNITHATGDQEIKLALTSDDGTWDAYVDFIE >CBM46==GUNB_PAELA-2 - Paenibacillus lautus >CBM37==Q9AJB4_RUMAL - Ruminococcus albus PKLSSTTGTTSSFAIPTAFNGDQLATMEAVYVNGGNAGPHNWTSFKEFETTFSPAYSEGKIKLQQ PEESEIEGTLYSATFENGTNYWSGRGSASVASSSSKAYEGSKSLYVSGRTDNWNGGEVEVNTSTF AFFNEVNDTTVTLKFQFWSGEIVNYTIKKSGSTVTGTAS KPGNSYSFSAMVNPAESTTVQLSMQYDQNGTTKYTQIAEGSCTAGKWTKLENTSFTIPSGASNV KMYVEAPDSLCDIYVDRAIIADKGYVA >CBM48==Q9RX51_DEIRA - Deinococcus radiodurans KKEFGGFSGFSGEDVPDPQAEQTFLNSKLNWAEREGGEHARTLRLYRDLLRLRREDPVLHNRQR >CBM38==O52973_BACCI-1 - Bacillus circulans ENLTTGHDGDVLWVRTVTGAGERVLLWNLGQDTRAVAEVKLPFTVPRRLLLHTEGREDLTLGA TGWSVAEGGAFGPDSVSDETVWWAERIPYDQEGAYHLNGWKYPESETGVLRSSTFELGGSGWIS GEAVLVG FKLGGAKDPDKAFINIVEADTGQVVARYGNSAFTDVGFPDPAQGMRLANMEQYKADLSGHIGK KLYIEIVDHATSDWGLIFADAF >CBM48==GLGB_ECOLI - Escherichia coli MSDRIDRDVINALIAGHFADPFSVLGMHKTTAGLEVRALLPDATDVWVIEPKTGRKLAKLECLDS >CBM38==O52973_BACCI-2 - Bacillus circulans RGFFSGVIPRRKNFFRYQLAVVWHGQQNLIDDPYRFGPLIQEMDAWLLSEGTHLRPYE TGWTVIEGDAFGPNSVSDETVWWAERIPYDQEGAYHLNGWKYPESETGVLRSSTFELGGSGWIT FKLGGGKHTDQVYVSVIEAETGNLIARYGNSAFTDVGFPDPAQGMRLANMEQYKADLSKHIGK >CBM48==PULA_KLEAE - Klebsiella aerogenes KLYLEIVDHGVSDWGLVFADAF KSSPLFTLGDGATVMKRVDFRNTGADQQTGLLVMTIDDGMQAGRQSGQPCRRHRGGDQRRAG KPDAAGLRRHIAPAERYSAGGGRPVAGERVQVAADGSVTLPAWSVAVLELPQASRRALACR
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>CBM49==GUN2_ORYSJ - Oryza sativa subsp. japonica (Rice) AAGHGARARGRLGQSLQHGIAANHTSLPHGANHQHASPVEIEQKATASWEKDGRTYHRYAVTV SNRSPAGGKTVEELHIGIGKLYGPVWGLEKAARYGYVLPSWTPSLPAGESAAFVYVHAAPPADV WVTGYKLV
>CBM49==Q9ZSP9_SOLLC - Solanum lycopersicum (Tomato) (Lycopersicon esculentum) HAGHSGYNQLLPVVPDPKPTPKPAPRTKVTPAPRPRVLPVPANAHVTIQQRATSSWALNGKTYY RYSAVVTNKSGKTVKNLKLSIVKLYGPLWGLTKYGNSFIFPAWLNSLPAGKSLEFVYIHTASPAIV SVSSYTLV
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Table S1. Non-parametric diversity estimators. Diversity estimates were calculated using four different methods involving parametric (exponential and two parameter hyperbola) and non- parametric estimators (bootstrap and jackknife). 16S sequences were assigned to clusters (Operational Taxonomical Units or OTUs) using four different thresholds to differentiate OTUs: 3%, 2%, 1% and 0% difference in sequence. The highlighted 99% sequence identity threshold was chosen for the phylotype representation in the phylogenetic tree (Fig. 1b).
OTU OTUs Jackknife % observed Bootstrap % observed definition observed Estimate (Jackknife) estimate (Bootstrap) 100% 463 739 +/- 48 63% 574 +/- 64 89% 99% 216 303 +/- 6 71% 254 +/- 24 84% 98% 122 165 +/- 1 74% 140 +/- 12 85% 97% 84 115 +/- 1 73% 97 +/- 9 87%
Table S2. Estimates of gross community structure based on sequence composition binning, and conserved single copy gene phylogenies (weighted for contig size). For the PhyloPythia binning only fragments classified at class or phylum level were considered.
Method % Spirochaetes % Fibrobacteres % other Sequence composition-based classifier: PhyloPythia 59 6 35 Single copy gene phylogenies: Ribosomal protein S3 (rpsC) 73 19 8 Ribosome recycling factor 79 4 17 Ribosome-binding factor A 59 0 41 Translation initiation factor 2 (IF-2; GTPase) 100 0 0 Polyribonucleotide nucleotidyl transferase 84 16 0 Imidazoleglycerol-phosphate dehydratase 0 20 80 Elongation factor EFG (fusA) 82 5 14 Membrane GTPase (lepA) 67 33 0 Ribosomal protein L2 (rplB) 63 26 11 Elongation factor EF-Tu (tufA) 82 18 0 Average +/- standard deviation 68 +/- 26 13 +/- 11 19 +/- 25
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Table S3. Summary of glycoside hydrolases (GHs) and carbohydrate-binding modules (CBMs) discovered in the P3 luminal microbiota. CAZy Pfam HMM Name Pfam P fam Description Known Activities (CAZy) Term ite Gut C om m unity Fam ily Accession m etagenom e ¶ fosm ids ¶
JGI ID 2004080001 2004175000 N ucleotide sequence length 61533145 459633 P rotein coding genes 82789 436
Glycoside hydrolase catalytic dom ains GH1 Glyco_hydro_1 P F00232.8 Glycosyl hydrolase family 1 -glucosidase, -galactosidase, -mannosidase, 22 (256 ppm) 0 others GH2 Glyco_hydro_2_C P F02836.6 Glycosyl hydrolases family 2, TIM -galactosidase, -mannosidase, others 23 (281 ppm) 2 (3818 ppm) barrel domain GH3 Glyco_hydro_3 P F00933.11 Glycosyl hydrolase family 3 N -1,4-glucosidase, -1,4-xylosidase, -1,3- 69 (670 ppm) 1 (1547 ppm) terminal domain glucosidase, -L-arabinofuranosidase, others GH4 Glyco_hydro_4 P F02056.5 Family 4 glycosyl hydrolase -glucosidase, -galactosidase, - 14 (192 ppm) 0 glucuronidase, others GH5 Cellulase P F00150.7 Cellulase (glycosyl hydrolase cellulase, -1,4-endoglucanase, -1,3- 56 (662 ppm) 1 (1971 ppm) family 5) glucosidase, -1,4-endoxylanase, -1,4- endomannanase, others GH6 Glyco_hydro_6 P F01341.7 Glycosyl hydrolases family 6 endoglucanase, cellobiohydrolase 0 0 GH7 Glyco_hydro_7 P F00840.10 Glycosyl hydrolase family 7 endoglucanase, cellobiohydrolase (fungal only) 0 0 GH8 Glyco_hydro_8 P F01270.7 Glycosyl hydrolases family 8 cellulase, -1,3-glucosidase, -1,4- 5 (70 ppm) 0 endoxylanase, -1,4-endomannanase, others GH9 Glyco_hydro_9 P F00759.8 Glycosyl hydrolase family 9 endoglucanase, cellobiohydrolase, - 9 (131 ppm) 1 (2428 ppm) glucosidase GH10 Glyco_hydro_10 P F00331.10 Glycosyl hydrolase family 10 xylanase, -1,3-endoxylanase 46 (572 ppm) 1 (2187 ppm) GH11 Glyco_hydro_11 P F00457.7 Glycosyl hydrolases family 11 xylanase 14 (110 ppm) 0 GH12 Glyco_hydro_12 P F01670.6 Glycosyl hydrolase family 12 endoglucanase, -1,3-1,4-glucanase, xyloglucan 00 hydrolase GH13 A lpha-amylase P F00128.11 A lpha amylase, catalytic domain -amylase, catalytic domain, and related 48 (661 ppm) 0 enzymes GH14 Glyco_hydro_14 P F01373.7 Glycosyl hydrolase family 14 -amylase 0 0 GH15 Glyco_hydro_15 P F00723.10 Glycosyl hydrolases family 15 glucoamylase, glucodextranase 0 0 GH16 Glyco_hydro_16 P F00722.9 Glycosyl hydrolases family 16 -1,3(4)-endoglucanase, others 1 (8 ppm) 0 GH17 Glyco_hydro_17 P F00332.8 Glycosyl hydrolases family 17 glucan endo-1,3- -D-glucosidase glucan 1,3- - 00 glucosidase, others GH18 Glyco_hydro_18 P F00704.16 Glycosyl hydrolases family 18 chitinase, endo- -N-acetylglucosaminidase, non- 17 (223 ppm) 0 catalytic proteins GH19 Glyco_hydro_19 P F00182.8 Chitinase class I chitinase 0 0 GH20 Glyco_hydro_20 P F00728.11 Glycosyl hydrolase family 20, -hexosaminidase, lacto-N-biosidase 15 (152 ppm) 0 catalytic domain GH21 deleted family GH22 Lys P F00062.10 C-type lysozyme/alpha- C-type lysozyme, -lactalbumin (eukaryotic 00 lactalbumin family only) GH23 SLT# P F01464.10 Transglycosylase S LT domain G-type lysozyme, peptidoglycan lytic 52 (294 ppm) 1 (751 ppm) transglycosylase GH24 P hage_lysozyme $ PF00959.9 Phage lysozyme lysozyme 0 0 GH25 Glyco_hydro_25 P F01183.10 Glycosyl hydrolases family 25 lysozyme 1 (5 ppm) 0 GH26 Glyco_hydro_26 P F02156.5 Glycosyl hydrolase family 26 -1,3-xylanase, mannanase 15 (197 ppm) 0 GH27 Melibiase PF02065.8 Melibiase -galactosidase, -N-acetylgalactosaminidase, 4 (51 ppm) 0 isomalto-dextranase GH28 Glyco_hydro_28 P F00295.7 Glycosyl hydrolases family 28 polygalacturonase, rhamnogalacturonase, 6 (92 ppm) 0 others GH29 A lpha_L_fucos P F01120.7 A lpha-L-fucosidase -L-fucosidase 0 0 GH30 Glyco_hydro_30 P F02055.6 O-Glycosyl hydrolase family 30 -1,6-glucanase, -xylosidase 0 0 GH31 Glyco_hydro_31 P F01055.15 Glycosyl hydrolases family 31 -glucosidase, -xylosidase, others 26 (349 ppm) 1 (2807 ppm) GH32 Glyco_hydro_32N P F00251.9 Glycosyl hydrolases family 32 N invertase, others 0 0 terminal GH33 B NR P F02012.9 B NR/A sp-box repeat sialidase, neuraminidase 0 0 GH34 Neur P F00064.8 Neuraminidase sialidase, neuraminidase (viral only) 0 0 GH35 Glyco_hydro_35 P F01301.9 Glycosyl hydrolases family 35 -galactosidase 3 (38 ppm) 0 § GH36 BLAST search galactosidase, N-acetylgalactosaminidase 5 to 7 0
GH37 Trehalase P F01204.8 Trehalase trehalase 0 0 GH38 Glyco_hydro_38 P F01074.11 Glycosyl hydrolases family 38 N- -mannosidase 11 (106 ppm) 0 terminal domain GH39 Glyco_hydro_39 P F01229.7 Glycosyl hydrolases family 39 -xylosidase, -L-iduronidase 3 (62 ppm) 0 GH40 deleted family GH41 deleted family GH42 Glyco_hydro_42 P F02449.5 B eta-galactosidase -galactosidase 24 (332 ppm) 1 (2754 ppm) # GH43 Glyco_hydro_43 P F04616.4 Glycosyl hydrolases family 43 xylanase, -xylosidase, -L- 16 (226 ppm) 1 (1906 ppm) arabinofuranosidase, arabinanase, others GH44 BLAST search § endoglucanase, xyloglucanase 6 0 GH45 Glyco_hydro_45 P F02015.6 Glycosyl hydrolase family 45 endoglucanase (mainly eukaryotic, 2 bacterial) 4 (38 ppm) 1 (1939 ppm) GH46 Glyco_hydro_46 P F01374.8 Glycosyl hydrolase family 46 chitosanase 0 0 GH47 Glyco_hydro_47 P F01532.10 Glycosyl hydrolase family 47 -mannosidase (mainly eukaryotic, 1 bacterial) 0 0 GH48 Glyco_hydro_48 P F02011.5 Glycosyl hydrolase family 48 endoglucanase, cellobiohydrolase 0 0 GH49 Glyco_hydro_49 P F03718.3 Glycosyl hydrolase family 49 dextranase, isopullulanase, others 0 0 § GH50 BLAST search -agarase 0 0 GH51 BLAST search § endoglucanase, -L-arabinofuranosidase 18 to 19 0 GH52 Glyco_hydro_52 P F03512.3 Glycosyl hydrolase family 52 -xylosidase 3 (47 ppm) 0 GH53 Glyco_hydro_53 # P F07745.2 Glycosyl hydrolase family 53 -1,4-endogalactanase 12 (154 ppm) 0 # GH54 A rabFuran-catal P F09206.1 A lpha-L-arabinofuranosidase B , -xylosidase, -L-arabinofuranosidase (mainly 00 catalytic eukaryotic, 2 bacterial) GH55 BLAST search § endo-1,3-glucanase, exo-1,3-glucanase (mainly 00 eukaryotic, 2 bacterial)
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CAZy Pfam HMM Name Pfam P fam Description Known Activities (CAZy) Term ite Gut C om m unity Fam ily Accession m etagenom e ¶ fosm ids ¶
JGI ID 2004080001 2004175000 N ucleotide sequence length 61533145 459633 P rotein coding genes 82789 436
Glycoside hydrolase catalytic dom ains GH56 Glyco_hydro_56 P F01630.8 Hyaluronidase hyaluronidase (eukaryotic only) 0 0 GH57 Glyco_hydro_57 P F03065.4 Glycosyl hydrolase family 57 -amylase, 4- -glucanotransferase, - 17 (274 ppm) 0 galactosidase, others GH58 BLAST search § endo-N-acetylneuraminidase or endo-sialidase 1 0 GH59 Glyco_hydro_59 P F02057.5 Glycosyl hydrolase family 59 galactocerebrosidase (mainly eukaryotic, 2 00 bacterial) GH60 deleted family GH61 Glyco_hydro_61 P F03443.4 Glycosyl hydrolase family 61 endoglucanase (fungal only) 0 0 GH62 Glyco_hydro_62 P F03664.3 Glycosyl hydrolase family 62 -L-arabinofuranosidase 0 0 GH63 Glyco_hydro_63 P F03200.5 Mannosyl oligosaccharide processing -glucosidase 0 0 glucosidase § GH64 BLAST search -1,3-glucanase 0 0 GH65 Glyco_hydro_65m P F03632.4 Glycosyl hydrolase family 65 trehalase, maltose phosphorylase, trehalose 6 (77 ppm) 0 central catalytic domain phosphorylase GH66 BLAST search § cycloisomaltooligosaccharide 00 glucanotransferase, dextranase GH67 Glyco_hydro_67M P F07488.1 Glycosyl hydrolase family 67 -glucuronidase, others 10 (96 ppm) 0 middle domain GH68 Glyco_hydro_68 P F02435.6 Levansucrase/Invertase levansucrase, others 0 0 GH69 renamed P L16 GH70 Glyco_hydro_70 P F02324.6 Glycosyl hydrolase family 70 dextransucrase, others 0 0 GH71 Glyco_hydro_71 P F03659.4 Glycosyl hydrolase family 71 -1,3-glucanase (mainly fungal, 1 bacterial) 0 0 GH72 Glyco_hydro_72 P F03198.3 Glycolipid anchored surface -1,3-glucanosyltransglycosylase (fungal only) 0 0 protein (GA S 1) GH73 Glucosaminidase P F01832.9 Mannosyl-glycoprotein endo-beta- endo- -N-acetylglucosaminidase, others 0 0 N-acetylglucosaminidase GH74 BLAST search § endoglucanase, cellobiohydrolase, 70 xyloglucanase GH75 Chitosanase P F07335.1 Fungal chitosanase chitosanase (mainly fungal) 0 0 GH76 Glyco_hydro_76 P F03663.4 Glycosyl hydrolase family 76 -1,6-mannanase 0 0 GH77 Glyco_hydro_77 P F02446.7 4-alpha-glucanotransferase 4- -glucanotransferase, amylomaltase 14 (242 ppm) 0 GH78 B ac_rhamnosid P F05592.1 B acterial alpha-L-rhamnosidase -L-rhamnosidase 0 0 GH79 Glyco_hydro_79n P F03662.3 Glycosyl hydrolase family 79, N- endo- -glucuronidase 0 0 terminal domain GH80 BLAST search § chitosanase 0 0 GH81 Glyco_hydro_81 P F03639.3 Glycosyl hydrolase family 81 -1,3-glucanase (mainly eukaryotic, 6 bacterial) 0 0
§ GH82 BLAST search carrageenase (2 bacterial) 0 0 GH83 HN P F00423.9 Hemagglutinin-neuraminidase hemaglutinin-neuraminidase (viral only) 0 0 GH84 Hyaluronidase_2 # P F07555.2 Hyaluronidase hyaluronidase, N-acetyl b-glucosaminidase 0 0 GH85 Glyco_hydro_85 P F03644.3 Glycosyl hydrolase family 85 endo- -N-acetylglucosaminidase 0 0 § GH86 BLAST search -agarase 0 0 § GH87 BLAST search -1,3-glucanase, mycodextranase 0 0 GH88 Glyco_hydro_88 P F07470.2 Glycosyl Hydrolase Family 88 d-4,5 unsaturated -glucuronyl hydrolase 9 (133 ppm) 0 GH89 NA GLU P F05089.2 A lpha-N-acetylglucosaminidase -N-acetylglucosaminidase 0 0 (NA GLU) GH90 BLAST search § endorhamnosidase (mainly viral, 3 bacterial) 0 0 GH91 BLAST search § inulin fructotransferase 1 0 # GH92 Glyco_hydro_92 P F07971.2 Glycosyl hydrolase family 92 -1,2-mannosidase 2 (29 ppm) 0 GH93 BLAST search § exo-arabinanase (mainly fungal, 4 bacterial) 0 0 GH94 BLAST search § cellobiose phosphorylase, chitobiose 68 to 132 1 to 2 phosphorylase, cellodextrin phosphorylase § GH95 BLAST search -L-fucosidase 12 to 31 0 GH96 BLAST search § -agarase (2 bacterial, 2 unclassified) 0 0 § GH97 BLAST search -glucosidase 0 0 # GH98 Glyco_hydro_98M P F08306.1 Glycosyl hydrolase family 98 endo- -galactosidase 1 (12 ppm) 0 GH99 BLAST search § endo- -1,2-mannosidase (mainly eukaryotic, 2 00 bacterial) GH100 Invertase_neut P F04853.2 P lant neutral invertase alkaline and neutral invertase 0 0 GH101 BLAST search § endo- -N-acetylgalactosaminidase 0 0 GH102 MltA P F03562.4 MltA N-terminal domain peptidoglycan lytic transglycosylase 0 0 GH103 TIGR: MltB # TIGR02282 MltB: lytic murein peptidoglycan lytic transglycosylase 3 (31 ppm) 0 transglycosylase B GH104 P hage_lysozyme $ P F00959 P hage lysozyme peptidoglycan lytic transglycosylase see GH24 GH105 Glyco_hydro_88 # P F07470.2 Glycosyl Hydrolase Family 88 unsaturated rhamnogalacturonyl hydrolase see GH88 GH106 BLAST search § -L-rhamnosidase 2 0 GH107 BLAST search § sulfated fucan endo-1,4-fucanase (3 bacterial) 0 0 GH108 DUF847 # P F05838.2 P redicted lysozyme (DUF847) N-acetylmuramidase 0 0 GH109 BLAST search § -N-acetylgalactosaminidase 3 to 5 0 § GH110 BLAST search -galactosidase 0 0
SUPPLEMENTARY INFORMATION Warnecke et al: Page 10 www.nature.com/nature 10 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
CAZy Pfam HMM Name Pfam P fam Description Known Activities (CAZy) Term ite Gut C om m unity Fam ily Accession m etagenom e ¶ fosm ids ¶
JGI ID 2004080001 2004175000 N ucleotide sequence length 61533145 459633 P rotein coding genes 82789 436
C arbohydrate-binding dom ains CB M1 CB M_1 P F00734.8 Fungal cellulose binding domain cellulose-binding domain (mainly fungal, 1 viral) 0 0 CB M2 CB M_2 P F00553.9 Cellulose binding domain cellulose-binding domain 0 0 CB M3 CB M_3 P F00942.8 Cellulose binding domain cellulose-binding domain 0 0 CBM4 CB M_4_9 & P F02018.7 Carbohydrate binding domain amorphous cellulose-, xylan- and glucan-binding 5 (35 ppm) 0 domain CBM5 CBM_5_12 ¥ P F02839.4 Carbohydrate binding domain cellulose-binding domain 0 0 CB M6 CB M_6 P F03422.5 Carbohydrate binding module amorphous cellulose- and xylan-binding domain 13 (79 ppm) 1 (862 ppm) (family 6) CB M7 deleted entry CBM8 BLAST search § cellulose-binding domain (2 bacterial, 2 00 eukaryotic) CBM9 CB M_4_9 & P F02018.7 Carbohydrate binding domain cellulose-binding domain see CB M4 CB M10 CB M_10 P F02013.6 Cellulose or protein binding cellulose-binding domain (aerobic bacteria) and 00 domain dockerin (anaerobic fungi) CBM11 CBM_11 # P F03425.3 Carbohydrate binding domain glucan-binding domain 3 (26 ppm) 0 (family 11) CBM12 CB M_5_12 ¥ P F02839.4 Carbohydrate binding domain chitin-binding domain see CB M5 CB M13 Ricin_B _lectin P F00652.11 Ricin-type beta-trefoil lectin mannose- and xylan-binding domain 0 0 domain CB M14 CB M_14 P F01607.12 Chitin binding P eritrophin-A chitin-binding domain 0 0 domain CB M15 CB M_15 P F03426.4 Carbohydrate binding domain xylan-binding domain (2 bacterial) 0 0 (family 15) CB M16 CB M_4_9 & P F02018.7 Carbohydrate binding domain carbohydrate-binding module 16 see CB M4 CBM17 CB M_17_28 P F03424.3 Carbohydrate binding domain amorphous cellulose- and cellooligosaccharide- 00 (family 17/28) binding domain CB M18 Chitin_bind_1 P F00187.8 Chitin recognition protein chitin-binding domain (eukaryotic only) 0 0 CB M19 CB M_19 P F03427.3 Carbohydrate binding domain chitin-binding domain (eukaryotic only) 0 0 (family 19) CB M20 CB M_20 P F00686.9 S tarch binding domain starch-binding domain 0 0 CB M21 CB M_21 P F03370.3 P utative phosphatase regulatory starch-binding domain (mainly eukaryotic, 1 00 subunit bacterial) CBM22 CB M_4_9 & P F02018.7 Carbohydrate binding domain xylan-binding domain see CB M4 CBM23 BLAST search § mannan-binding domain (3 bacterial) 0 0 § CBM24 BLAST search -1,3-glucan (mutan)-binding domain (fungal 00 only) CB M25 CB M_25 P F03423.3 Carbohydrate binding domain starch-binding domain 0 0 (family 25) CBM26 BLAST search § starch-binding domain 0 0 CBM27 CBM27 # P F09212.1 Carbohydrate binding module 27 mannan-binding domain 0 0 CBM28 CB M_17_28 P F03424.3 Carbohydrate binding domain amorphous cellulose- and cellooligosaccharide- see CB M17 (family 17/28) binding domain CBM29 BLAST search § mannan/glucomannan-binding domain (1 00 eukaryotic) CBM30 BLAST search § cellulose-binding domain 1 to 8 0 § CBM31 BLAST search -1,3-xylan binding domain (4 bacterial) 0 0 CB M32 F5_F8_type_C P F00754.14 F5/8 type C domain galactose- and lactose-binding domain 4 (22 ppm) 0 CB M33 Chitin_bind_3 P F03067.5 Chitin binding domain chitin-binding domain 0 0 CB M34 A lpha_amylase_N P F02903.4 A lpha amylase, N-terminal ig-like starch-binding domain 0 0 domain § CBM35 BLAST search mannan- xylan- and -galactan-binding domain 0 to 1 0 CBM36 BLAST search § xylan-binding domain 2 to 13 0 to 1 CBM37 BLAST search § broad binding specificity 1 0 CBM38 BLAST search § inulin-binding domain 0 0 CBM39 BLAST search § -1,3-glucan binding domain (eukaryotic only) 0 0 CB M40 S ialidase P F02973.6 S ialidase, N-terminal domain sialic acid-binding domain 0 0 CBM41 PUD# P F03714.4 B acterial pullanase-associated -glucan-, amylose-, amylopectin-, and pullulan- 00 domain binding domain CBM42 AbfB# P F05270.3 A lpha-L-arabinofuranosidase B arabinose-binding domain 0 0 (ABFB) # CBM43 X8 P F07983.2 X8 domain -1,3-glucan binding domain (eukaryotic only) 0 0 CBM44 BLAST search § cellulose- and xyloglucan-binding domain (2 00 bacterial) CBM45 BLAST search § starch-binding domain (eukaryotic only) 0 0 CBM46 BLAST search § cellulose-binding domain 0 0 CB M47 F5_F8_type_C # P F00754.14 F5/8 type C domain fucose-binding domain see CB M32 CBM48 BLAST search § glycogen-binding domain 0 to 1 0 CBM49 BLAST search § crystalline cellulose-binding domain (eukaryotic 00 only)
SUPPLEMENTARY INFORMATION Warnecke et al: Page 11 www.nature.com/nature 11 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
CAZy Pfam HMM Name Pfam P fam Description Known Activities (CAZy) Term ite Gut C om m unity Fam ily Accession m etagenom e ¶ fosm ids ¶
JGI ID 2004080001 2004175000 N ucleotide sequence length 61533145 459633 P rotein coding genes 82789 436
Other dom ains oftentim es associated with GH catalytic dom ains A lpha-amylase_C P F02806.6 A lpha amylase, C-terminal all-beta -amylase, C-terminal all- domain; associated 00 domain with GH13 A lpha-L-A F_C P F06964.1 A lpha-L-arabinofuranosidase C- -L-arabinofuranosidase, C-terminal domain; 10 (67 ppm) 0 terminus associated with GH51 A lpha-mann_mid P F09261.1 A lpha mannosidase, middle middle domain; associated with GH38 15 (56 ppm) 0 domain B ig_1 P F02369.6 B acterial Ig-like domain (group 1) B acterial Ig-like domain (group 1) 0 0 B ig_2 P F02368.7 B acterial Ig-like domain (group 2) B acterial Ig-like domain (group 2) 140 (540 ppm) 0 B ig_3 P F07523.2 B acterial Ig-like domain (group 3) B acterial Ig-like domain (group 3) 22 (72 ppm) 0 B ig_4 P F07532.1 B acterial Ig-like domain (group 4) B acterial Ig-like domain (group 4) 0 0 B gal_small_N P F02929.6 B eta galactosidase small chain -galactosidase, small chain; associated with 5 (53 ppm) 1 (1932 ppm) GH2 CB M_X P F06204.1 P utative carbohydrate binding associated with GH94 44 (136 ppm) 1 (418 ppm) domain CelD_N P F02927.4 N-terminal ig-like domain of N-terminal Ig-like domain of cellulase; 5 (22 ppm) 1 (607 ppm) cellulase associated with GH9 CHB _HE X P F03173.3 P utative carbohydrate binding P utative carbohydrate binding domain; 00 domain associated with GH20 CHB _HE X_C P F03174.3 Chitobiase/beta-hexosaminidase Chitobiase/beta-hexosaminidase C-terminal 00 C-terminal domain domain; associated with GH20 ChiC P F06483.2 Chitinase C Chitinase C; associated with GH18 0 0 ChitinaseA _N P F08329.1 Chitinase A , N-terminal domain Chitinase A , N-terminal domain; associated with 00 GH18 Cohesin P F00963.8 Cohesin domain Cohesin domain 0 0 Dockerin_1 P F00404.8 Dockerin type I repeat Dockerin type I repeat 0 0 fn3 P F00041.10 Fibronectin type III domain Fibronectin type III domain 45 (181 ppm) 0 GDE _C P F06202.3 A mylo-alpha-1,6-glucosidase A mylo-alpha-1,6-glucosidase 1 (12 ppm) 0 Glucodextran_B P F09136.1 Glucodextranase, domain B Glucodextranase, domain B ; associated with 00 GH15 Glucodextran_N P F09137.1 Glucodextranase, domain N Glucodextranase, domain N; associated with 00 GH15 Glyco_hydro_2_N P F02837.7 Glycosyl hydrolases family 2, sugar-binding domain 26 (178 ppm) 2 (2206 ppm) sugar binding domain Glyco_hydro_2 P F00703.10 Glycosyl hydrolases family 2, immunoglobulin-like -sandwich domain 4 (21 ppm) 0 immunoglobulin-like beta- sandwich domain Glyco_hydro_3_C P F01915.11 Glycosyl hydrolase family 3 C C-terminal domain (glycan-binding?) 42 (402 ppm) 1 (2317 ppm) terminal domain Glyco_hydro_20b P F02838.5 Glycosyl hydrolase family 20, domain 2 0 0 domain 2 Glyco_hydro_32C P F08244.1 Glycosyl hydrolases family 32 C C-terminal domain 0 0 terminal Glyco_hydro_38C P F07748.2 Glycosyl hydrolases family 38 C- C-terminal domain 12 (170 ppm) 0 terminal domain Glyco_hydro_42M P F08532.1 B eta-galactosidase trimerisation trimerisation domain 20 (163 ppm) 1 (1371 ppm) domain Glyco_hydro_42C P F08533.1 B eta-galactosidase C-terminal C-terminal domain 8 (23 ppm) 1 (392 ppm) domain Glyco_hydro_65N P F03636.4 Glycosyl hydrolase family 65, N- N-terminal domain 1 (10 ppm) 0 terminal domain Glyco_hydro_65C P F03633.4 Glycosyl hydrolase family 65, C- C-terminal domain 3 (8 ppm) 0 terminal domain Glyco_hydro_67N P F03648.4 Glycosyl hydrolase family 67 N- N-terminal domain 2 (11 ppm) 0 terminus Glyco_hydro_67C P F07477.1 Glycosyl hydrolase family 67 C- C-terminal domain 11 (112 ppm) 0 terminus Glyco_hydro_98C P F08307.1 Glycosyl hydrolase family 98 C- C-terminal domain 0 0 terminal domain Glyco_transf_36 P F06165.1 Glycosyltransferase family 36 associated with GH94 47 (248 ppm) 1 (738 ppm) GT36_A F P F06205.2 Glycosyltransferase 36 associated with GH94 45 (189 ppm) 1 (568 ppm) associated family He_P IG P F05345.2 P utative Ig domain P utative Ig-like domain 11 (24 ppm) 2 (627 ppm) Isoamylase_N P F02922.7 Isoamylase N-terminal domain Isoamylase N-terminal domain; associated with 15 (67 ppm) 0 GH13 TIG P F01833.13 IP T/TIG domain Ig-like domain 0 0
Footnotes ¶ P fam HMM hits are counted if their e-value is smaller than 1e-4. B LA S T hits are counted if their e-value is smaller than 1e-6. The value in parenthesis is the ratio between the total nucleotide length of the hits for this family and the total nucleotide l # CA Zy does not provide weblinks to P fam for this family, but this P fam HMM recognizes the sequences of this family. § No P fam HMM is available for this family. B LA S T searches were conducted with segments of selected sequences listed at CA Zy corresponding to this family. $ The CA Zy website links to P fam P F00959.9 (P hage_lysozyme) for both, GH24 and GH104. & The CA Zy website links to P fam P F02018.7 (CB M_4_9) for all, CB M4, CB M9, CB M16, and CB M22. ¥ The CA Zy website links to P fam P F02839.4 (CB M_5_12) for both, CB M5 and CB M12. The CA Zy website links to P fam P F03424.3 (CB M_17_28) for both, CB M17 and CB M28.
SUPPLEMENTARY INFORMATION Warnecke et al: Page 12 www.nature.com/nature 12 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Table S4. Summary of the P3 luminal microbiota GH and CBM domains, their PhyloPhytia binning information, proteomics, and activity results. CAZy P fam HMM Nam e Known Activities (CAZy)P hyloP hytia P roteom ics Activity Fam ily treponem a fibrobacter data m ining hybridization activity screen m etagenom e (fosm ids) active (inactive) JGI ID Nucleotide sequence length P rotein coding genes
Glycoside hydrolase catalytic dom ains GH1 Glyco_hydro_1 -glucosidase, -galactosidase, -mannosidase, 50 1 others GH2 Glyco_hydro_2_C -galactosidase, -mannosidase, others 4 (2) 0 GH3 Glyco_hydro_3 -1,4-glucosidase, -1,4-xylosidase, -1,3- 14 (1) 0 1 glucosidase, -L-arabinofuranosidase, others GH4 Glyco_hydro_4 -glucosidase, -galactosidase, - 30 2 glucuronidase, others GH5 Cellulase cellulase, -1,4-endoglucanase, -1,3- 6 (1) 0 2 11 (0) 8 (2) 7 (2 partial) glucosidase, -1,4-endoxylanase, -1,4- endomannanase, others GH6 Glyco_hydro_6 endoglucanase, cellobiohydrolase 0 0 GH7 Glyco_hydro_7 endoglucanase, cellobiohydrolase (fungal only) 0 0 GH8 Glyco_hydro_8 cellulase, -1,3-glucosidase, -1,4- 00 endoxylanase, -1,4-endomannanase, others GH9 Glyco_hydro_9 endoglucanase, cellobiohydrolase, - 0 2 (1) 3 (4) 4 (1) glucosidase GH10 Glyco_hydro_10 xylanase, -1,3-endoxylanase 11 (1) 0 1 GH11 Glyco_hydro_11 xylanase 4 0 GH12 Glyco_hydro_12 endoglucanase, -1,3-1,4-glucanase, xyloglucan 00 hydrolase GH13 A lpha-amylase -amylase, catalytic domain, and related 60 2 enzymes GH14 Glyco_hydro_14 -amylase 0 0 GH15 Glyco_hydro_15 glucoamylase, glucodextranase 0 0 GH16 Glyco_hydro_16 -1,3(4)-endoglucanase, others 0 0 GH17 Glyco_hydro_17 glucan endo-1,3- -D-glucosidase glucan 1,3- - 00 glucosidase, others GH18 Glyco_hydro_18 chitinase, endo- -N-acetylglucosaminidase, non- 40 catalytic proteins GH19 Glyco_hydro_19 chitinase 0 0 GH20 Glyco_hydro_20 -hexosaminidase, lacto-N-biosidase 1 0 GH21 deleted family GH22 Lys C-type lysozyme, -lactalbumin (eukaryotic 00 only) GH23 SLT# G-type lysozyme, peptidoglycan lytic 11 (1) 0 transglycosylase GH24 P hage_lysozyme $ lysozyme 0 0 GH25 Glyco_hydro_25 lysozyme 1 0 GH26 Glyco_hydro_26 -1,3-xylanase, mannanase 3 0 GH27 Melibiase -galactosidase, -N-acetylgalactosaminidase, 00 isomalto-dextranase GH28 Glyco_hydro_28 polygalacturonase, rhamnogalacturonase, 10 others GH29 A lpha_L_fucos -L-fucosidase 0 0 GH30 Glyco_hydro_30 -1,6-glucanase, -xylosidase 0 0 GH31 Glyco_hydro_31 -glucosidase, -xylosidase, others 7 (1) 0 GH32 Glyco_hydro_32N invertase, others 0 0 GH33 B NR sialidase, neuraminidase 0 0 GH34 Neur sialidase, neuraminidase (viral only) 0 0 GH35 Glyco_hydro_35 -galactosidase 1 0 GH36 BLAST search § galactosidase, N-acetylgalactosaminidase
GH37 Trehalase trehalase 0 0 GH38 Glyco_hydro_38 -mannosidase 3 0 GH39 Glyco_hydro_39 -xylosidase, -L-iduronidase 2 0 GH40 deleted family GH41 deleted family GH42 Glyco_hydro_42 -galactosidase 4 (1) 0 1 # GH43 Glyco_hydro_43 xylanase, -xylosidase, -L- 6 (1) 0 arabinofuranosidase, arabinanase, others GH44 BLAST search § endoglucanase, xyloglucanase GH45 Glyco_hydro_45 endoglucanase (mainly eukaryotic, 2 bacterial) 0 (1) 1 (0) 1 (0) GH46 Glyco_hydro_46 chitosanase 0 0 GH47 Glyco_hydro_47 -mannosidase (mainly eukaryotic, 1 bacterial) 0 0 GH48 Glyco_hydro_48 endoglucanase, cellobiohydrolase 0 0 GH49 Glyco_hydro_49 dextranase, isopullulanase, others 0 0 § GH50 BLAST search -agarase § GH51 BLAST search endoglucanase, -L-arabinofuranosidase GH52 Glyco_hydro_52 -xylosidase 0 0 # GH53 Glyco_hydro_53 -1,4-endogalactanase 2 0 GH54 A rabFuran-catal # -xylosidase, -L-arabinofuranosidase (mainly 00 eukaryotic, 2 bacterial) GH55 BLAST search § endo-1,3-glucanase, exo-1,3-glucanase (mainly eukaryotic, 2 bacterial)
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CAZy Pfam HMM Name Known Activities (CAZy)PhyloPhytia Proteomics Activity Family treponema fibrobacter data mining hybridization activity screen metagenome (fosmids) active (inactive) JGI ID Nucleotide sequence length Protein coding genes
Glycoside hydrolase catalytic domains GH56 Glyco_hydro_56 hyaluronidase (eukaryotic only) 0 0 GH57 Glyco_hydro_57 -amylase, 4- -glucanotransferase, - 60 galactosidase, others GH58 BLAST search § endo-N-acetylneuraminidase or endo-sialidase GH59 Glyco_hydro_59 galactocerebrosidase (mainly eukaryotic, 2 00 bacterial) GH60 deleted family GH61 Glyco_hydro_61 endoglucanase (fungal only) 0 0 GH62 Glyco_hydro_62 -L-arabinofuranosidase 0 0 GH63 Glyco_hydro_63 processing -glucosidase 0 0 GH64 BLAST search § -1,3-glucanase GH65 Glyco_hydro_65m trehalase, maltose phosphorylase, trehalose 00 phosphorylase GH66 BLAST search § cycloisomaltooligosaccharide glucanotransferase, dextranase GH67 Glyco_hydro_67M -glucuronidase, others 4 0 GH68 Glyco_hydro_68 levansucrase, others 0 0 GH69 renamed PL16 GH70 Glyco_hydro_70 dextransucrase, others 0 0 GH71 Glyco_hydro_71 -1,3-glucanase (mainly fungal, 1 bacterial) 0 0 GH72 Glyco_hydro_72 -1,3-glucanosyltransglycosylase (fungal only) 0 0 GH73 Glucosaminidase endo- -N-acetylglucosaminidase, others 0 0 GH74 BLAST search § endoglucanase, cellobiohydrolase, xyloglucanase GH75 Chitosanase chitosanase (mainly fungal) 0 0 GH76 Glyco_hydro_76 -1,6-mannanase 0 0 GH77 Glyco_hydro_77 4--glucanotransferase, amylomaltase 4 0 GH78 Bac_rhamnosid -L-rhamnosidase 0 0 GH79 Glyco_hydro_79n endo- -glucuronidase 0 0 GH80 BLAST search § chitosanase GH81 Glyco_hydro_81 -1,3-glucanase (mainly eukaryotic, 6 bacterial) 0 0
GH82 BLAST search § carrageenase (2 bacterial) GH83 HN hemaglutinin-neuraminidase (viral only) 0 0 GH84 Hyaluronidase_2 # hyaluronidase, N-acetyl b-glucosaminidase 0 0 GH85 Glyco_hydro_85 endo- -N-acetylglucosaminidase 0 0 GH86 BLAST search § -agarase GH87 BLAST search § -1,3-glucanase, mycodextranase GH88 Glyco_hydro_88 d-4,5 unsaturated -glucuronyl hydrolase 3 0 1 GH89 NAGLU -N-acetylglucosaminidase 0 0 GH90 BLAST search § endorhamnosidase (mainly viral, 3 bacterial) GH91 BLAST search § inulin fructotransferase GH92 Glyco_hydro_92 # -1,2-mannosidase 0 0 GH93 BLAST search § exo-arabinanase (mainly fungal, 4 bacterial) GH94 BLAST search § cellobiose phosphorylase, chitobiose phosphorylase, cellodextrin phosphorylase GH95 BLAST search § -L-fucosidase GH96 BLAST search § -agarase (2 bacterial, 2 unclassified) GH97 BLAST search § -glucosidase GH98 Glyco_hydro_98M # endo- -galactosidase 0 0 GH99 BLAST search § endo- -1,2-mannosidase (mainly eukaryotic, 2 bacterial) GH100 Invertase_neut alkaline and neutral invertase 0 0 GH101 BLAST search § endo- -N-acetylgalactosaminidase GH102 MltA peptidoglycan lytic transglycosylase 0 0 GH103 TIGR: MltB # peptidoglycan lytic transglycosylase 0 0 GH104 Phage_lysozyme $ peptidoglycan lytic transglycosylase GH105 Glyco_hydro_88 # unsaturated rhamnogalacturonyl hydrolase GH106 BLAST search § -L-rhamnosidase GH107 BLAST search § sulfated fucan endo-1,4-fucanase (3 bacterial) GH108 DUF847 # N-acetylmuramidase 0 0 GH109 BLAST search § -N-acetylgalactosaminidase GH110 BLAST search § -galactosidase
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CAZy Pfam HMM Name Known Activities (CAZy)PhyloPhytia Proteomics Activity Family treponema fibrobacter data mining hybridization activity screen metagenome (fosmids) active (inactive) JGI ID Nucleotide sequence length Protein coding genes
Carbohydrate-binding domains CBM1 CBM_1 cellulose-binding domain (mainly fungal, 1 viral) 0 0 CBM2 CBM_2 cellulose-binding domain 0 0 CBM3 CBM_3 cellulose-binding domain 0 0 CBM4 CBM_4_9 & amorphous cellulose-, xylan- and glucan-binding 001 domain CBM5 CBM_5_12 ¥ cellulose-binding domain 0 0 CBM6 CBM_6 amorphous cellulose- and xylan-binding domain 2 (1) 0
CBM7 deleted entry CBM8 BLAST search § cellulose-binding domain (2 bacterial, 2 eukaryotic) CBM9 CBM_4_9 & cellulose-binding domain CBM10 CBM_10 cellulose-binding domain (aerobic bacteria) and 00 dockerin (anaerobic fungi) CBM11 CBM_11 # glucan-binding domain 0 0 CBM12 CBM_5_12 ¥ chitin-binding domain CBM13 Ricin_B_lectin mannose- and xylan-binding domain 0 0 CBM14 CBM_14 chitin-binding domain 0 0 CBM15 CBM_15 xylan-binding domain (2 bacterial) 0 0 CBM16 CBM_4_9 & carbohydrate-binding module 16 CBM17 CBM_17_28 amorphous cellulose- and cellooligosaccharide- 00 binding domain CBM18 Chitin_bind_1 chitin-binding domain (eukaryotic only) 0 0 CBM19 CBM_19 chitin-binding domain (eukaryotic only) 0 0 CBM20 CBM_20 starch-binding domain 0 0 CBM21 CBM_21 starch-binding domain (mainly eukaryotic, 1 00 bacterial) CBM22 CBM_4_9 & xylan-binding domain CBM23 BLAST search § mannan-binding domain (3 bacterial) CBM24 BLAST search § -1,3-glucan (mutan)-binding domain (fungal only) CBM25 CBM_25 starch-binding domain 0 0 CBM26 BLAST search § starch-binding domain CBM27 CBM27 # mannan-binding domain 0 0 CBM28 CBM_17_28 amorphous cellulose- and cellooligosaccharide- binding domain CBM29 BLAST search § mannan/glucomannan-binding domain (1 eukaryotic) CBM30 BLAST search § cellulose-binding domain CBM31 BLAST search § -1,3-xylan binding domain (4 bacterial) CBM32 F5_F8_type_C galactose- and lactose-binding domain 0 1 CBM33 Chitin_bind_3 chitin-binding domain 0 0 CBM34 Alpha_amylase_N starch-binding domain 0 0 CBM35 BLAST search § mannan- xylan- and -galactan-binding domain CBM36 BLAST search § xylan-binding domain CBM37 BLAST search § broad binding specificity CBM38 BLAST search § inulin-binding domain CBM39 BLAST search § -1,3-glucan binding domain (eukaryotic only) CBM40 Sialidase sialic acid-binding domain 0 0 CBM41 PUD # -glucan-, amylose-, amylopectin-, and pullulan- 00 binding domain CBM42 AbfB # arabinose-binding domain 0 0 CBM43 X8 # -1,3-glucan binding domain (eukaryotic only) 0 0 CBM44 BLAST search § cellulose- and xyloglucan-binding domain (2 bacterial) CBM45 BLAST search § starch-binding domain (eukaryotic only) CBM46 BLAST search § cellulose-binding domain CBM47 F5_F8_type_C # fucose-binding domain CBM48 BLAST search § glycogen-binding domain CBM49 BLAST search § crystalline cellulose-binding domain (eukaryotic only)
SUPPLEMENTARY INFORMATION Warnecke et al: Page 15 www.nature.com/nature 15 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
CAZy Pfam HMM Name Known Activities (CAZy)PhyloPhytia Proteomics Activity Family treponema fibrobacter data mining hybridization activity screen metagenome (fosmids) active (inactive) JGI ID Nucleotide sequence length Protein coding genes
Other domains oftentimes associated with GH catalytic domains Alpha-amylase_C -amylase, C-terminal all- domain; associated 00 with GH13 Alpha-L-AF_C -L-arabinofuranosidase, C-terminal domain; 10 associated with GH51 Alpha-mann_mid middle domain; associated with GH38 3 0 Big_1 Bacterial Ig-like domain (group 1) 0 0 Big_2 Bacterial Ig-like domain (group 2) 7 0 Big_3 Bacterial Ig-like domain (group 3) 0 0 Big_4 Bacterial Ig-like domain (group 4) 0 0 Bgal_small_N -galactosidase, small chain; associated with (1) 0 GH2 CBM_X associated with GH94 8 (1) 0 8 CelD_N N-terminal Ig-like domain of cellulase; 01 (1) associated with GH9 CHB_HEX Putative carbohydrate binding domain; 00 associated with GH20 CHB_HEX_C Chitobiase/beta-hexosaminidase C-terminal 00 domain; associated with GH20 ChiC Chitinase C; associated with GH18 0 0 ChitinaseA_N Chitinase A, N-terminal domain; associated with 00 GH18 Cohesin Cohesin domain 0 0 Dockerin_1 Dockerin type I repeat 0 0 fn3 Fibronectin type III domain 4 0 GDE_C Amylo-alpha-1,6-glucosidase 0 0 Glucodextran_B Glucodextranase, domain B; associated with 00 GH15 Glucodextran_N Glucodextranase, domain N; associated with 00 GH15 Glyco_hydro_2_N sugar-binding domain 5 (2) 2 Glyco_hydro_2 immunoglobulin-like -sandwich domain 0 0 Glyco_hydro_3_C C-terminal domain (glycan-binding?) 8 (1) 1 3 Glyco_hydro_20b domain 2 0 0 Glyco_hydro_32C C-terminal domain 0 0 Glyco_hydro_38C C-terminal domain 2 0 Glyco_hydro_42M trimerisation domain 4 (1) 0 Glyco_hydro_42C C-terminal domain 1 (1) 0 Glyco_hydro_65N N-terminal domain 0 0 Glyco_hydro_65C C-terminal domain 0 0 Glyco_hydro_67N N-terminal domain 0 0 Glyco_hydro_67C C-terminal domain 2 0 Glyco_hydro_98C C-terminal domain 0 0 Glyco_transf_36 associated with GH94 12 (1) 0 8 GT36_AF associated with GH94 13 (1) 0 8 He_PIG Putative Ig-like domain 1 0 (1) Isoamylase_N Isoamylase N-terminal domain; associated with 20 GH13 TIG Ig-like domain 0 0
Footnotes ¶ Pfam HMM hits are counted if their e-value is smaller than 1e-4. BLAST hits are counted if their e-value is smaller than 1e-6. The value in parenthesis is the ratio between the total nucleotide length of the hits for this family and the total nucleotide l
# CAZy does not provide weblinks to Pfam for this family, but this Pfam HMM recognizes the sequences of this family. § No Pfam HMM is available for this family. BLAST searches were conducted with segments of selected sequences listed at CAZy corresponding to this family. $ The CAZy website links to Pfam PF00959.9 (Phage_lysozyme) for both, GH24 and GH104. & The CAZy website links to Pfam PF02018.7 (CBM_4_9) for all, CBM4, CBM9, CBM16, and CBM22. ¥ The CAZy website links to Pfam PF02839.4 (CBM_5_12) for both, CBM5 and CBM12. The CAZy website links to Pfam PF03424.3 (CBM_17_28) for both, CBM17 and CBM28.
SUPPLEMENTARY INFORMATION Warnecke et al: Page 16 www.nature.com/nature 16 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Table S5. Comparison of abundance of selected GH and CBM domains in different single organism genomes and metagenome datasets. CAZy Pfam HMM Name Known Activities (CAZy)Human Gut Community Soil (Diversa Fibrobacter Saccharophagus Family Silage)¶ succinogenes¶ degradans¶
subject 7¶ subject 8¶
JGI ID 2004002000 2004002001 2001200001 2001800000 635640000 Nucle otide se que nce le ngth 15817685 20486813 152406385 4024184 5057531 Prote in coding ge ne s 20523 25983 184374 3341 4017
Glycoside hydrolase catalytic domains GH1 Glyco_hydro_1 -glucosidase, -galactosidase, -mannosidase, 20 (1209 ppm) 23 (1158 ppm) 9 (46 ppm) 0 2 (536 ppm) others GH2 Glyco_hydro_2_C -galactosidase, -mannosidase, others 13 (616 ppm) 17 (668 ppm) 7 (34 ppm) 1 (207 ppm) 6 (1102 ppm) GH3 Glyco_hydro_3 -1,4-glucosidase, -1,4-xylosidase, -1,3- 20 (780 ppm) 23 (682 ppm) 44 (160 ppm) 2 (351 ppm) 6 (807 ppm) glucosidase, -L-arabinofuranosidase, others GH4 Glyco_hydro_4 -glucosidase, -galactosidase, - 4 (250 ppm) 5 (206 ppm) 7 (38 ppm) 0 0 glucuronidase, others GH5 Cellulase cellulase, -1,4-endoglucanase, -1,3- 1 (49 ppm) 1 (44 ppm) 2 (10 ppm) 11 (2483 ppm) 17 (2834 ppm) glucosidase, -1,4-endoxylanase, -1,4- endomannanase, others GH6 Glyco_hydro_6 endoglucanase, cellobiohydrolase 0 0 3 (12 ppm) 0 1 (209 ppm) GH7 Glyco_hydro_7 endoglucanase, cellobiohydrolase (fungal only) 0 0 0 0 0 GH8 Glyco_hydro_8 cellulase, -1,3-glucosidase, -1,4- 0 1 (55 ppm) 1 (6 ppm) 6 (1602 ppm) 0 endoxylanase, -1,4-endomannanase, others GH9 Glyco_hydro_9 endoglucanase, cellobiohydrolase, - 0 0 2 (12 ppm) 8 (2901 ppm) 3 (823 ppm) glucosidase GH10 Glyco_hydro_10 xylanase, -1,3-endoxylanase 0 2 (97 ppm) 11 (47 ppm) 7 (1689 ppm) 5 (928 ppm) GH11 Glyco_hydro_11 xylanase 0 0 0 4 (595 ppm) 2 (243 ppm) GH12 Glyco_hydro_12 endoglucanase, -1,3-1,4-glucanase, xyloglucan 0 0 1 (3 ppm) 0 0 hydrolase GH13 Alpha-amylase -amylase, catalytic domain, and related 27 (1636 ppm) 45 (2213 ppm) 42 (228 ppm) 3 (768 ppm) 10 (2272 ppm) enzymes GH14 Glyco_hydro_14 -amylase 0 0 0 0 0 GH15 Glyco_hydro_15 glucoamylase, glucodextranase 0 0 17 (90 ppm) 0 1 (267 ppm) GH16 Glyco_hydro_16 -1,3(4)-endoglucanase, others 0 1 (33 ppm) 8 (29 ppm) 4 (620 ppm) 8 (1059 ppm) GH17 Glyco_hydro_17 glucan endo-1,3- -D-glucosidase glucan 1,3- - 000 0 0 glucosidase, others GH18 Glyco_hydro_18 chitinase, endo- -N-acetylglucosaminidase, non- 1 (58 ppm) 3 (156 ppm) 11 (49 ppm) 2 (458 ppm) 5 (1123 ppm) catalytic proteins GH19 Glyco_hydro_19 chitinase 0 0 0 0 0 GH20 Glyco_hydro_20 -hexosaminidase, lacto-N-biosidase 2 (100 ppm) 6 (259 ppm) 15 (69 ppm) 0 2 (447 ppm) GH22 Lys C-type lysozyme, -lactalbumin (eukaryotic 000 0 0 only) GH23 SLT # G-type lysozyme, peptidoglycan lytic 4 (93 ppm) 1 (17 ppm) 37 (85 ppm) 2 (175 ppm) 4 (273 ppm) transglycosylase GH24 Phage_lysozyme $ lysozyme 0 0 0 0 0 GH25 Glyco_hydro_25 lysozyme 8 (255 ppm) 4 (102 ppm) 6 (18 ppm) 0 0 GH26 Glyco_hydro_26 -1,3-xylanase, mannanase 0 1 (33 ppm) 0 4 (1011 ppm) 1 (191 ppm) GH27 Melibiase -galactosidase, -N-acetylgalactosaminidase, 3 (163 ppm) 8 (408 ppm) 1 (8 ppm) 1 (248 ppm) 1 (196 ppm) isomalto-dextranase GH28 Glyco_hydro_28 polygalacturonase, rhamnogalacturonase, 0 1 (47 ppm) 1 (6 ppm) 0 1 (225 ppm) others GH29 Alpha_L_fucos -L-fucosidase 0 4 (230 ppm) 5 (25 ppm) 0 0 GH30 Glyco_hydro_30 -1,6-glucanase, -xylosidase 1 (67 ppm) 1 (65 ppm) 0 0 2 (578 ppm) GH31 Glyco_hydro_31 -glucosidase, -xylosidase, others 9 (623 ppm) 14 (688 ppm) 11 (54 ppm) 0 1 (278 ppm) GH32 Glyco_hydro_32N invertase, others 11 (536 ppm) 17 (635 ppm) 1 (4 ppm) 0 0 GH33 BNR sialidase, neuraminidase 0 0 0 0 0 GH34 Neur sialidase, neuraminidase (viral only) 0 0 0 0 0 GH35 Glyco_hydro_35 -galactosidase 2 (118 ppm) 1 (49 ppm) 3 (13 ppm) 0 0 GH37 Trehalase trehalase 0 0 2 (9 ppm) 0 0 GH38 Glyco_hydro_38 -mannosidase 2 (77 ppm) 2 (60 ppm) 6 (26 ppm) 0 0 GH39 Glyco_hydro_39 -xylosidase, -L-iduronidase 0 0 1 (7 ppm) 0 0 GH42 Glyco_hydro_42 -galactosidase 6 (421 ppm) 6 (282 ppm) 3 (16 ppm) 0 0 GH43 Glyco_hydro_43 # xylanase, -xylosidase, -L- 4 (229 ppm) 4 (165 ppm) 5 (27 ppm) 13 (2795 ppm) 13 (2340 ppm) arabinofuranosidase, arabinanase, others GH45 Glyco_hydro_45 endoglucanase (mainly eukaryotic, 2 bacterial) 0 0 0 4 (741 ppm) 0 GH46 Glyco_hydro_46 chitosanase 0 0 0 0 0 GH47 Glyco_hydro_47 -mannosidase (mainly eukaryotic, 1 bacterial) 0 0 1 (5 ppm) 0 0 GH48 Glyco_hydro_48 endoglucanase, cellobiohydrolase 0 0 0 0 0 GH49 Glyco_hydro_49 dextranase, isopullulanase, others 0 0 0 0 0 GH52 Glyco_hydro_52 -xylosidase 0 0 0 0 0 GH53 Glyco_hydro_53 # -1,4-endogalactanase 1 (43 ppm) 7 (247 ppm) 4 (16 ppm) 2 (470 ppm) 3 (596 ppm) GH54 ArabFuran-catal # -xylosidase, -L-arabinofuranosidase (mainly 0 0 2 (6 ppm) 1 (242 ppm) 0 eukaryotic, 2 bacterial)
SUPPLEMENTARY INFORMATION Warnecke et al: Page 17 www.nature.com/nature 17 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
CAZy P fam HMM Nam e Known Activities (CAZy)H um an Gut C om m unity S oil (Diversa Fibrobacter S accharophagus Fam ily Silage) ¶ succinogenes ¶ degradans ¶
subject 7 ¶ subject 8 ¶
JGI ID 2004002000 2004002001 2001200001 2001800000 635640000 Nucleotide sequence length 15817685 20486813 152406385 4024184 5057531 P rotein coding genes 20523 25983 184374 3341 4017
Glycoside hydrolase catalytic dom ains GH56 Glyco_hydro_56 hyaluronidase (eukaryotic only) 0 0 0 0 0 GH57 Glyco_hydro_57 -amylase, 4- -glucanotransferase, - 0 0 3 (18 ppm) 3 (753 ppm) 0 galactosidase, others GH59 Glyco_hydro_59 galactocerebrosidase (mainly eukaryotic, 2 000 0 0 bacterial) GH61 Glyco_hydro_61 endoglucanase (fungal only) 0 0 0 0 0 GH62 Glyco_hydro_62 -L-arabinofuranosidase 0 0 1 (5 ppm) 0 0 GH63 Glyco_hydro_63 processing -glucosidase 0 0 0 0 0 GH65 Glyco_hydro_65m trehalase, maltose phosphorylase, trehalose 0 1 (32 ppm) 5 (24 ppm) 0 0 phosphorylase GH67 Glyco_hydro_67M -glucuronidase, others 0 1 (34 ppm) 2 (10 ppm) 0 1 (192 ppm) GH68 Glyco_hydro_68 levansucrase, others 0 0 0 1 (324 ppm) 0 GH70 Glyco_hydro_70 dextransucrase, others 0 0 0 0 0 GH71 Glyco_hydro_71 -1,3-glucanase (mainly fungal, 1 bacterial) 0 0 0 0 0 GH72 Glyco_hydro_72 -1,3-glucanosyltransglycosylase (fungal only) 0 0 0 0 0 GH73 Glucosaminidase endo- -N-acetylglucosaminidase, others 0 2 (41 ppm) 3 (8 ppm) 0 2 (166 ppm) GH75 Chitosanase chitosanase (mainly fungal) 0 0 0 0 0 GH76 Glyco_hydro_76 -1,6-mannanase 0 0 0 0 0 GH77 Glyco_hydro_77 4- -glucanotransferase, amylomaltase 10 (664 ppm) 11 (608 ppm) 11 (68 ppm) 1 (471 ppm) 1 (317 ppm) GH78 B ac_rhamnosid -L-rhamnosidase 0 4 (276 ppm) 0 0 0 GH79 Glyco_hydro_79n endo- -glucuronidase 0 0 0 0 1 (190 ppm) GH81 Glyco_hydro_81 -1,3-glucanase (mainly eukaryotic, 6 bacterial) 0 0 0 0 1 (406 ppm)
GH83 HN hemaglutinin-neuraminidase (viral only) 0 0 0 0 0 GH84 Hyaluronidase_2 # hyaluronidase, N-acetyl b-glucosaminidase 0 3 (107 ppm) 1 (4 ppm) 0 0 GH85 Glyco_hydro_85 endo- -N-acetylglucosaminidase 1 (56 ppm) 0 0 0 0 GH88 Glyco_hydro_88 d-4,5 unsaturated -glucuronyl hydrolase 4 (234 ppm) 0 5 (25 ppm) 0 4 (836 ppm) GH89 NAGLU -N-acetylglucosaminidase 0 1 (65 ppm) 0 0 0 # GH92 Glyco_hydro_92 -1,2-mannosidase 0 0 9 (41 ppm) 0 0 # GH98 Glyco_hydro_98M endo- -galactosidase 0 0 0 0 0 GH100 Invertase_neut alkaline and neutral invertase 0 0 0 0 0 GH102 MltA peptidoglycan lytic transglycosylase 0 0 3 (9 ppm) 0 0 GH103 TIGR: MltB # peptidoglycan lytic transglycosylase 0 0 19 (80 ppm) 0 1 (173 ppm) GH108 DUF847 # N-acetylmuramidase 0 0 2 (6 ppm) 0 1 (98 ppm)
C arbohydrate-binding dom ains CBM1 CBM_1 cellulose-binding domain (mainly fungal, 1 viral) 0 0 0 0 0 CB M2 CB M_2 cellulose-binding domain 0 2 (25 ppm) 3 (6 ppm) 0 19 (1070 ppm) CB M3 CB M_3 cellulose-binding domain 0 0 1 (2 ppm) 0 0 CBM4 CBM_4_9 & amorphous cellulose-, xylan- and glucan-binding 0 4 (86 ppm) 0 4 (434 ppm) 5 (412 ppm) domain CBM5 CB M_5_12 ¥ cellulose-binding domain 0 0 0 0 2 (52 ppm) CB M6 CB M_6 amorphous cellulose- and xylan-binding domain 0 1 (16 ppm) 2 (5 ppm) 32 (2895 ppm) 45 (3238 ppm)
CB M10 CB M_10 cellulose-binding domain (aerobic bacteria) and 0 0 0 0 4 (72 ppm) dockerin (anaerobic fungi) CBM11 CBM_11 # glucan-binding domain 0 0 0 2 (277 ppm) 0 CB M13 Ricin_B _lectin mannose- and xylan-binding domain 1 (26 ppm) 5 (98 ppm) 4 (10 ppm) 0 9 (720 ppm) CB M14 CB M_14 chitin-binding domain 0 0 0 0 0 CB M15 CB M_15 xylan-binding domain (2 bacterial) 0 0 0 0 0 CBM16 CBM_4_9 & carbohydrate-binding module 16 CB M17 CB M_17_28 amorphous cellulose- and cellooligosaccharide- 000 0 0 binding domain CB M18 Chitin_bind_1 chitin-binding domain (eukaryotic only) 0 0 0 0 0 CB M19 CB M_19 chitin-binding domain (eukaryotic only) 0 0 0 0 0 CB M20 CB M_20 starch-binding domain 0 0 1 (2 ppm) 0 2 (113 ppm) CB M21 CB M_21 starch-binding domain (mainly eukaryotic, 1 000 0 0 bacterial) CB M25 CB M_25 starch-binding domain 0 0 0 0 0 CBM27 CBM27 # mannan-binding domain 0 0 0 0 0 CB M32 F5_F8_type_C galactose- and lactose-binding domain 10 (243 ppm) 23 (447 ppm) 12 (30 ppm) 1 (99 ppm) 26 (1835 ppm) CB M33 Chitin_bind_3 chitin-binding domain 0 0 0 0 1 (126 ppm) CB M34 A lpha_amylase_N starch-binding domain 3 (61 ppm) 4 (67 ppm) 0 0 0 § CBM35 BLAST search mannan- xylan- and -galactan-binding domain CBM40 Sialidase sialic acid-binding domain 0 1 (27 ppm) 0 0 0 # CBM41 PUD -glucan-, amylose-, amylopectin-, and pullulan- 0 0 1 (2 ppm) 0 1 (63 ppm) binding domain CBM42 AbfB# arabinose-binding domain 0 0 1 (3 ppm) 0 0 # CBM43 X8 -1,3-glucan binding domain (eukaryotic only) 0 0 0 0 0
SUPPLEMENTARY INFORMATION Warnecke et al: Page 18 www.nature.com/nature 18 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
CAZy Pfam HMM Name Known Activities (CAZy)Human Gut Community Soil (Diversa Fibrobacter Saccharophagus Family Silage)¶ succinogenes¶ degradans¶
subject 7¶ subject 8¶
JGI ID 2004002000 2004002001 2001200001 2001800000 635640000 Nucle otide se que nce le ngth 15817685 20486813 152406385 4024184 5057531 Prote in coding ge ne s 20523 25983 184374 3341 4017
Other domains oftentimes associated with GH catalytic domains Alpha-amylase_C -amylase, C-terminal all- domain; associated 1 (15 ppm) 1 (10 ppm) 0 0 1 (52 ppm) with GH13 Alpha-L-AF_C -L-arabinofuranosidase, C-terminal domain; 5 (162 ppm) 7 (207 ppm) 7 (22 ppm) 0 1 (116 ppm) associated with GH51 Alpha-mann_mid middle domain; associated with GH38 2 (29 ppm) 2 (18 ppm) 5 (8 ppm) 0 0 Big_1 Bacterial Ig-like domain (group 1) 0 0 1 (2 ppm) 0 0 Big_2 Bacterial Ig-like domain (group 2) 22 (330 ppm) 41 (472 ppm) 29 (47 ppm) 0 1 (49 ppm) Big_3 Bacterial Ig-like domain (group 3) 4 (54 ppm) 6 (65 ppm) 0 0 0 Big_4 Bacterial Ig-like domain (group 4) 2 (24 ppm) 3 (27 ppm) 0 0 0 Bgal_small_N -galactosidase, small chain; associated with 9 (374 ppm) 7 (270 ppm) 0 1 (203 ppm) 0 GH2 CBM_X associated with GH94 3 (35 ppm) 5 (46 ppm) 18 (23 ppm) 1 (47 ppm) 1 (38 ppm) CelD_N N-terminal Ig-like domain of cellulase; 0 0 2 (4 ppm) 4 (264 ppm) 3 (160 ppm) associated with GH9 CHB_HEX Putative carbohydrate binding domain; 0 0 1 (3 ppm) 0 1 (107 ppm) associated with GH20 CHB_HEX_C Chitobiase/beta-hexosaminidase C-terminal 0 0 0 0 1 (38 ppm) domain; associated with GH20 ChiC Chitinase C; associated with GH18 0 0 0 0 1 (107 ppm) ChitinaseA_N Chitinase A, N-terminal domain; associated with 000 02 (129 ppm) GH18 Cohesin Cohesin domain 0 0 2 (5 ppm) 0 0 Dockerin_1 Dockerin type I repeat 2 (8 ppm) 5 (15 ppm) 0 0 0 fn3 Fibronectin type III domain 9 (136 ppm) 13 (153 ppm) 27 (44 ppm) 0 5 (235 ppm) GDE_C Amylo-alpha-1,6-glucosidase 0 0 8 (44 ppm) 0 0 Glucodextran_B Glucodextranase, domain B; associated with 000 0 0 GH15 Glucodextran_N Glucodextranase, domain N; associated with 0 0 2 (9 ppm) 0 1 (170 ppm) GH15 Glyco_hydro_2_N sugar-binding domain 12 (338 ppm) 16 (320 ppm) 18 (53 ppm) 2 (239 ppm) 8 (784 ppm) Glyco_hydro_2 immunoglobulin-like -sandwich domain 8 (154 ppm) 8 (120 ppm) 5 (10 ppm) 1 (86 ppm) 5 (303 ppm) Glyco_hydro_3_C C-terminal domain (glycan-binding?) 14 (671 ppm) 20 (655 ppm) 28 (104 ppm) 1 (157 ppm) 5 (817 ppm) Glyco_hydro_20b domain 2 0 0 0 0 1 (79 ppm) Glyco_hydro_32C C-terminal domain 2 (33 ppm) 1 (12 ppm) 1 (2 ppm) 0 0 Glyco_hydro_38C C-terminal domain 1 (46 ppm) 0 3 (21 ppm) 0 0 Glyco_hydro_42M trimerisation domain 5 (198 ppm) 5 (134 ppm) 3 (12 ppm) 0 0 Glyco_hydro_42C C-terminal domain 2 (22 ppm) 0 3 (3 ppm) 0 0 Glyco_hydro_65N N-terminal domain 0 0 2 (9 ppm) 0 0 Glyco_hydro_65C C-terminal domain 0 1 (8 ppm) 2 (2 ppm) 0 0 Glyco_hydro_67N N-terminal domain 0 1 (14 ppm) 0 0 1 (76 ppm) Glyco_hydro_67C C-terminal domain 0 1 (19 ppm) 7 (22 ppm) 0 1 (139 ppm) Glyco_hydro_98C C-terminal domain 0 0 0 0 0 Glyco_transf_36 associated with GH94 3 (61 ppm) 5 (80 ppm) 21 (44 ppm) 0 2 (129 ppm) GT36_AF associated with GH94 2 (34 ppm) 5 (66 ppm) 18 (30 ppm) 0 1 (53 ppm) He_PIG Putative Ig-like domain 1 (8 ppm) 0 16 (14 ppm) 0 31 (874 ppm) Isoamylase_N Isoamylase N-terminal domain; associated with 6 (97 ppm) 10 (119 ppm) 25 (41 ppm) 1 (63 ppm) 3 (154 ppm) GH13 TIG Ig-like domain 0 0 8 (13 ppm) 0 4 (209 ppm)
Footnotes ¶ Pfam HMM hits are counted if their e-value is smaller than 1e-4. BLAST hits are counted if their e-value is smaller than 1e-6. The value in parenthesis is the ratio between the total nucleotide length of the hits for this family and the total nucleotide l
# CAZy does not provide weblinks to Pfam for this family, but this Pfam HMM recognizes the sequences of this family. § No Pfam HMM is available for this family. BLAST searches were conducted with segments of selected sequences listed at CAZy corresponding to this family.
$ The CAZy website links to Pfam PF00959.9 (Phage_lysozyme) for both, GH24 and GH104. & The CAZy website links to Pfam PF02018.7 (CBM_4_9) for all, CBM4, CBM9, CBM16, and CBM22. ¥ The CAZy website links to Pfam PF02839.4 (CBM_5_12) for both, CBM5 and CBM12. The CAZy website links to Pfam PF03424.3 (CBM_17_28) for both, CBM17 and CBM28.
SUPPLEMENTARY INFORMATION Warnecke et al: Page 19 www.nature.com/nature 19 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Table S6. Comparison of abundance of selected GH and CBM domains in different single organism genomes (continued). CAZy Pfam HMM Name Known Activities (CAZy) Cytophaga Thermobifida Caldicellulosiruptor Clostridium Family hutchinsonii ¶ fusca ¶ sa ccha rolyticus ¶ thermocellum ¶
JGI ID 400030000 620040000 625650000 400320000 Nucle otide se que nce le ngth 4433218 3642249 2788317 3783150 Prote in coding ge ne s 3592 3117 2602 3163
Glycoside hydrolase catalytic domains GH1 Glyco_hydro_1 -glucosidase, -galactosidase, -mannosidase, 1 (300 ppm) 2 (756 ppm) 1 (486 ppm) 2 (688 ppm) others GH2 Glyco_hydro_2_C -galactosidase, -mannosidase, others 0 0 3 (938 ppm) 1 (243 ppm) GH3 Glyco_hydro_3 -1,4-glucosidase, -1,4-xylosidase, -1,3- 6 (928 ppm) 2 (384 ppm) 2 (482 ppm) 2 (363 ppm) glucosidase, -L-arabinofuranosidase, others GH4 Glyco_hydro_4 -glucosidase, -galactosidase, - 0 1 (356 ppm) 2 (893 ppm) 0 glucuronidase, others GH5 Cellulase cellulase, -1,4-endoglucanase, -1,3- 4 (893 ppm) 3 (707 ppm) 5 (1484 ppm) 10 (2515 ppm) glucosidase, -1,4-endoxylanase, -1,4- endomannanase, others GH6 Glyco_hydro_6 endoglucanase, cellobiohydrolase 0 2 (525 ppm) 0 0 GH7 Glyco_hydro_7 endoglucanase, cellobiohydrolase (fungal only) 0 0 0 0 GH8 Glyco_hydro_8 cellulase, -1,3-glucosidase, -1,4- 5 (1228 ppm) 0 0 1 (281 ppm) endoxylanase, -1,4-endomannanase, others GH9 Glyco_hydro_9 endoglucanase, cellobiohydrolase, - 6 (1870 ppm) 2 (749 ppm) 2 (919 ppm) 16 (5729 ppm) glucosidase GH10 Glyco_hydro_10 xylanase, -1,3-endoxylanase 3 (646 ppm) 2 (528 ppm) 5 (1703 ppm) 5 (1262 ppm) GH11 Glyco_hydro_11 xylanase 1 (127 ppm) 1 (147 ppm) 0 1 (148 ppm) GH12 Glyco_hydro_12 endoglucanase, -1,3-1,4-glucanase, xyloglucan 00 0 0 hydrolase GH13 Alpha-amylase -amylase, catalytic domain, and related 4 (1114 ppm) 6 (1824 ppm) 4 (1545 ppm) 2 (562 ppm) enzymes GH14 Glyco_hydro_14 -amylase 0 0 0 0 GH15 Glyco_hydro_15 glucoamylase, glucodextranase 1 (246 ppm) 2 (612 ppm) 1 (391 ppm) 1 (299 ppm) GH16 Glyco_hydro_16 -1,3(4)-endoglucanase, others 2 (267 ppm) 0 1 (152 ppm) 2 (324 ppm) GH17 Glyco_hydro_17 glucan endo-1,3- -D-glucosidase glucan 1,3- - 00 0 0 glucosidase, others GH18 Glyco_hydro_18 chitinase, endo- -N-acetylglucosaminidase, non- 0 2 (638 ppm) 0 3 (746 ppm) catalytic proteins GH19 Glyco_hydro_19 chitinase 0 0 0 0 GH20 Glyco_hydro_20 -hexosaminidase, lacto-N-biosidase 0 0 1 (340 ppm) 0 GH22 Lys C-type lysozyme, -lactalbumin (eukaryotic 00 0 0 only) GH23 SLT # G-type lysozyme, peptidoglycan lytic 4 (317 ppm) 0 3 (393 ppm) 2 (182 ppm) transglycosylase GH24 Phage_lysozyme $ lysozyme 0 0 0 0 GH25 Glyco_hydro_25 lysozyme 0 0 0 0 GH26 Glyco_hydro_26 -1,3-xylanase, mannanase 1 (208 ppm) 0 1 (334 ppm) 2 (509 ppm) GH27 Melibiase -galactosidase, -N-acetylgalactosaminidase, 0 0 1 (429 ppm) 0 isomalto-dextranase GH28 Glyco_hydro_28 polygalacturonase, rhamnogalacturonase, 0 0 2 (752 ppm) 0 others GH29 Alpha_L_fucos -L-fucosidase 0 0 0 0 GH30 Glyco_hydro_30 -1,6-glucanase, -xylosidase 0 0 1 (476 ppm) 0 GH31 Glyco_hydro_31 -glucosidase, -xylosidase, others 1 (298 ppm) 1 (353 ppm) 1 (463 ppm) 0 GH32 Glyco_hydro_32N invertase, others 0 0 0 0 GH33 BNR sialidase, neuraminidase 0 0 0 0 GH34 Neur sialidase, neuraminidase (viral only) 0 0 0 0 GH35 Glyco_hydro_35 -galactosidase 0 0 0 0 GH37 Trehalase trehalase 0 0 0 0 GH38 Glyco_hydro_38 -mannosidase 0 0 0 0 GH39 Glyco_hydro_39 -xylosidase, -L-iduronidase 0 0 3 (1360 ppm) 0 GH42 Glyco_hydro_42 -galactosidase 0 1 (338 ppm) 1 (459 ppm) 0 GH43 Glyco_hydro_43 # xylanase, -xylosidase, -L- 2 (369 ppm) 1 (241 ppm) 4 (1232 ppm) 4 (919 ppm) arabinofuranosidase, arabinanase, others GH45 Glyco_hydro_45 endoglucanase (mainly eukaryotic, 2 bacterial) 0 0 0 0 GH46 Glyco_hydro_46 chitosanase 0 0 0 0 GH47 Glyco_hydro_47 -mannosidase (mainly eukaryotic, 1 bacterial) 0 0 0 0 GH48 Glyco_hydro_48 endoglucanase, cellobiohydrolase 0 1 (524 ppm) 1 (670 ppm) 2 (988 ppm) GH49 Glyco_hydro_49 dextranase, isopullulanase, others 0 0 0 0 GH52 Glyco_hydro_52 -xylosidase 0 0 0 0 GH53 Glyco_hydro_53 # -1,4-endogalactanase 0 0 0 1 (240 ppm) GH54 ArabFuran-catal # -xylosidase, -L-arabinofuranosidase (mainly 00 0 0 eukaryotic, 2 bacterial)
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CAZy P fam H MM N am e K nown A ctivities (C A Zy) C ytophaga Therm obifida Caldicellulosiruptor Clostridium Fam ily hutchinsonii ¶ fusca ¶ saccharolyticus ¶ therm ocellum ¶
JGI ID 400030000 620040000 625650000 400320000 Nucleotide sequence length 4433218 3642249 2788317 3783150 P rotein coding genes 3592 3117 2602 3163
Glycoside hydrolase catalytic dom ains GH56 Glyco_hydro_56 hyaluronidase (eukaryotic only) 0 0 0 0 GH57 Glyco_hydro_57 -amylase, 4- -glucanotransferase, - 1 (213 ppm) 0 0 0 galactosidase, others GH59 Glyco_hydro_59 galactocerebrosidase (mainly eukaryotic, 2 00 0 0 bacterial) GH61 Glyco_hydro_61 endoglucanase (fungal only) 0 0 0 0 GH62 Glyco_hydro_62 -L-arabinofuranosidase 0 0 0 0 GH63 Glyco_hydro_63 processing -glucosidase 0 0 0 0 GH65 Glyco_hydro_65m trehalase, maltose phosphorylase, trehalose 0 1 (340 ppm) 2 (833 ppm) 0 phosphorylase GH67 Glyco_hydro_67M -glucuronidase, others 0 0 1 (356 ppm) 0 GH68 Glyco_hydro_68 levansucrase, others 0 0 0 0 GH70 Glyco_hydro_70 dextransucrase, others 0 0 0 0 GH71 Glyco_hydro_71 -1,3-glucanase (mainly fungal, 1 bacterial) 0 0 0 0 GH72 Glyco_hydro_72 -1,3-glucanosyltransglycosylase (fungal only) 0 0 0 0 GH73 Glucosaminidase endo- -N-acetylglucosaminidase, others 1 (97 ppm) 0 0 0 GH75 Chitosanase chitosanase (mainly fungal) 0 0 0 0 GH76 Glyco_hydro_76 -1,6-mannanase 0 0 0 0 GH77 Glyco_hydro_77 4- -glucanotransferase, amylomaltase 1 (328 ppm) 1 (442 ppm) 0 0 GH78 B ac_rhamnosid -L-rhamnosidase 0 0 2 (867 ppm) 0 GH79 Glyco_hydro_79n endo- -glucuronidase 0 0 0 0 GH81 Glyco_hydro_81 -1,3-glucanase (mainly eukaryotic, 6 bacterial) 0 1 (531 ppm) 0 1 (504 ppm)
GH83 HN hemaglutinin-neuraminidase (viral only) 0 0 0 0 GH84 Hyaluronidase_2 # hyaluronidase, N-acetyl b-glucosaminidase 0 0 0 0 GH85 Glyco_hydro_85 endo- -N-acetylglucosaminidase 0 0 0 0 GH88 Glyco_hydro_88 d-4,5 unsaturated -glucuronyl hydrolase 0 0 2 (755 ppm) 0 GH89 NAGLU -N-acetylglucosaminidase 0 0 0 0 # GH92 Glyco_hydro_92 -1,2-mannosidase 0 0 0 0 GH98 Glyco_hydro_98M # endo- -galactosidase 0 0 0 0 GH100 Invertase_neut alkaline and neutral invertase 0 0 0 0 GH102 MltA peptidoglycan lytic transglycosylase 0 0 0 0 GH103 TIGR: MltB # peptidoglycan lytic transglycosylase 0 0 0 0 GH108 DUF847 # N-acetylmuramidase 0 0 0 0
C arbohydrate-binding dom ains CBM1 CBM_1 cellulose-binding domain (mainly fungal, 1 viral) 0 0 0 0 CBM2 CBM_2 cellulose-binding domain 0 14 (1134 ppm) 0 0 CB M3 CB M_3 cellulose-binding domain 0 2 (133 ppm) 10 (898 ppm) 19 (1278 ppm) CBM4 CB M_4_9 & amorphous cellulose-, xylan- and glucan-binding 2 (208 ppm) 1 (115 ppm) 9 (1504 ppm) 12 (1458 ppm) domain CBM5 CB M_5_12 ¥ cellulose-binding domain 0 0 0 0 CB M6 CB M_6 amorphous cellulose- and xylan-binding domain 2 (162 ppm) 1 (96 ppm) 1 (136 ppm) 17 (1653 ppm)
CB M10 CB M_10 cellulose-binding domain (aerobic bacteria) and 00 0 0 dockerin (anaerobic fungi) CBM11 CB M_11 # glucan-binding domain 1 (129 ppm) 0 0 1 (139 ppm) CB M13 Ricin_B _lectin mannose- and xylan-binding domain 0 1 (112 ppm) 0 1 (108 ppm) CB M14 CB M_14 chitin-binding domain 0 0 0 0 CB M15 CB M_15 xylan-binding domain (2 bacterial) 0 0 0 0 CB M17 CB M_17_28 amorphous cellulose- and cellooligosaccharide- 0 0 1 (238 ppm) 0 binding domain CB M18 Chitin_bind_1 chitin-binding domain (eukaryotic only) 0 0 0 0 CB M19 CB M_19 chitin-binding domain (eukaryotic only) 0 0 0 0 CB M20 CB M_20 starch-binding domain 0 1 (78 ppm) 1 (110 ppm) 0 CB M21 CB M_21 starch-binding domain (mainly eukaryotic, 1 00 0 0 bacterial) CB M25 CB M_25 starch-binding domain 0 0 0 0 CBM27 CBM27 # mannan-binding domain 0 0 0 0 CB M32 F5_F8_type_C galactose- and lactose-binding domain 1 (83 ppm) 1 (108 ppm) 1 (125 ppm) 1 (92 ppm) CB M33 Chitin_bind_3 chitin-binding domain 0 2 (334 ppm) 0 0 CB M34 A lpha_amylase_N starch-binding domain 0 0 0 1 (90 ppm) CBM40 Sialidase sialic acid-binding domain 0 0 0 0 # CBM41 PUD -glucan-, amylose-, amylopectin-, and pullulan- 0 0 1 (113 ppm) 0 binding domain CBM42 AbfB# arabinose-binding domain 0 0 0 4 (429 ppm) CBM43 X8 # -1,3-glucan binding domain (eukaryotic only) 0 0 0 0
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CAZy Pfam HMM Name Known Activities (CAZy) Cytophaga Thermobifida Caldicellulosiruptor Clostridium Family hutchinsonii ¶ fusca ¶ sa ccha rolyticus ¶ thermocellum ¶
JGI ID 400030000 620040000 625650000 400320000 Nucle otide se que nce le ngth 4433218 3642249 2788317 3783150 Prote in coding ge ne s 3592 3117 2602 3163
Other domains oftentimes associated with GH catalytic domains Alpha-amylase_C -amylase, C-terminal all- domain; associated 0 1 (67 ppm) 0 0 with GH13 Alpha-L-AF_C -L-arabinofuranosidase, C-terminal domain; 0 0 1 (219 ppm) 1 (163 ppm) associated with GH51 Alpha-mann_mid middle domain; associated with GH38 0 0 0 0 Big_1 Bacterial Ig-like domain (group 1) 0 0 0 1 (84 ppm) Big_2 Bacterial Ig-like domain (group 2) 0 0 2 (169 ppm) 1 (63 ppm) Big_3 Bacterial Ig-like domain (group 3) 0 0 0 0 Big_4 Bacterial Ig-like domain (group 4) 0 0 2 (130 ppm) 1 (44 ppm) Bgal_small_N -galactosidase, small chain; associated with 0 0 2 (581 ppm) 0 GH2 CBM_X associated with GH94 0 0 2 (138 ppm) 3 (152 ppm) CelD_N N-terminal Ig-like domain of cellulase; 4 (252 ppm) 1 (75 ppm) 0 4 (292 ppm) associated with GH9 CHB_HEX Putative carbohydrate binding domain; 00 0 0 associated with GH20 CHB_HEX_C Chitobiase/beta-hexosaminidase C-terminal 00 0 0 domain; associated with GH20 ChiC Chitinase C; associated with GH18 0 0 0 0 ChitinaseA_N Chitinase A, N-terminal domain; associated with 00 0 0 GH18 Cohesin Cohesin domain 0 0 0 29 (3558 ppm) Dockerin_1 Dockerin type I repeat 0 0 0 138 (2297 ppm) fn3 F ibronect in t ype III domain 1 (53 ppm) 4 (275 ppm) 0 7 (440 ppm) GDE_C Amylo-alpha-1,6-glucosidase 1 (248 ppm) 0 0 1 (290 ppm) Glucodextran_B Glucodextranase, domain B; associated with 00 0 0 GH15 Glucodextran_N Glucodextranase, domain N; associated with 00 0 0 GH15 Glyco_hydro_2_N sugar-binding domain 0 1 (125 ppm) 5 (902 ppm) 1 (79 ppm) Glyco_hydro_2 immunoglobulin-like -sandwich domain 0 0 3 (359 ppm) 1 (90 ppm) Glyco_hydro_3_C C-terminal domain (glycan-binding?) 4 (658 ppm) 2 (397 ppm) 2 (510 ppm) 1 (170 ppm) Glyco_hydro_20b domain 2 0 0 0 0 Glyco_hydro_32C C-terminal domain 0 0 0 0 Glyco_hydro_38C C-terminal domain 0 0 0 0 Glyco_hydro_42M trimerisation domain 0 1 (172 ppm) 1 (228 ppm) 0 Glyco_hydro_42C C-terminal domain 0 0 1 (62 ppm) 0 Glyco_hydro_65N N-terminal domain 0 1 (213 ppm) 2 (551 ppm) 0 Glyco_hydro_65C C-terminal domain 0 0 2 (111 ppm) 0 Glyco_hydro_67N N-terminal domain 0 0 1 (132 ppm) 0 Glyco_hydro_67C C-terminal domain 0 0 1 (242 ppm) 0 Glyco_hydro_98C C-terminal domain 0 0 0 0 Glyco_transf_36 associated with GH94 0 0 2 (237 ppm) 4 (343 ppm) GT36_AF associated with GH94 0 0 2 (186 ppm) 3 (213 ppm) He_PIG Putative Ig-like domain 0 0 0 0 Isoamylase_N Isoamylase N-terminal domain; associated with 1 (58 ppm) 2 (144 ppm) 2 (185 ppm) 1 (67 ppm) GH13 TIG Ig-like domain 0 0 0 0
Footnotes ¶ Pfam HMM hits are counted if their e-value is smaller than 1e-4. BLAST hits are counted if their e-value is smaller than 1e-6. The value in parenthesis is the ratio between the total nucleotide length of the hits for this family and the total nucleotide l
# CAZy does not provide weblinks to Pfam for this family, but this Pfam HMM recognizes the sequences of this family. § No Pfam HMM is available for this family. BLAST searches were conducted with segments of selected sequences listed at CAZy corresponding to this family. $ The CAZy website links to Pfam PF00959.9 (Phage_lysozyme) for both, GH24 and GH104. & The CAZy website links to Pfam PF02018.7 (CBM_4_9) for all, CBM4, CBM9, CBM16, and CBM22. ¥ The CAZy website links to Pfam PF02839.4 (CBM_5_12) for both, CBM5 and CBM12. The CAZy website links to Pfam PF03424.3 (CBM_17_28) for both, CBM17 and CBM28.
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Table S7. Phylogenetic characterization of the termite gut metagenome sequence dataset, based on compositional phylogenetic analysis 43. Shown are clades containing 50 kb of sequence for fragments 1 kb. Taxonomic group # fragments %a # bp %a Bacteria 18,869 96 28,048,863 96 Bacteroidetes 189 1 287,830 1 Fibrobacteres 434 2 828,179 3 Firmicutes 640 3 963,754 3 Clostridia 39 <1 98,404 <1 Proteobacteria 1,614 8 2,579,469 9 Betaproteobacteria 197 1 287,933 1 Gammaproteobacteria 47 <1 92,769 <1 Deltaproteobacteria 43 <1 85,112 <1 Epsilonproteobacteria 111 1 125,930 <1 Spirochaetes 4,648 24 9,487,929 33 Spirochaetales Treponema 4,500 23 9,288,738 32 Archaea 584 3 762,065 3 Euryarchaeota 196 1 269,315 1 Other 251 1 311,181 1 Total 19,720 29,164,892 a percentages are given at different taxonomic levels, hence add up to more than 100%; data in shaded rows was assigned to the sample-derived classes for the Fibrobacteres and Treponema clades of the model, all other assignments are to classes trained from publicly available data (generic model component).
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Table S8. Counts of genes classified to COGs corresponding to different hydrogenase families.
Hydrogenase class COG Gene count in termite hindgut metagenome
total Fibrobacter Treponema other
Ni-Fe hydrogen-uptake COG0374 (Ni,Fe-hydrogenase I 0 0 0 0 hydrogenase large subunit)
COG1740 (Ni,Fe-hydrogenase I 0 0 0 0 small subunit
Ni-Fe hydrogen-evolving COG3261 (Ni,Fe-hydrogenase III 1 0 0 1 hydrogenase large subunit)
COG3260 (Ni,Fe-hydrogenase III 1 0 0 1 small subunit)
Metal-free uptake hydrogenase COG4074 (H2-forming N5,N10- 0 0 0 0 methylenetetrahydromethanopterin dehydrogenase)
Iron-only hydrogenase COG4624 (Iron only hydrogenase 124 0 24 100 (reversible) large subunit, C-terminal domain)
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Table S9. Fe-only hydrogenases (COG4624, large subunit, C-terminal domain) identified in the P3 luminal microbiota. Expressed genes identified in the metaproteomic analysis are highlighted in blue. Family Gene_OID IMG/M annotation Contig/read # family 1 2004147267 Methyl-accepting chemotaxis protein Contig41712 family 1 2004145065 Iron only hydrogenase large subunit, C-terminal domain Contig41140 family 1 2004144833 Iron only hydrogenase large subunit, C-terminal domain Contig41062 family 1 2004144069 Methyl-accepting chemotaxis protein Contig40793 family 1 2004139220 Methyl-accepting chemotaxis protein Contig38638 family 1 2004138928 Methyl-accepting chemotaxis protein Contig38500 family 1 2004138343 Sigma-54 dependent transcriptional regulator, Fis family Contig38190 family 1 2004135624 Iron only hydrogenase large subunit, C-terminal domain Contig36773 family 1 2004135138 Iron only hydrogenase large subunit, C-terminal domain Contig36510 family 1 2004133729 Methyl-accepting chemotaxis protein Contig35731 family 1 2004131875 Methyl-accepting chemotaxis protein Contig34710 family 1 2004130511 Methyl-accepting chemotaxis protein Contig33880 family 1 2004130436 Ferredoxin 2 Contig33825 family 1 2004125995 Iron only hydrogenase large subunit, C-terminal domain Contig31061 family 1 2004123920 Ferredoxin 2 Contig29740 family 1 2004123628 Methyl-accepting chemotaxis protein Contig29555 family 1 2004120652 Iron only hydrogenase large subunit, C-terminal domain Contig27679 family 1 2004119843 Iron only hydrogenase large subunit, C-terminal domain Contig27164 family 1 2004119364 Iron only hydrogenase large subunit, C-terminal domain Contig26877 family 1 2004116165 Iron only hydrogenase large subunit, C-terminal domain Contig24838 family 1 2004115852 Methyl-accepting chemotaxis protein Contig24630 family 1 2004115530 Iron only hydrogenase large subunit, C-terminal domain Contig24431 family 1 2004115224 Iron only hydrogenase large subunit, C-terminal domain Contig24239 family 1 2004113529 Sigma-54 dependent transcriptional regulator, Fis family Contig23149 family 1 2004110612 Iron only hydrogenase large subunit, C-terminal domain Contig21035 family 1 2004108337 Ferredoxin 2 Contig19382 family 1 2004107815 Iron only hydrogenase large subunit, C-terminal domain Contig18989 family 1 2004106533 Sigma-54 dependent transcriptional regulator, Fis family Contig18043 family 1 2004100524 Iron only hydrogenase large subunit, C-terminal domain Contig13615 family 1 2004094811 Iron only hydrogenase large subunit, C-terminal domain Contig9317 family 1 2004090341 Iron only hydrogenase large subunit, C-terminal domain Contig5988 family 1 2004088633 Iron only hydrogenase large subunit, C-terminal domain Contig4679 family 1 2004088033 Contig4225 family 1 2004086764 Iron only hydrogenase large subunit, C-terminal domain Contig3281 family 1 2004086733 Iron only hydrogenase large subunit, C-terminal domain Contig3259 family 1 2004084573 Iron only hydrogenase large subunit, C-terminal domain Contig1675 family 1 2004083504 Iron only hydrogenase large subunit, C-terminal domain Contig870 family 1 2004083482 Iron only hydrogenase large subunit, C-terminal domain Contig856 family 2 2004083911 Uncharacterized anaerobic dehydrogenase Contig1178 family 2 2004095107 Iron only hydrogenase large subunit, C-terminal domain Contig9545 family 2 2004131651 Uncharacterized anaerobic dehydrogenase Contig34592 family 2 2004145969 NADH dehydrogenase/NADH Contig41400 family 3 2004160714 Iron only hydrogenase large subunit, C-terminal domain BHZN39579_g2 family 3 2004148312 Iron only hydrogenase large subunit, C-terminal domain BHZN3955_g1 family 3 2004146072 Iron only hydrogenase large subunit, C-terminal domain Contig41428 family 3 2004145706 Iron only hydrogenase large subunit, C-terminal domain Contig41331 family 3 2004144780 Iron only hydrogenase large subunit, C-terminal domain Contig41045
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Family Gene_OID IMG/M annotation Contig/read # family 3 2004142657 Iron only hydrogenase large subunit, C-terminal domain Contig40246 family 3 2004142656 Iron only hydrogenase large subunit, C-terminal domain Contig40246 family 3 2004141757 Iron only hydrogenase large subunit, C-terminal domain Contig39862 family 3 2004139922 Iron only hydrogenase large subunit, C-terminal domain Contig38965 family 3 2004138311 NADH dehydrogenase/NADH Contig38171 family 3 2004136169 Iron only hydrogenase large subunit, C-terminal domain Contig37066 family 3 2004133409 Iron only hydrogenase large subunit, C-terminal domain Contig35567 family 3 2004133408 Iron only hydrogenase large subunit, C-terminal domain Contig35567 family 3 2004132119 Iron only hydrogenase large subunit, C-terminal domain Contig34839 family 3 2004128968 Iron only hydrogenase large subunit, C-terminal domain Contig32917 family 3 2004128967 Iron only hydrogenase large subunit, C-terminal domain Contig32917 family 3 2004126522 Uncharacterized anaerobic dehydrogenase Contig31391 family 3 2004123602 Iron only hydrogenase large subunit, C-terminal domain Contig29540 family 3 2004119568 Iron only hydrogenase large subunit, C-terminal domain Contig27003 family 3 2004119452 Iron only hydrogenase large subunit, C-terminal domain Contig26935 family 3 2004118909 Iron only hydrogenase large subunit, C-terminal domain Contig26581 family 3 2004117939 Iron only hydrogenase large subunit, C-terminal domain Contig25966 family 3 2004111139 Uncharacterized anaerobic dehydrogenase Contig21412 family 3 2004110961 Iron only hydrogenase large subunit, C-terminal domain Contig21282 family 3 2004107649 Iron only hydrogenase large subunit, C-terminal domain Contig18868 family 3 2004106470 Iron only hydrogenase large subunit, C-terminal domain Contig17999 family 3 2004105320 Iron only hydrogenase large subunit, C-terminal domain Contig17144 family 3 2004101268 Iron only hydrogenase large subunit, C-terminal domain Contig14158 family 3 2004100209 Iron only hydrogenase large subunit, C-terminal domain Contig13393
family 3 2004098523 Iron only hydrogenase large subunit, C-terminal domain Contig12149 family 3 2004097668 NADH dehydrogenase/NADH Contig11484 family 3 2004096748 Iron only hydrogenase large subunit, C-terminal domain Contig10773 family 3 2004093306 Iron only hydrogenase large subunit, C-terminal domain Contig8200 family 3 2004091623 Iron only hydrogenase large subunit, C-terminal domain Contig6946 family 3 2004091513 Iron only hydrogenase large subunit, C-terminal domain Contig6870 family 3 2004090116 Iron only hydrogenase large subunit, C-terminal domain Contig5808 family 3 2004087563 Iron only hydrogenase large subunit, C-terminal domain Contig3857 family 3 2004086063 Iron only hydrogenase large subunit, C-terminal domain Contig2785 family 3 2004085995 Iron only hydrogenase large subunit, C-terminal domain Contig2738 family 3 2004083009 Iron only hydrogenase large subunit, C-terminal domain Contig520 family 3 2004087291 Iron only hydrogenase large subunit, C-terminal domain Contig3659 family 3 2004113334 Iron only hydrogenase large subunit, C-terminal domain Contig23005 family 3 2004084376 Iron only hydrogenase large subunit, C-terminal domain Contig1522 family 4 2004145520 Iron only hydrogenase large subunit, C-terminal domain Contig41281 family 4 2004143447 Predicted Fe-S protein Contig40571 family 4 2004143119 Iron only hydrogenase large subunit, C-terminal domain Contig40438 family 4 2004142364 Predicted Fe-S protein Contig40123 family 4 2004142003 Predicted Fe-S protein Contig39974 family 4 2004141813 Iron only hydrogenase large subunit, C-terminal domain Contig39888 family 4 2004140344 Iron only hydrogenase large subunit, C-terminal domain Contig39175 family 4 2004137623 Iron only hydrogenase large subunit, C-terminal domain Contig37820 family 4 2004136305 Iron only hydrogenase large subunit, C-terminal domain Contig37142 family 4 2004132739 Contig35189 family 4 2004130999 Predicted Fe-S protein Contig34175
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Family Gene_OID IMG/M annotation Contig/read # family 4 2004122985 Predicted Fe-S protein Contig29147 family 4 2004118032 Iron only hydrogenase large subunit, C-terminal domain Contig26030 family 4 2004117531 Iron only hydrogenase large subunit, C-terminal domain Contig25710 family 4 2004113736 Predicted Fe-S protein Contig23289 family 4 2004112441 Iron only hydrogenase large subunit, C-terminal domain Contig22346 family 4 2004110033 Iron only hydrogenase large subunit, C-terminal domain Contig20612 family 4 2004107974 Iron only hydrogenase large subunit, C-terminal domain Contig19110 family 4 2004106935 Predicted Fe-S protein Contig18338 family 4 2004104986 Predicted Fe-S protein Contig16892 family 4 2004094651 Iron only hydrogenase large subunit, C-terminal domain Contig9194 family 4 2004092344 Iron only hydrogenase large subunit, C-terminal domain Contig7486 family 4 2004085753 Predicted Fe-S protein Contig2559 family 4 2004085275 Predicted Fe-S protein Contig2200 family 4 2004084806 Iron only hydrogenase large subunit, C-terminal domain Contig1848 family 4 2004086462 Predicted Fe-S protein Contig3065 family 5 2004084868 Ferredoxin 2 Contig1895 family 5 2004103550 Contig15845 family 5 2004117823 Methyl-accepting chemotaxis protein Contig25893 family 5 2004133476 Iron only hydrogenase large subunit, C-terminal domain Contig35600 family 5 2004137292 Methyl-accepting chemotaxis protein Contig37649 family 5 2004145010 Methyl-accepting chemotaxis protein Contig41124 family 5 2004123386 Contig29398 family 6 2004088165 Iron only hydrogenase large subunit, C-terminal domain Contig4324 family 6 2004088501 Fe-hydrogenase large subunit family protein Contig4580 family 6 2004091626 Iron only hydrogenase large subunit, C-terminal domain Contig6948 family 6 2004096774 Iron only hydrogenase large subunit, C-terminal domain Contig10793 family 6 2004097531 Iron only hydrogenase large subunit, C-terminal domain Contig11376 family 6 2004104141 Iron only hydrogenase large subunit, C-terminal domain Contig16272 family 6 2004104158 Iron only hydrogenase large subunit, C-terminal domain Contig16283 family 6 2004116450 Iron only hydrogenase large subunit, C-terminal domain Contig25030 family 6 2004118259 Iron only hydrogenase large subunit, C-terminal domain Contig26175 family 6 2004121757 Fe-hydrogenase large subunit family protein Contig28364 family 6 2004123063 Iron only hydrogenase large subunit, C-terminal domain Contig29195 family 6 2004131441 Fe-hydrogenase large subunit family protein Contig34452 family 6 2004131442 Iron only hydrogenase large subunit, C-terminal domain Contig34452 family 6 2004132679 Iron only hydrogenase large subunit, C-terminal domain Contig35152 family 6 2004137321 Fe-hydrogenase large subunit family protein Contig37664 family 6 2004145474 Iron only hydrogenase large subunit, C-terminal domain Contig41267 family 6 2004141812 Contig39888 family 7 2004096510 Iron only hydrogenase large subunit, C-terminal domain Contig10596 family 7 2004102798 Iron only hydrogenase large subunit, C-terminal domain Contig15296 family 7 2004130014 Iron only hydrogenase large subunit, C-terminal domain Contig33577 family 7 2004139317 NADH dehydrogenase/NADH Contig38678 family 7 2004147498 Iron only hydrogenase large subunit, C-terminal domain Contig41753 family 7 2004149219 Iron only hydrogenase large subunit, C-terminal domain BHZN6343_g1 family 8 2004086463 Iron only hydrogenase large subunit, C-terminal domain Contig3066 family 8 2004097310 Iron only hydrogenase large subunit, C-terminal domain Contig11202 family 8 2004116251 Predicted Fe-S protein Contig24896 family 8 2004125308 Iron only hydrogenase large subunit, C-terminal domain Contig30621
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Family Gene_OID IMG/M annotation Contig/read # family 8 2004127099 Predicted Fe-S protein Contig31758 family 8 2004147499 Iron only hydrogenase large subunit, C-terminal domain Contig41753 family 10 2004088865 Ferredoxin 2 Contig4854 family 10 2004124058 Iron only hydrogenase large subunit, C-terminal domain Contig29832 family 10 2004128298 Iron only hydrogenase large subunit, C-terminal domain Contig32507 family 10 2004145200 Methyl-accepting chemotaxis protein Contig41182
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Table S10. Gene clusters overrepresented in termite P3 luminal microbiota versus soil, ocean and human gut metagenome datasets. Termite Gene_OIDs of Termite P3 metaproteome Sargasso Human a c b COG/NOG/TOG Description representative FC p-value lumenb analysis Seab Soil Colonb NOG14630 Hypothetical repeat containing protein 2004131930 1.3E-04 82 (1.00) 0 (0.00) 0 (0.00) 0 (0.00) COG2373 Large extracellular alpha-helical protein 2004146652 R 2.2E-04 201 (0.83) 28 (0.01) 83 (0.16) 0 (0.00) NOG18930 Fibronectin type III domain protein 2004133748 4.0E-04 79 (0.87) 44 (0.04) 9 (0.05) 2 (0.04) COG1262 Uncharacterized conserved protein 2004132642 S 4.4E-04 205 (0.75) 247 (0.08) 106 (0.18) 0 (0.00) Uncharacterized protein conserved in COG2604 S 4.5E-04 51 (0.98) 5 (0.01) 1 (0.01) 0 (0.00) bacteria 2004142827 NOG06353 Integrase domain protein 2004141667 4.9E-04 58 (0.95) 1 (0.00) 6 (0.04) 0 (0.00) Iron only hydrogenase large subunit, C- COG4624 R 5.3E-04 145 (0.69) 211 (0.08) 11 (0.02) 24 (0.20) terminal domain 2004145706 NOG45161 Alpha amylase family protein 2004146628 5.5E-04 60 (0.95) 0 (0.00) 7 (0.05) 0 (0.00) COG4886 Leucine-rich repeat (LRR) protein 2004146824 S 7.2E-04 133 (0.65) 502 (0.20) 51 (0.11) 4 (0.04) COG1543 Uncharacterized conserved protein 2004121747 S 8.3E-04 51 (0.89) 24 (0.04) 9 (0.07) 0 (0.00)
NOG18207 Hypothetical protein 2004145197 9.4E-04 53 (0.95) 0 (0.00) 6 (0.05) 0 (0.00) COG3378 Predicted ATPase 2004143224 R 1.0E-03 98 (0.80) 48 (0.03) 11 (0.04) 9 (0.13) Predicted oxidoreductases of the COG1453 R 1.0E-03 110 (0.78) 47 (0.03) 3 (0.01) 14 (0.18) aldo/keto reductase family 2004136416 COG4804 Uncharacterized conserved protein 2004137258 S 1.3E-03 80 (0.76) 7 (0.01) 8 (0.03) 12 (0.20)
NOG44579 Conserved protein 2004146659 2.2E-03 100 (0.67) 1 (0.00) 0 (0.00) 28 (0.33) Uncharacterized ABC-type transport COG1079 2004139432 R 2.4E-03 59 (0.65) 252 (0.21) 20 (0.12) 1 (0.02) system, permease component ABC-type uncharacterized transport COG4603 R 2.4E-03 64 (0.65) 252 (0.23) 26 (0.10) 1 (0.02) system, permease component 2004139431 TOG1 (TIGR02145) Hypothetical protein 2004082485 482 (0.98) 1 (2) 18 (0.00) 7 (0.01) 3 (0.01) TOG2 Hypothetical protein 2004147571 145 (0.93) 13 (1833) 1 (0.00) 1 (0.00) 6 (0.07) TOG3 Hypothetical protein 2004084370 121 (0.97) 40 (0.03) 0 (0.00) 0 (0.00) TOG4 (TIGR0178) Hypothetical protein 2004083157 103 (0.91) 0 (0.00) 0 (0.00) 6 (0.09) TOG5 (TIGR0224) Hypothetical protein 2004083056 97 (0.84) 11 (0.01) 6 (0.02) 8 (0.13) TOG6 Hypothetical protein 2004083890 83 (1.00) 2 (2) 3 (0.00) 0 (0.00) 0 (0.00) TOG7 Hypothetical protein 2004082393 78 (0.89) 1 (2) 21 (0.02) 5 (0.03) 3 (0.06) TOG8 (PF01590) Hypothetical protein 2004082587 72 (0.96) 2 (0.00) 6 (0.04) 0 (0.00) TOG9 Hypothetical protein 2004082635 67 (0.97) 3 (24) 1 (0.00) 1 (0.01) 1 (0.03) TOG10 (PF01627) Hypothetical protein 2004082388 60 (0.99) 1 (0.00) 1 (0.01) 0 (0.00) TOG11 Hypothetical protein 2004083498 60 (1.00) 1 (0.00) 0 (0.00) 0 (0.00) TOG12 Hypothetical protein 2004084111 60 (0.81) 15 (0.02) 13 (0.08) 4 (0.10) TOG13 (TIGR02722) Hypothetical protein 2004088261 58 (0.95) 29 (0.04) 2 (0.01) 0 (0.00) TOG14 Hypothetical protein 2004083452 56 (1.00) 0 (0.00) 0 (0.00) 0 (0.00) TOG15 Hypothetical protein 2004084219 52 (0.96) 19 (0.03) 1 (0.01) 0 (0.00) TOG16 Hypothetical protein 2004082452 51 (1.00) 0 (0.00) 0 (0.00) 0 (0.00) TOG17 Hypothetical protein 2004085120 50 (0.97) 0 (0.00) 0 (0.00) 1 (0.03) a FC – COG functional category, R= “general function prediction only”, S=”function unknown”; b Number of proteins in the dataset, relative representation in the specific metagenome is in parenthesis; c appearances of Termite metagenome orthologous group (TOG) peptides in the proteomic dataset: number of peptides identified (number of spectral counts)
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Table S11. Operational taxonomic unit (OTU) representatives of 16S rRNA sequences obtained from the P3 luminal fluid of Nasutitermes spp. PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # 1 290cost002-P3L-1850 EF454252 19 Fibrobacteres TG3-1 79.6 Thermanaeromonas toyohensis AB062280.1 2 290cost002-P3L-1281 EF453894 6 Contig41540 2 Spirochaetes TTG-2 90.4 Spirochaeta (Treponema) caldaria M71240.1 3 290cost002-P3L-1173 EF453818 3 Contig41291 2 Spirochaetes TTG-1 89.9 Spirochaeta (Treponema) caldaria M71240.1 4 290cost002-P3L-1616 EF454087 3 Contig38075 2 Fibrobacteres TG3-1 80.2 Thermanaeromonas toyohensis AB062280.1 5 290cost002-P3L-1831 EF454236 3 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 6 290cost002-P3L-1330 EF453929 3 Contig38078 2 Fibrobacteres TG3-1 79.8 Thermanaeromonas toyohensis AB062280.1 7 290cost002-P3L-1580 EF454061 2 Fibrobacteres TG3-1 79.8 Thermanaeromonas toyohensis AB062280.1 8 290cost002-P3L-1788 EF454199 2 Fibrobacteres TG3-1 80.0 Thermanaeromonas toyohensis AB062280.1 9 290cost002-P3L-1581 EF454062 2 Spirochaetes TTG-2 90.2 Spirochaeta (Treponema) caldaria M71240.1 10 290cost002-P3L-2273 EF454524 2 Fibrobacteres TG3-1 79.8 Thermanaeromonas toyohensis AB062280.1 11 290cost002-P3L-1714 EF454151 2 Fibrobacteres TG3-1 79.4 Thermanaeromonas toyohensis AB062280.1 12 290cost002-P3L-1936 EF454311 2 Fibrobacteres TG3-1 79.8 Thermanaeromonas toyohensis AB062280.1 13 290cost002-P3L-1710 EF454148 2 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 14 290cost002-P3L-1174 EF453819 1 Fibrobacteres TG3-1 79.5 Fibrobacter isolate L35547.1 15 290cost002-P3L-1474 EF454022 1 Contig41557 2 Spirochaetes TTG-10 93.1 Treponema isolate strain SPIT5 AM182455.1 16 290cost002-P3L-1290 EF453902 1 Spirochaetes TTG-1 90.2 Spirochaeta (Treponema) caldaria M71240.1 17 290cost002-P3L-1362 EF453951 1 Fibrobacteres TG3-1 79.4 Thermanaeromonas toyohensis AB062280.1 18 290cost002-P3L-1792 EF454203 1 Fibrobacteres TG3-1 79.6 Fibrobacter isolate L35547.1 19 290cost002-P3L-1292 EF453904 1 Contig7288 2 Spirochaetes TTG-10 91.7 Treponema isolate strain SPIT5 AM182455.1 20 290cost002-P3L-2618 EF454739 1 Fibrobacteres TG3-1 79.4 Thermanaeromonas toyohensis AB062280.1 21 290cost002-P3L-1195 EF453837 1 Spirochaetes TTG-3 89.8 Spirochaeta (Treponema) caldaria M71240.1 22 290cost002-P3L-2418 EF454620 1 Fibrobacteres TG3-1 79.6 Thermanaeromonas toyohensis AB062280.1 23 290cost002-P3L-1232 EF453863 1 Spirochaetes TTG-10 92.0 Treponema azotonutricium ZAS-9 AF320287.1 24 290cost002-P3L-1484 EF454025 1 Fibrobacteres TG3-1 79.9 Thermanaeromonas toyohensis AB062280.1 25 290cost002-P3L-1542 EF454030 1 Bacteroidetes Bacteroidales 84.9 Alistipes finegoldii AJ518874.1 26 290cost002-P3L-2378 EF454595 1 Proteobacteria Deltaproteobacteria 84.6 Pelobacter acidigallici X77216.1 27 290cost002-P3L-1211 EF453849 1 Fibrobacteres TG3-1 79.8 Thermanaeromonas toyohensis AB062280.1 28 290cost002-P3L-1190 EF453832 1 Spirochaetes TTG-2 90.2 Spirochaeta (Treponema) caldaria M71240.1 29 290cost002-P3L-1297 EF453909 1 Contig41389 2 Spirochaetes TTG-1 89.8 Spirochaeta (Treponema) caldaria M71240.1 30 290cost002-P3L-1558 EF454042 1 Fibrobacteres TG3-1 79.6 Thermanaeromonas toyohensis AB062280.1 31 290cost002-P3L-1197 EF453839 1 Acidobacteria Holophagales 86.9 Holophaga foetida X77215.1 32 290cost002-P3L-1243 EF453870 1 Spirochaetes TTG-1 90.1 Spirochaeta (Treponema) caldaria M71240.1 33 290cost002-P3L-1249 EF453874 1 Spirochaetes TTG-10 93.0 Treponema isolate strain SPIT5 AM182455.1
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # 34 290cost002-P3L-1291 EF453903 1 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 Bacteroidales, 35 290cost002-P3L-1253 EF453876 1 Bacteroidetes Marinilabiliaceae 85.2 Ruminofilibacter xylanolyticum str. S1 DQ141183.1 36 290cost002-P3L-2041 EF454386 1 Proteobacteria Deltaproteobacteria 84.5 Deltaproteobacterium str. S2551 AF177428.1 37 290cost002-P3L-1750 EF454175 1 Spirochaetes TSG-3 80.5 "Spirochaeta bajacaliforniensis" M71239.1 38 290cost002-P3L-1777 EF454191 1 Contig40418 2 Spirochaetes TTG-4 89.2 Spirochaeta (Treponema) caldaria M71240.1 39 290cost002-P3L-2121 EF454429 1 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 40 290cost002-P3L-1847 EF454249 1 Fibrobacteres TG3-1 79.5 Thermanaeromonas toyohensis AB062280.1 41 290cost002-P3L-1810 EF454220 1 Spirochaetes TTG-1 90.2 Spirochaeta (Treponema) caldaria M71240.1 42 290cost002-P3L-1194 EF453836 1 Contig39460 2 Spirochaetes TTG-1 90.4 Spirochaeta (Treponema) caldaria M71240.1 43 290cost002-P3L-1382 EF453966 1 Fibrobacteres TG3-1 79.4 Thermanaeromonas toyohensis AB062280.1 44 290cost002-P3L-1770 EF454186 1 Fibrobacteres TG3-1 79.6 Thermanaeromonas toyohensis AB062280.1 45 290cost002-P3L-1269 EF453887 <1 Contig13944 2 Acidobacteria Holophagales 87.3 Holophaga foetida X77215.1 46 290cost002-P3L-1573 EF454054 <1 Contig37655 2 Proteobacteria Deltaproteobacteria 84.6 Pelobacter acidigallici X77216.1 47 290cost002-P3L-1283 EF453896 <1 Spirochaetes TTG-1 90.1 Spirochaeta (Treponema) caldaria M71240.1 48 290cost002-P3L-1230 EF453861 <1 Fibrobacteres TG3-2 76.7 Brevibacillus isolate WF146 AY950801.1 49 290cost002-P3L-1384 EF453967 <1 Spirochaetes TTG-4 89.5 Spirochaeta (Treponema) caldaria M71240.1 50 290cost002-P3L-1582 EF454063 <1 Contig24754 2 Spirochaetes TTG-4 89.1 Spirochaeta (Treponema) caldaria M71240.1 51 290cost002-P3L-1761 EF454182 <1 Spirochaetes TTG-1 90.0 Spirochaeta (Treponema) caldaria M71240.1 52 290cost002-P3L-1868 EF454266 <1 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 53 290cost002-P3L-2001 EF454358 <1 Fibrobacteres TG3-2 76.0 Butyrate-producing isolate L2-50 AJ270491.2 54 290cost002-P3L-1314 EF453919 <1 ZB3 79.5 Clostridium sp. str. PPf35E10 AY548785.1 55 290cost002-P3L-1628 EF454096 <1 Bacteroidetes Bacteroidales 85.0 Paludibacter propionicigenes AB078842.2 56 290cost002-P3L-1189 EF453831 <1 Contig41631 9 2 Fibrobacteres TFG-1 84.1 Fibrobacter succinogenes M62685.1 57 290cost002-P3L-2170 EF454461 <1 Fibrobacteres TFG-1 85.0 Fibrobacter intestinalis M62686.1 58 290cost002-P3L-1613 EF454084 <1 Spirochaetes TTG-10 92.1 Treponema isolate strain SPIT5 AM182455.1 59 290cost002-P3L-1300 EF453912 <1 Spirochaetes TTG-10 92.1 Treponema isolate strain SPIT5 AM182455.1 60 290cost002-P3L-2057 EF454395 <1 Contig4242 5 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 60 Contig3094 Fibrobacteres TG3-1 61 290cost002-P3L-2234 EF454503 <1 Firmicutes Lachnospiraceae 86.9 Clostridium sp. str. XB90 AJ229234.1 62 290cost002-P3L-1869 EF454267 <1 Spirochaetes TSG-2 81.6 Treponema isolate strain I:W:T040 AF182832.1 63 290cost002-P3L-1386 EF453968 <1 Spirochaetes TTG-7 88.4 Treponema primitia ZAS-2 AF093252.1 64 290cost002-P3L-1393 EF453973 <1 Spirochaetes TTG-1 90.0 Spirochaeta (Treponema) caldaria M71240.1 65 290cost002-P3L-1376 EF453961 <1 Fibrobacteres TG3-1 79.9 Thermanaeromonas toyohensis AB062280.1 66 290cost002-P3L-1669 EF454124 <1 Fibrobacteres TG3-1 79.4 Thermanaeromonas toyohensis AB062280.1
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # 67 290cost002-P3L-1178 EF453822 <1 Contig39436 2 Fibrobacteres TFG-1 84.1 Fibrobacter intestinalis M62687.1 68 290cost002-P3L-1618 EF454088 <1 Spirochaetes TSG-2 81.7 "Spirochaeta bajacaliforniensis" M71239.1 69 290cost002-P3L-1445 EF454015 <1 Spirochaetes TTG-1 90.2 Spirochaeta (Treponema) caldaria M71240.1 70 290cost002-P3L-556 EF454868 <1 Spirochaetes TTG-1 90.3 Spirochaeta (Treponema) caldaria M71240.1 71 290cost002-P3L-1377 EF453962 <1 Spirochaetes TTG-10 91.6 Treponema isolate strain SPIT5 AM182455.1 72 290cost002-P3L-2083 EF454411 <1 Spirochaetes TTG-8 91.5 Treponema primitia ZAS-1 AF093251.1 73 290cost002-P3L-1904 EF454293 <1 Spirochaetes TTG-10 92.1 Treponema isolate strain SPIT5 AM182455.1 74 290cost002-P3L-1623 EF454093 <1 Contig18672 2 Spirochaetes TTG-10 90.9 Treponema primitia ZAS-2 AF093252.1 75 290cost002-P3L-1405 EF453983 <1 Spirochaetes TTG-10 92.5 Treponema isolate strain SPIT5 AM182455.1 76 290cost002-P3L-750 EF454953 <1 ZB3 79.6 Clostridium sp. str. PPf35E10 AY548785.1 77 290cost002-P3L-1947 EF454317 <1 Bacteroidetes Bacteroidales 84.0 Paludibacter propionicigenes AB078842.2 Bacteroidales, 78 290cost002-P3L-2684 EF454785 <1 Bacteroidetes Marinilabiliaceae 85.1 Ruminofilibacter xylanolyticum str. S1 DQ141183.1 79 290cost002-P3L-2433 EF454628 <1 Contig40689 2 Fibrobacteres TFG-1 84.6 Fibrobacter intestinalis M62686.1 80 290cost002-P3L-1576 EF454057 <1 Contig41384 2 Fibrobacteres TFG-1 84.2 Fibrobacter intestinalis M62687.1 81 290cost002-P3L-1210 EF453848 <1 Spirochaetes TTG-4 89.4 Spirochaeta (Treponema) caldaria M71240.1 82 290cost002-P3L-1325 EF453927 <1 Spirochaetes TTG-1 89.8 Spirochaeta (Treponema) caldaria M71240.1 83 290cost002-P3L-1395 EF453975 <1 Spirochaetes TTG-1 89.9 Spirochaeta (Treponema) caldaria M71240.1 84 290cost002-P3L-1342 EF453938 <1 Spirochaetes TTG-5 90.5 Treponema azotonutricium ZAS-9 AF320287.1 85 290cost002-P3L-2660 EF454768 <1 Spirochaetes TTG-1 90.3 Spirochaeta (Treponema) caldaria M71240.1 86 290cost002-P3L-1607 EF454080 <1 Spirochaetes TTG-1 90.0 Spirochaeta (Treponema) caldaria M71240.1 87 290cost002-P3L-1204 EF453844 <1 Spirochaetes TTG-10 92.5 Treponema azotonutricium ZAS-9 AF320287.1 88 290cost002-P3L-1653 EF454112 <1 Spirochaetes TTG-10 91.8 Treponema isolate strain SPIT5 AM182455.1 89 290cost002-P3L-1331 EF453930 <1 Spirochaetes TTG-10 91.7 Treponema isolate strain SPIT5 AM182455.1 90 290cost002-P3L-1340 EF453937 <1 Spirochaetes TTG-10 92.7 Treponema isolate strain SPIT5 AM182455.1 91 290cost002-P3L-1895 EF454285 <1 Spirochaetes TTG-10 92.6 Treponema isolate strain SPIT5 AM182455.1 92 290cost002-P3L-1360 EF453949 <1 Fibrobacteres TG3-1 79.8 Thermanaeromonas toyohensis AB062280.1 93 290cost002-P3L-1606 EF454079 <1 Fibrobacteres TG3-1 79.5 Thermanaeromonas toyohensis AB062280.1 94 290cost002-P3L-2652 EF454762 <1 Fibrobacteres TG3-2 76.4 Brevibacillus isolate WF146 AY950801.1 95 290cost002-P3L-1153 EF453801 <1 Acidobacteria Holophagales 86.6 Holophaga foetida X77215.1 96 290cost002-P3L-2521 EF454677 <1 Acidobacteria 82.3 Acidobacteria str. Ellin345 CP000360.1 97 290cost002-P3L-2379 EF454596 <1 Acidobacteria 82.5 Acidobacteriaceae str. Gsoil 149 AB245339.1 98 290cost002-P3L-858 EF454982 <1 Acidobacteria 82.3 Acidobacteriaceae str. Gsoil 149 AB245339.1 99 290cost002-P3L-603 EF454889 <1 Bacteroidetes Bacteroidales 83.3 Alistipes finegoldii AJ518874.1 100 290cost002-P3L-2320 EF454557 <1 Bacteroidetes Bacteroidales 85.4 Paludibacter propionicigenes AB078842.2
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # 101 290cost002-P3L-1182 EF453826 <1 Fibrobacteres TFG-1 84.4 Fibrobacter intestinalis M62686.1 102 290cost002-P3L-2166 EF454459 <1 Fibrobacteres TFG-1 84.5 Fibrobacter intestinalis M62686.1 103 290cost002-P3L-2390 EF454604 <1 Fibrobacteres TFG-1 84.1 Fibrobacter intestinalis M62687.1 104 290cost002-P3L-969 EF455006 <1 Contig39720 10 10 Fibrobacteres TFG-1 84.5 Fibrobacter intestinalis M62687.1 104 Contig40980 Fibrobacteres TFG-1 104 Contig16110 Fibrobacteres TFG-1 104 Contig20300 Fibrobacteres TFG-1 105 290cost002-P3L-1224 EF453857 <1 Fibrobacteres TFG-1 84.0 Fibrobacter succinogenes M62685.1 Deltaproteobacteria, Desulfovibrionales, 106 290cost002-P3L-1410 EF453987 <1 Proteobacteria Desulfovibrionaceae 92.1 Desulfovibrio sp. str. LNB1 AY554145.1 Gammaproteobacteria, 107 290cost002-P3L-2069 EF454402 <1 Proteobacteria Pseudomonadaceae 100.0 Pseudomonas sp. str. DVS13A AY864637.1 108 290cost002-P3L-1223 EF453856 <1 Spirochaetes TSG-2 81.3 Treponema isolate strain I:W:T040 AF182832.1 109 290cost002-P3L-1614 EF454085 <1 Spirochaetes TTG-2 89.8 Spirochaeta (Treponema) caldaria M71240.1 110 290cost002-P3L-1603 EF454077 <1 Spirochaetes TTG-1 90.2 Spirochaeta (Treponema) caldaria M71240.1 111 290cost002-P3L-1681 EF454129 <1 Spirochaetes TTG-1 89.6 Spirochaeta (Treponema) caldaria M71240.1 112 290cost002-P3L-1733 EF454163 <1 Spirochaetes TTG-4 89.2 Treponema isolate strain SPIT5 AM182455.1 113 290cost002-P3L-1753 EF454177 <1 Spirochaetes TTG-1 90.2 Spirochaeta (Treponema) caldaria M71240.1 114 290cost002-P3L-766 EF454959 <1 Spirochaetes TTG-7 88.8 Spirochaeta (Treponema) caldaria M71240.1 115 290cost002-P3L-1791 EF454202 <1 Spirochaetes TTG-5 90.7 Treponema azotonutricium ZAS-9 AF320287.1 116 290cost002-P3L-443 EF454814 <1 Spirochaetes TTG-6 90.5 Treponema isolate strain SPIT5 AM182455.1 117 290cost002-P3L-1207 EF453845 <1 Spirochaetes TTG-1 90.4 Spirochaeta (Treponema) caldaria M71240.1 118 290cost002-P3L-1272 EF453888 <1 Spirochaetes TTG-10 91.9 Treponema isolate strain SPIT5 AM182455.1 119 290cost002-P3L-1458 EF454019 <1 Spirochaetes TTG-10 92.1 Treponema isolate strain SPIT5 AM182455.1 120 290cost002-P3L-1586 EF454067 <1 Contig40676 2 Spirochaetes TTG-10 92.0 Treponema isolate strain SPIT5 AM182455.1 121 290cost002-P3L-558 EF454869 <1 Spirochaetes TTG-10 92.4 Treponema isolate strain SPIT5 AM182455.1 122 290cost002-P3L-1546 EF454034 <1 Spirochaetes TTG-10 92.0 Treponema isolate strain SPIT5 AM182455.1 123 290cost002-P3L-1483 EF454024 <1 Spirochaetes TTG-8 92.0 Treponema isolate strain SPIT5 AM182455.1 124 290cost002-P3L-636 EF454904 <1 Spirochaetes TTG-10 92.2 Treponema primitia ZAS-2 AF093252.1 125 290cost002-P3L-2145 EF454444 <1 Spirochaetes TTG-10 93.1 Treponema isolate strain SPIT5 AM182455.1 126 290cost002-P3L-1803 EF454213 <1 Spirochaetes TTG-10 91.6 Treponema azotonutricium ZAS-9 AF320287.1 127 290cost002-P3L-1875 EF454273 <1 Spirochaetes TTG-10 91.3 Treponema azotonutricium ZAS-9 AF320287.1 128 290cost002-P3L-2228 EF454497 <1 Spirochaetes TTG-10 91.9 Treponema isolate strain SPIT5 AM182455.1 129 290cost002-P3L-2341 EF454571 <1 Fibrobacteres TG3-1 79.4 Thermanaeromonas toyohensis AB062280.1
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # 130 290cost002-P3L-1175 EF453820 <1 Acidobacteria 82.1 Acidobacteriaceae str. Gsoil 149 AB245339.1 131 290cost002-P3L-1241 EF453868 <1 Contig30608 2 Acidobacteria Holophagales 85.9 Holophaga foetida X77215.1 132 290cost002-P3L-2407 EF454612 <1 Acidobacteria Holophagales 85.6 Holophaga foetida X77215.1 133 290cost002-P3L-693 EF454928 <1 Acidobacteria 82.6 Acidobacteriaceae str. Gsoil 149 AB245339.1 134 290cost002-P3L-685 EF454925 <1 Aminanaerobia TG5 84.3 Dethiosulfovibrio russensis AF234544.1 135 290cost002-P3L-1187 EF453830 <1 Bacteroidetes Bacteroidales 84.4 Paludibacter propionicigenes AB078842.2 136 290cost002-P3L-1305 EF453914 <1 Bacteroidetes Bacteroidales 84.1 Paludibacter propionicigenes AB078842.2 137 290cost002-P3L-1802 EF454212 <1 Bacteroidetes Bacteroidales 84.7 Alistipes finegoldii AJ518874.1 138 290cost002-P3L-1961 EF454327 <1 Bacteroidetes Bacteroidales 83.4 Ruminobacillus xylanolyticum str. G1 DQ178248.1 139 290cost002-P3L-2080 EF454409 <1 Bacteroidetes Bacteroidales 84.9 Alistipes finegoldii AJ518874.1 140 290cost002-P3L-2184 EF454472 <1 Bacteroidetes Bacteroidales 84.7 Alistipes finegoldii AJ518874.1 141 290cost002-P3L-2216 EF454492 <1 Bacteroidetes Bacteroidales 82.8 Bacteroides str. 22C AY554420.1 142 290cost002-P3L-2517 EF454675 <1 Chlorobi 78.3 Desulfobacteraceae str. MSL86 AB110542.2 143 290cost002-P3L-1309 EF453917 <1 Cyanobacteria 91.7 Rumen isolate str. YS2 AF544207.1 144 290cost002-P3L-1371 EF453956 <1 Cyanobacteria 89.9 Rumen isolate str. YS2 AF544207.1 145 290cost002-P3L-421 EF454802 <1 Deferribacteres 86.4 Geovibrio str. Lincoln Park 3 AF157057.1 146 290cost002-P3L-2571 EF454709 <1 Endomicrobia 79.4 Acidobacteriaceae str. Gsoil 149 AB245339.1 147 290cost002-P3L-1177 EF453821 <1 Fibrobacteres TFG-1 84.4 Fibrobacter intestinalis M62687.1 148 290cost002-P3L-1894 EF454284 <1 Fibrobacteres TFG-1 84.7 Fibrobacter intestinalis M62686.1 149 290cost002-P3L-2095 EF454418 <1 Contig41368 2 Fibrobacteres TFG-1 84.4 Fibrobacter isolate L35547.1 150 290cost002-P3L-2239 EF454506 <1 Fibrobacteres TFG-1 84.3 Fibrobacter intestinalis M62687.1 151 290cost002-P3L-1289 EF453901 <1 Firmicutes Acidaminococcaceae 87.9 Dehalobacter sp. E2 AY673991.1 152 290cost002-P3L-1430 EF454003 <1 Firmicutes Lachnospiraceae 89.2 Eubacterium siraeum L34625.1 153 290cost002-P3L-1599 EF454073 <1 Firmicutes Lachnospiraceae 90.9 Sporobacter termitidis Z49863.1 154 290cost002-P3L-1640 EF454103 <1 Firmicutes Catabacteraceae 82.8 Clostridium sp. str. FCB90-3 AJ229251.1 155 290cost002-P3L-1650 EF454110 <1 Firmicutes Catabacteraceae 82.6 Sedimentibacter sp. D7 AY766467.1 156 290cost002-P3L-1924 EF454305 <1 Firmicutes Peptostreptococcaceae 92.1 Anaerovorax odorimutans str. NorPut AJ251215.1 157 290cost002-P3L-2244 EF454508 <1 Firmicutes Lachnospiraceae 91.8 Sporobacter termitidis Z49863.1 Ethanologenbacterium harbinense str. 158 290cost002-P3L-2299 EF454544 <1 Firmicutes Lachnospiraceae 83.8 X-29 AY833421.1 159 290cost002-P3L-2304 EF454547 <1 Firmicutes Acidaminococcaceae 87.6 Sporomusa rhizae str. RS AM158322.1 160 290cost002-P3L-2413 EF454616 <1 Firmicutes Lachnospiraceae 90.0 Eubacterium siraeum L34625.1 161 290cost002-P3L-2450 EF454637 <1 Firmicutes Catabacteraceae 82.9 Sedimentibacter sp. D7 AY766467.1 Lactobacillales, Enterococcus malodoratus str. 162 290cost002-P3L-2602 EF454727 <1 Firmicutes Enterococcaceae 92.9 ATCC43197 AF061012.1
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # Lactobacillales, 163 290cost002-P3L-2633 EF454749 <1 Firmicutes Enterococcaceae 92.8 Enterococcus avium AF061008.1 Clostridium scindens str. JCM 10420 M- 164 290cost002-P3L-446 EF454815 <1 Firmicutes Lachnospiraceae 87.6 18 AB020729.1 165 290cost002-P3L-568 EF454875 <1 Firmicutes Lachnospiraceae 83.9 Acetanaerobacterium elongatum str. Z1 AY518589.1 166 290cost002-P3L-2033 EF454380 <1 Proteobacteria Deltaproteobacteria 83.4 Sulfate-reducing bacterium str. Hxd3 Y17698.1 Deltaproteobacteria, 167 290cost002-P3L-2608 EF454731 <1 Proteobacteria Desulfovibrionales 95.1 Oxalobacter formigenes str. OXC U49755.1 Deltaproteobacteria, Desulfovibrionales, 168 290cost002-P3L-532 EF454852 <1 Proteobacteria Desulfovibrionaceae 90.7 Desulfovibrio sp. str. LNB2 AY554146.1 Deltaproteobacteria, Desulfovibrionales, 169 290cost002-P3L-618 EF454896 <1 Proteobacteria Desulfovibrionaceae 92.1 Bilophila wadsworthia str. NB-12 AB117562.1 170 290cost002-P3L-430 EF454808 <1 Spirochaetes T. primitia group 91.2 Treponema primitia ZAS-2 AF093252.1 171 290cost002-P3L-657 EF454914 <1 Spirochaetes TLG-1 83.2 Leptospira inadai Z21634.1 172 290cost002-P3L-632 EF454901 <1 Spirochaetes TSG-1 85.5 "Spirochaeta bajacaliforniensis" M71239.1 173 290cost002-P3L-1129 EF453791 <1 Spirochaetes TTG-1 89.8 Spirochaeta (Treponema) caldaria M71240.1 174 290cost002-P3L-1231 EF453862 <1 Contig41516 7 Spirochaetes TTG-7 88.8 Treponema primitia ZAS-2 AF093252.1 174 Contig38802 Spirochaetes TTG-7 174 Contig11194 Spirochaetes TTG-7 175 290cost002-P3L-1239 EF453867 <1 Spirochaetes TTG-5 90.9 Treponema azotonutricium ZAS-9 AF320287.1 176 290cost002-P3L-1301 EF453913 <1 Spirochaetes TTG-4 89.4 Treponema isolate strain SPIT5 AM182455.1 177 290cost002-P3L-1392 EF453972 <1 Spirochaetes TTG-5 90.7 Treponema azotonutricium ZAS-9 AF320287.1 178 290cost002-P3L-1422 EF453997 <1 Spirochaetes TTG-6 90.7 Spirochaeta (Treponema) caldaria M71240.1 179 290cost002-P3L-1667 EF454122 <1 Spirochaetes TTG-1 89.4 Spirochaeta (Treponema) caldaria M71240.1 180 290cost002-P3L-1703 EF454143 <1 Spirochaetes TTG-4 88.5 Spirochaeta (Treponema) caldaria M71240.1 181 290cost002-P3L-1728 EF454159 <1 Spirochaetes TTG-2 89.6 Treponema primitia ZAS-1 AF093251.1 182 290cost002-P3L-1731 EF454161 <1 Spirochaetes TTG-1 89.0 Spirochaeta (Treponema) caldaria M71240.1 183 290cost002-P3L-1794 EF454205 <1 Spirochaetes TTG-1 89.8 Spirochaeta (Treponema) caldaria M71240.1 184 290cost002-P3L-1823 EF454228 <1 Contig25203 2 Spirochaetes TTG-7 88.3 Spirochaeta (Treponema) caldaria M71240.1 185 290cost002-P3L-1859 EF454259 <1 Contig41088 2 Spirochaetes TTG-7 88.1 Treponema azotonutricium ZAS-9 AF320287.1 186 290cost002-P3L-1879 EF454277 <1 Spirochaetes TTG-2 89.0 Spirochaeta (Treponema) caldaria M71240.1 187 290cost002-P3L-2106 EF454423 <1 Spirochaetes TTG-5 89.6 Spirochaeta (Treponema) caldaria M71240.1 188 290cost002-P3L-2386 EF454600 <1 Contig41269 10 Spirochaetes TTG-7 88.4 Spirochaeta (Treponema) caldaria M71240.1 188 Contig35356 Spirochaetes TTG-7 188 Contig8763 Spirochaetes TTG-7
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # 188 Contig132 Spirochaetes TTG-7 189 290cost002-P3L-2594 EF454723 <1 Spirochaetes TTG-2 89.0 Spirochaeta (Treponema) caldaria M71240.1 190 290cost002-P3L-418 EF454799 <1 Spirochaetes TTG-7 88.0 Spirochaeta (Treponema) caldaria M71240.1 191 290cost002-P3L-599 EF454887 <1 Spirochaetes TTG-7 88.5 Treponema primitia ZAS-2 AF093252.1 192 290cost002-P3L-742 EF454947 <1 Spirochaetes TTG-2 89.8 Spirochaeta (Treponema) caldaria M71240.1 193 290cost002-P3L-746 EF454951 <1 Spirochaetes TTG-7 88.6 Treponema azotonutricium ZAS-9 AF320287.1 194 290cost002-P3L-899 EF454989 <1 Spirochaetes TTG-5 90.1 Treponema azotonutricium ZAS-9 AF320287.1 195 290cost002-P3L-1157 EF453804 <1 Spirochaetes TTG-9 92.9 Treponema primitia ZAS-2 AF093252.1 196 290cost002-P3L-1258 EF453880 <1 Spirochaetes TTG-9 91.9 Treponema primitia ZAS-2 AF093252.1 197 290cost002-P3L-1293 EF453905 <1 Spirochaetes TTG-9 91.3 Treponema primitia ZAS-2 AF093252.1 198 290cost002-P3L-1645 EF454106 <1 Spirochaetes TTG-9 92.6 Treponema primitia ZAS-2 AF093252.1 199 290cost002-P3L-535 EF454854 <1 Spirochaetes TTG-9 92.6 Treponema primitia ZAS-2 AF093252.1 200 290cost002-P3L-1160 EF453807 <1 Spirochaetes TTG-10 91.8 Treponema isolate strain SPIT5 AM182455.1 201 290cost002-P3L-1171 EF453817 <1 Spirochaetes TTG-10 92.3 Treponema primitia ZAS-2 AF093252.1 202 290cost002-P3L-1214 EF453850 <1 Spirochaetes TTG-10 91.9 Treponema isolate strain SPIT5 AM182455.1 203 290cost002-P3L-1591 EF454071 <1 Spirochaetes TTG-10 92.5 Treponema primitia ZAS-1 AF093251.1 204 290cost002-P3L-1598 EF454072 <1 Spirochaetes TTG-10 91.4 Treponema isolate strain SPIT5 AM182455.1 205 290cost002-P3L-1656 EF454114 <1 Spirochaetes TTG-10 92.1 Treponema isolate strain SPIT5 AM182455.1 206 290cost002-P3L-1688 EF454133 <1 Spirochaetes TTG-10 91.8 Spirochaeta (Treponema) caldaria M71240.1 207 290cost002-P3L-1708 EF454146 <1 Spirochaetes TTG-10 92.4 Treponema isolate strain SPIT5 AM182455.1 208 290cost002-P3L-1874 EF454272 <1 Spirochaetes TTG-10 91.8 Treponema primitia ZAS-2 AF093252.1 209 290cost002-P3L-505 EF454845 <1 Spirochaetes TTG-10 92.5 Treponema isolate strain SPIT5 AM182455.1 210 290cost002-P3L-559 EF454870 <1 Spirochaetes TTG-10 91.5 Treponema isolate strain SPIT5 AM182455.1 211 290cost002-P3L-660 EF454916 <1 Spirochaetes TTG-10 92.0 Treponema isolate strain SPIT5 AM182455.1 212 290cost002-P3L-738 EF454945 <1 Spirochaetes TTG-10 91.6 Treponema isolate strain SPIT5 AM182455.1 213 290cost002-P3L-762 EF454956 <1 Spirochaetes TTG-10 91.8 Treponema primitia ZAS-2 AF093252.1 214 290cost002-P3L-2049 EF454390 <1 Fibrobacteres TG3-1 79.3 Thermanaeromonas toyohensis AB062280.1 215 290cost002-P3L-2381 EF454598 <1 Fibrobacteres TG3-1 79.7 Thermanaeromonas toyohensis AB062280.1 216 290cost002-P3L-2679 EF454781 <1 ZB3 78.7 Clostridium sp. str. JC3 AB093546.1 Alphaproteobacteria, Contig5625 2 Proteobacteria Oleomonas 77.3 Petrobacter sp. DM-3 DQ539621.1 BHZN43990 2 Bacteroidetes Bacteroidales 93.1 Bacillus strain NIH L11886.1 Deltaproteobacteria, Desulfovibrionales, Desulfovibrio vulgaris str. Contig20711 2 Proteobacteria Desulfovibrionaceae 90.8 Hildenborough AE017285.1
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PCR library Metagenome Closest cultivated species / isolate 1 2 3 4 5 6 7 8 OTU OTU rep. Acc. # % % Phylum Phylog. group % Name Acc. # Contig18107 2 Acidobacteria Holophagales 83.9 Holophaga foetida X77215.1 Contig40113 2 Spirochaetes TTG-7 91.0 Treponema azotonutricium ZAS-9 AF320287.1 Contig2434 2 Spirochaetes TTG-7 83.1 Spirochaeta xylanolyticus AY735097.1 1 OTUs were defined at 99% sequence identity; 2 OTU representative; 3 Genbank accession number for OTU representative; 4 Percentage in PCR library; 5 Percentage in metagenome; 6 phylogenetic group as depicted in Fig. 1b; 7 percent sequence identity with closest cultivated species; 8 Genbank accession number; 9 fosmid Contig88; 10 fosmid contig110.
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Costa Rican termite 290cost002 A N. ephratae, AB037328 N. polygynus, AB037326 N. corniger, AB037327 N. nigriceps, AB037329 N. novarumhebridarum, AB037325 N. matangensis, AB037324 N. matangensiformis, AB109489 N. takasagoensis, DQ493747 N. triodiae, AB037330 N. magnus, AB037331 N. walkeri, AB037332 N. exitiosus, AB037333 N. princeps, AB037334 N. pinocchio, AB037336 N. bikpelanus, AB037335 Microcerotermes spp.
0.05
Costa Rican termite 290cost002 B N. corniger, AB037327 N. nigriceps, AB037329 N. polygynus, AB037326 N. walkeri, AB037332 N. ephratae, AB037328 N. magnus, AB037331 N. triodiae, AB037330 N. exitiosus, AB037333 N. princeps, AB037334 N. matangensis, AB037324 N. takasagoensis, DQ493747 N. matangensiformis, AB109489 N. novarumhebridarum, AB037325 N. pinocchio, AB037336 N. bikpelanus, AB037335 Microcerotermes spp.
0.05
Fig. S1. Phylogenetic identification of termite host species 290cost002. The sequence of the mitochondrial cytochrome oxidase II (COII) gene was determined and aligned to all available Isoptera sequences, only species of the higher termite (Termitidae) genera Nasutitermes and Microcerotermes are shown. A, DNA nucleotide-based dendrogram using 661 unambigously aligned and filtered positions. B, DNA sequence was translated into amino acid sequence and a dendrogram was constructed using 228 unambiguously aligned and filtered positions. The trees were calculated using TREE-PUZZLE (Schmidt et al. 2002). Branching pattern confidence is visualised as follows: no circle, >50%; open circle, >70%; filled circle, >90%. The slightly contradictory tree topologies based on nucleotide and amino acid sequences is due to a large number of silent mutations in this gene. The collected specimens were most closely related to N. ephratae (by nt comparison, A) and N. corniger (by aa comparison, B) and we therefore only assign our specimens to Nasutitermes sp. in lieu of a comprehensive analysis of multiple collections of this and other closely related Nasutitermes throughout the region.
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OTUs
Fig. S2. Accumulation curves of 16S rRNA genes obtained from the P3 luminal microbiota . Accumulation curves were constructed by plotting the number of unique Operational taxonomic units (OTUs) at 99% sequence identity found in a given number of clones versus the number of clones (averaged over a 1000 random permutations of the initial clone order). For comparison, besides an accumulation curve for the total number of OTUs, accumulation curves for the Spirochaetes related OTUs and the Fibrobacteres including TG3-related OTUs are shown, too. For the the total OTU accumulation curve, neither the exponential nor the two parameter hyperbola models offered good fits, so they were dropped. The non-parametric estimates for this data set produced more meaningful estimates of the total diversity (Table S1). Based on this estimates, 71 to 84% of the total OTU diversity has been sequenced.
www.nature.com/nature 39 290cost002-P3L-1173 290cost002-P3L-1731 290cost002-P3L-1243 290cost002-P3L-1290 290cost002-P3L-1607 Fig. S3. Phylogenetic diversity of P3 290cost002-P3L-1810 290cost002 metagenome Contig39460 luminal microbiota within the phylum 290cost002-P3L-1297 290cost002-P3L-1761 Spirochaetes 290cost002-P3L-1794 . From a PCR-based 290cost002-P3L-1603 TTG-1 290cost002-P3L-1667 290cost002-P3L-1445 inventory and from the metagenome 290cost002 metagenome Contig41389 290cost002-P3L-1283 libraries 1703 and 14 near-full length 16S 290cost002-P3L-556 290cost002-P3L-1325 290cost002-P3L-1395 rRNA gene sequences, respectively, were 290cost002-P3L-1129 290cost002-P3L-2660 used in a Maximum Likelihood analysis 290cost002-P3L-1681 290cost002-P3L-1753 290cost002-P3L-1194 (RAxML). The Phylogram was constructed 290cost002-P3L-1207 290cost002-P3L-1393 290cost002-P3L-1728 using 1289 unambiguously aligned and 290cost002-P3L-1879 290cost002-P3L-2594 filtered nucleotide positions. Genbank 290cost002-P3L-1614 290cost002-P3L-1190 TTG-2 290cost002-P3L-1581 accession numbers are given. Bar, 10% 290cost002-P3L-742 290cost002-P3L-1281 estimated sequence divergence. 290cost002 metagenome Contig41540 290cost002-P3L-1195 TTG-3 290cost002 metagenome Contig40418 290cost002-P3L-1384 290cost002-P3L-1777 290cost002-P3L-1210 TTG-4 290cost002-P3L-1703 290cost002-P3L-1301 290cost002-P3L-1733 290cost002-P3L-1582 290cost002-P3L-2106 290cost002-P3L-899 290cost002-P3L-1239 TTG-5 290cost002-P3L-1342 290cost002-P3L-1392 290cost002-P3L-1791 290cost002-P3L-443 290cost002-P3L-1422 TTG-6 290cost002-P3L-1823 290cost002-P3L-1859 290cost002-P3L-1231 290cost002 metagenome Contig41516 290cost002-P3L-2386 290cost002 metagenome Contig25203 290cost002-P3L-599 termite gut clone NL1, U40791.1 termite gut homogenate clone M1NP2-94, AB191968.1 termite gut homogenate clone M1NP1-77, AB191853.1 TTG-7 termite gut homogenate clone M1NP2-44, AB191901.1 termite gut clone , AB191821.1 termite gut homogenate clone M1NP1-53, AB191910.1 termite gut homogenate clone M2PT2-26, AB191883.1 termite gut homogenate clone M2PT2-78, AB191939.1 termite gut homogenate clone M1PT4-11, AB191954.1 290cost002-P3L-1386 290cost002-P3L-746 290cost002-P3L-418 290cost002-P3L-766 290cost002-P3L-1483 290cost002-P3L-2083 termite gut homogenate clone M1PL1-76, AB191929.1 TTG-8 termite gut homogenate clone M2PT2-87, AB191796.1 termite gut wall clone, AB231063.1 termite gut homogenate clone BCf4-14, AB062823.1 termite gut clone NkS5, AB084954.1 290cost002-P3L-1293 290cost002-P3L-535 290cost002-P3L-1258 TTG-9 290cost002-P3L-1645 290cost002-P3L-1157 termite gut homogenate clone M2PT2-47, AB191941.1 290cost002-P3L-1292 290cost002-P3L-2228 290cost002-P3L-1377 290cost002 metagenome Contig40676 290cost002-P3L-1586 290cost002-P3L-1214 290cost002-P3L-1458 290cost002-P3L-1160 290cost002-P3L-1300 290cost002-P3L-1904 290cost002-P3L-762 290cost002-P3L-559 290cost002-P3L-1598 290cost002-P3L-1272 290cost002-P3L-660 290cost002-P3L-1623 290cost002-P3L-1875 290cost002-P3L-1331 290cost002-P3L-1546 290cost002-P3L-1653 TTG-10 290cost002-P3L-1688 290cost002-P3L-1803 290cost002-P3L-1232 290cost002-P3L-636 290cost002-P3L-1171 290cost002-P3L-1204 290cost002-P3L-1613 290cost002-P3L-1340 290cost002-P3L-1405 290cost002-P3L-558 290cost002-P3L-1708 290cost002 metagenome Contig41557 290cost002-P3L-1895 290cost002-P3L-1656 290cost002-P3L-1474 290cost002-P3L-1591 290cost002-P3L-1874 290cost002-P3L-738 290cost002-P3L-505 290cost002-P3L-2145 290cost002-P3L-1249 Microcerotermes gut clones, AB243268.1 termite gut homogenate clone Tc-25, AB189683.1 Treponema primitia ZAS-1, AF093251.1 Treponema primitia ZAS-2, AF093252.1 termite gut homogenate clone RsTz-25, AB192140.1 Reticulitermes flavipes gut clone, DQ009704.2 termite gut homogenate clone RFS82, AF068427.1 termite gut clone NkS94, AB084971.1 Microcerotermes gut clones, AB243270.1 T. primitia Spirochaeta sp, AJ419822.1 290cost002-P3L-430 group termite gut wall clone RsW01-034, AB198469.1 termite gut homogenate clone BCf5-23, AB062829.1 termite gut homogenate clone Rs-J42 sp., AB088875.1 termite gut homogenate clone RsTu1-69, AB192195.1 Treponema azotonutricium ZAS-9, AF320287.1 termite hindgut clone mpsp15, X89051.1 Mixotricha paradoxa clone, AJ458944.1 termite hindgut clone mpsp16, X89052.1 Treponema str. SPIT5, AM182455.1 Spirochaeta (Treponema) caldaria, M71240.1 T. pallidum & amino acid fermentors T. bryantii & saccharolytic strains Spirochaeta str. Grapes, AF357917.2 Spirochaeta coccoides SPN1, AJ698092.1 Spirochaeta bajacaliforniensis, M71239.1 290cost002-P3L-632 TSG-1 Spirochaeta aurantia, AY599019.1 290cost002-P3L-1618 290cost002-P3L-1869 290cost002-P3L-1223 TSG-2 termite gut clone, AB191844.1 termite gut homogenate clone M2PT2-76, AB191843.1 290cost002-P3L-1750 TSG-3 290cost002-P3L-657 termite gut homogenate clone M1PT4-10, AB191983.1 TLG-1 termite gut homogenate clone Rs-H88, AB089124.1 fluidized bed anaerobic digestor clone vadinBA43, U81652.2 Leptospira 0.10 www.nature.com/nature 40 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Fibrobacter succinogenes OS119, AB275501.1 Fig. S4. Phylogenetic diversity of Fibrobacter succinogenes RS216, AB275507.1 Fibrobacter succinogenes OS112, AB275498.1 P3 luminal microbiota within the Fibrobacter succinogenes OS102, AB275496.1 Fibrobacter succinogenes RS224, AB275510.1 phylum Fibrobacteres. From a Fibrobacter succinogenes RS235, AB275514.1 Fibrobacter succinogenes OS128, AB275503.1 Fibrobacter PCR-based inventory and from the Fibrobacter succinogenes OS103, AB275497.1 Fibrobacter succinogenes AS225, AB275493.1 metagenome libraries 1703 and 14 Fibrobacter succinogenes S85 ATCC 1916, AJ496032.1 Fibrobacter succinogenes, M62685.1 near-full length 16S rRNA gene Fibrobacter succinogenes HM2, AJ496186.1 Fibrobacter succinogenes, M62692.1 sequences, respectively, were used Fibrobacter species, L35548.1 Fibrobacter species, L35547.1 in a Maximum Likelihood analysis Fibrobacter succinogenes, M62688.1 (RaxML). The Phylogram was Fibrobacter succinogenes, M62693.1 Fibrobacter intestinales, M62687.1 constructed using 1289 unambi- Fibrobacter intestinales, M62686.1 Fibrobacter intestinales, M62690.1 guously aligned and filtered termite gut homogenate clone M1NP1-43, AB192086.1 termite gut homogenate clone M1PT4-60, AB192097.1 nucleotide positions. Genbank termite gut clone, AB192088.1 termite gut homogenate clone M1NP2-42, AB192087.1 TFG-1 accession numbers are given. Bar, Microcerotermes gut clone, AB243279.1 10% estimated sequence diver- termite gut homogenate clone M2PT2-81, AB192095.1 termite gut homogenate clone M1PT4-02, AB192084.1 gence. Microcerotermes gut clone, AB248830.1 termite gut homogenate clone M1NP1-73, AB192079.1 Microcerotermes gut clone, AB243276.1 termite gut homogenate clone M1NP2-17, AB192080.1 termite gut homogenate clone M1PT4-84, AB192081.1 Microcerotermes gut clone, AB248829.1 Microcerotermes gut clone, AB243277.1 termite gut homogenate clone M2PT2-74, AB192092.1 termite gut homogenate clone M2PT2-66, AB192094.1 termite gut homogenate clone M2PT2-85, AB192090.1 termite gut homogenate clone M1PT4-22, AB192089.1 termite gut homogenate clone M1PT4-12, AB192076.1 termite gut homogenate clone M2PB4-47, AB192074.1 Microcerotermes gut clone, AB243278.1 termite gut homogenate clone M2PT2-01, AB192077.2 290cost002 metagenome Contig41631 290cost002-P3L-1189 290cost002-P3L-2239 290cost002 metagenome Contig39436 290cost002-P3L-1178 290cost002-P3L-969 290cost002 metagenome Contig39720 290cost002-P3L-2095 290cost002-P3L-1177 290cost002-P3L-1576 290cost002-P3L-1224 290cost002-P3L-2390 290cost002-P3L-1894 290cost002-P3L-2433 290cost002 metagenome Contig40689 290cost002-P3L-2166 290cost002-P3L-2170 290cost002-P3L-1182 290cost002-P3L-1362 290cost002-P3L-2057 290cost002-P3L-2618 290cost002-P3L-1174 290cost002-P3L-1382 TG3-1 290cost002-P3L-1850 290cost002-P3L-1669 290cost002-P3L-1606 290cost002-P3L-1868 290cost002-P3L-1847 290cost002-P3L-1792 290cost002-P3L-1360 290cost002-P3L-2273 290cost002-P3L-1580 290cost002-P3L-1558 290cost002-P3L-2341 290cost002-P3L-2049 290cost002-P3L-1714 290cost002-P3L-2418 290cost002-P3L-1291 290cost002-P3L-1788 290cost002-P3L-1484 290cost002 metagenome Contig38078 290cost002-P3L-1330 290cost002-P3L-1770 290cost002-P3L-2121 290cost002-P3L-1616 290cost002-P3L-1710 290cost002-P3L-2381 290cost002-P3L-1211 290cost002-P3L-1936 290cost002-P3L-1831 290cost002-P3L-1376 termite gut homogenate clone M1PT4-23, AB192108.1 termite gut homogenate clone M1PL1-46, AB192101.1 termite gut homogenate clone M1PT4-09, AB192098.2 termite gut homogenate clone M1NP1-24, AB192099.1 termite gut clone, AB192102.1 termite gut clone, AB248828.1 termite gut homogenate clone M1PL1-67, AB192106.2 Microcerotermes gut clone, AB243294.1 termite gut homogenate clone M2PB4-44, AB192107.1 Guerrero Negro microbial mat clone, DQ329627.1 Guerrero Negro mat microbial clone, DQ329620.1 peat bog clone B122, AM162455.1 Guerrero Negro microbial mat clone, DQ329625.1 290cost002-P3L-1230 290cost002-P3L-2652 290cost002-P3L-2001 termite gut clone, AB192111.2 Microcerotermes gut clone, AB243293.1 Macrotermes gilvus gut clone MgMjD-057 , AB234545.2 TG3-2 termite gut homogenate clone M2PB4-14, AB192109.1 termite gut homogenate clone M1PT4-30, AB192110.1 Riftia pachyptila’s tube clone R76-B150, AF449262.1
0.10
www.nature.com/nature 41 69 Nasutitermes clone Nt2-095, AB255910 67 290cost002-P3L-1187 91 Micrcerotermes clone M2PB4-61, AB191992 89 99 290cost002-P3L-1305 290cost002-P3L-1947 Macrotermes clone MgMjD-069, AB234417 100 Alistipes massiliensis; , AY547271 97 Bacteroides putredinis , L16497 Rikenella microfusus , L16498 94 290cost002-P3L-1253 290cost002-P3L-2684 70 Microcerotermes clone M1NP1-14, AB191984 51 Microcerotermes clone M2PB4-50, AB191986 Macrotermes clone MgMjD-011, AB234393 57 290cost002-P3L-2216 58 Microcerotermes clone M2PB4a-005, AB243253 90 88 Macrotermes clone MgMjR-050, AB234433 87 290cost002-P3L-1961 Reticulitermes clone RPK-31, AB192262 Reticulitermes clone RsTz-26, AB192164 98 Nasutitermes clone Nt2-022, AB255907 94 290cost002-P3L-1628 85 290cost002-P3L-2320 99 Cubitermes clone COB P3-5, AY160852 Cubitermes clone COB P5-29, AY160853 79 Alkaliflexus imshenetskii , AJ784993 Ruminofilibacter xylanolyticum , DQ141183 62 Anaerophaga thermohalophila , AJ418048 Marinilabilia salmonicolor , D12672 57 Bacteroides acidofaciens, AB021157 53 78 Bacteroides vulgatus, AB050111 88 Bacteroides fragilis , M61006 Bacteroides stercoris, X83953 Aquatic clone ML602M-17, AF449781 Sediment clone Y4, AB116461 Sediment clone KM93, AY216441 Cytophaga fermentans , M58766 Bacteroides splanchnicus, L16496 94 290cost002-P3L-2080 96 97 290cost002-P3L-2184 96 290cost002-P3L-1542 90 290cost002-P3L-1802 87 Nasutitermes clone Nt2-060, AB255906 90 Macrotermes clone MgMjD-040, AB234373 Microcerotermes clone M1PT4-06, AB192004 89 71 Reticulitermes clone RsTu1-27, AB192207 Reticulitermes clone Rs-E47, AB088921 Reticulitermes clone Rs-D44, AB088930 50 91 Cow rumen clone GRC99, DQ673564 94 Reticulitermes clone RsaHf415, AY571426 90 Pachnoda ephippiata larval clone PeH22, AJ576339 77 Cubitermes clone COB P4-1, AY160848 98 Nasutitermes clone Nt2-110, AB255911 95 290cost002-P3L-603 Nasutitermes clone Nt2-146, AB255913 100 Chlorobium limicola , M31769 99 Chlorobium vibrioforme , Y10649 96 Chlorobium ferrooxidans , Y18253 Chloroherpeton thalassium , AF170103 0.1 Fig. S5. 16S rRNA Phylogeny of Bacteroidetes-associated Nasutitermes gut clones. 99% OTU representatives of 16S rRNA sequencces amplified from Nasutitermes P3 lumen fluid are marked in red. Tree- Puzzle Maximum likelihood analysis was based on 844 unambiguously aligned nucleotides, HKY method for substitution across sites with uniform rate change. The Tree-Puzzle support values shown above nodes represent 5,000 puzzling steps. www.nature.com/nature 42 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
91 Hot Springs clone SM2A12, AF445709
87 Hot Springs clone SM2F06, AF445728 82 Denitrifying bioreactor clone DB-97, DQ836764
72 Biofilter clone BIfdi48, AJ318130 99 Microcerotermes clone M1NP2-68, AB192129
51 97 Reticulitermes clone RsTu1-32, AB192241
290cost002-P3L-2517
Rhizosphere clone RB205, AB240316
60 Thermophilic sludge clone TA55 Ba 21, AY297971 Hot Spring clone OPB56, AF027009 98 92 Freshwater clone LiUU-9-330, AY509521 Sludge clone A12b, AF234699
Rhizosphere clone RB029, AB240289
89 Arid soil clone 0319-6E22, AF234130
Soil clone S1220, AF507716
72 69 Hot Spring clone SM1A03, AF445646
Hot Spring clone SM1B09, AF445657
Uranium mine waste clone JG30a-KF-39, AJ536877
97 Chlorobium limicola , M31769 94 Chlorobium vibrioforme , Y10649 90 Chlorobium ferrooxidans , Y18253
86 Chloroherpeton thalassium , AF170103
84 100 Hot Spring clone SM1C06, AF445663
Hot Spring clone SM1B03, AF445653
72 Sediment clone K-273, AJ428452
59 Flooded soil clone BSV40, AJ229196
57 Hot Spring clone PK74, AY555793
83 Hot Spring clone PK329, AY555805 Rice paddy clone BSV26, AJ229188
76 Ruminofilibacter xylanolyticum , DQ141183 Cytophaga fermentans , M58766 84 Bacteroides fragilis , M61006
Rhodothermus marinus , AF217499
0.1
Fig. S6. Phylogeny of a Chlorobi-associated Nasutitermes gut clone. 16S rRNA sequences amplified from Nasutitermes P3 lumen fluid are marked in red. Tree-Puzzle Maximum likelihood analysis was based on 1028 unambiguously aligned nucleotides, HKY method for substitution across sites with uniform rate change. The Tree- Puzzle support values shown above nodes represent 10,000 puzzling steps. www.nature.com/nature 43 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
89 290cost002-P3L-Contig13944* A 290cost002-P3L-1269 290cost002-P3L-1153 99 290cost002-P3L-1197 99 290cost002-P3L-2407 89 100 290cost002-P3L-Contig30608* 290cost002-P3L-1241 290cost002-P3L-Contig18107*
98 99 Geothrix fermentans, U41563 Lake Washington sediment clone pLW-58, DQ066996 74 Holophaga foetida, X77215 70 Acidobacteria mats chemoautotrophic cave clone ss_LKC22_UA66, AM180887 98 termite host gut homogenate clone M1PL1-36, AB192122 termite gut homogenate clone M1NP1-62, AB192121 66 290cost002-P3L-1175 B 100 290cost002-P3L-858 100 290cost002-P3L-2379 96 290cost002-P3L-693 76 290cost002-P3L-2521 99 termite gut homogenate clone M1PT4-70, AB192123
99 fungus-growing termite Macrotermes gilvus gut homogenate clone MgMjD-009, AB234549 70 77 host hindgut caecum clone Aci 1, AY222310 subsurface soil beneath grassland clone 5g10, AY177760 forested wetland clone FW32, AF523992
62 Acidobacterium capsulatum, D26171
78 deep-sea octacoral clone ctg CGOF354, DQ395842 soil isolate Ellin310, AF498692 soil isolate Ellin5058, AY234475 87 La Andina Chile Piuquenes copper mine tailings Acidobacteriaceae bacterium CH1, DQ355184
95 fushan forest soils Taiwan clone FAC86, DQ451525 termite gut homogenate clone RsTu1-92, AB192240
98 98 Edaphobacter modestum str. Jbg-1, DQ528760 77 termite gut clone TAA166, AY587230 91 Edaphobacter modestum str. Wbg-1, DQ528761 99 99 termite gut homogenate clone Rs-M39 bacterium, AB089126
100 termite gut clone TAA48, AY587229 termite gut clone TAA43, AY587228 68 Acidobacteria bacterium Ellin345, CP000360
100 Solibacter usitatus str. Ellin6076, NZ AAIA01000029 97 soil isolate Ellin342, AF498724 sponge symbiont clone PAUC26f, AF186410 95 Treponema denticola, M71236 Outgroups 78 91 Treponema pallidum, M88726 Treponema primitia str. ZAS-2, AF093252
93 Clostridium aceticum str. DSM 1496, Y18183 Moorella thermoacetica str. DSM 521, AY656675
72 89 Escherichia coli K12, NC 000913 Pseudomonas aeruginosa PAO1, AE004501 Rhodopseudomonas palustris, L11664
0.1
Fig. S7. Phylogeny of 16s rRNA sequences affiliating with the phylum Acidobacteria recovered from Nasutitermes P3 lumen contents. Tree-Puzzle Maximum likelihood analysis of metagenome sequences identified in the present study (highlighted in red) was based on 1044 unambiguously aligned nucleotides. Sequences marked with (*) are partial gene fragments and were added later to the tree by parsimony methods. 16s rRNA sequences from phyla Spirochaetes, Firmicutes, and Proteobacteria were used to outgroup the unrooted tree. The Tree-Puzzle support values shown above nodes represent confidence values from a 10,000 puzzling step analysis of the dataset. Bar represents evolutionary distance given as 0.1 changes per nucleotide position.
www.nature.com/nature 44 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
92 Anabaena circinalis str. 86, AJ133151.1 Anabaena planctonica NIES-810 str. NIES 810 NIES-8, AB093488.1 55 Nostoc ellipsosporum str. V, AJ630450.1 56 Trichormus variabilis str. KCTC AG10026, DQ234830.1 Cylindrospermopsis raciborskii str. 23B, AF516731.1
Chlorogloeopsis sp. str. PCC 6718, AF132777.1 64 Oscillatoria princeps str. NIVA CYA 150, AB045961.1 Trichodesmium hildebrandtii str. puff, AF091322.1 68 Prochlorothrix hollandica, AJ007907.1 Synechococcus sp. str. C1, AF132772.1 74 89 Synechocystis sp. clone 36P1, AY845229.1 Spirulina subsalsa str. AB2002/06, AY575934.1 99 Gloeobacter violaceus str. PCC 7421, AF132790.1 81 Euglena gracilis str. Z, NC 001603.2 100 Mantoniella squamata str. CCAP 1965/1, X90641.1
Chlamydomonas reinhardii -- chloroplast, X03269.1 50 human transverse colon biopsy clone M019, AY916143.1 57 rumen clone 4C0d-2, AB034016.1 60 rat feces clone rc5-46, AY239440.1
57 84 Rumen isolate str. YS2, AF544207.1 99 290cost002-P3L-309 84 97 290cost002-P3L-1371 termite gut homogenate clone Rs-H34, AB089123.1 59 mouse cecum clone C23 g15, AY992501.1 90 deep-sea mud volcano clone Napoli-3B-41; BC07-3B-4, AY592714.1 55 80 microbial structure rhizosphere biofilm Sapporo ro, AB240501.1 82 freshwater clone PRD01a012B, AF289160.1 72 94 cyanobacterium clone SM1D11, AF445677.1 silica sinter depositing geothermal power station , AY222299.1 100 deep marine sediment clone MB-B2-105, AY093470.1 drinking water system simulator clone HOClCi9, AY328558.1 68 farm soil adjacent to silage storage bunker clone , AY921818.1 88 napthalene-contaminated soil clone 30, AY853673.1 water 10 m downstream manure clone 254ds10, AY212703.1
0.1 Fig. S8. 16S rRNA phylogeny of termite gut clones recovered from Nasutitermes P3 lumen fluid affiliating with the phylum Cyanobacteria. Termite metagenome sequences are highlighted in red. Tree-Puzzle Maximum likelihood analysis was based on 958 unambiguously aligned nucleotides, HKY method for substitution across sites with uniform rate change. Firmicutes sequences (not shown) were used to outgroup this tree. The Tree- Puzzle support values shown above nodes represent 10,000 puzzling steps.
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66 Clostridium leptum str. 10900, AF262239.1 65 Dorea longicatena str. III-35, AJ132842.1 adult human fecal matter clone adhufec236, AF132250.1 96 Clostridium jejuense str. HY-35-12T, AY494606.1 82 Clostridium xylanovorans str. HESP1; DSM 12503, AF116920.1 Clostridium aminovalericum, X73436.1 chicken ileum/cecum clone cc124, DQ057368.1 Coprococcus catus, AB038359.1 57 human sigmoid colon biopsy clone NW71, AY916309.1 rabbit caecum clone 950, AJ863530.1 Ruminococcus productus str. M-2, AB196512.1 68 54 290cost002-P3L-2234 50 290cost002-P3L- 446 rat feces clone rc2-27, AY239426.1 76 91 Catonella morbi, X87151.1 human oral cavity clone FL037, AY349369.1 81 Johnsonella ignava, X87152.1 termite gut clone RsaP112, AY571392.1 91 89 termite gut homogenate clone BCf10-10, AB062805.1 75 termite gut clone RsaHw471, AY571391.1 79 Clostridium propionicum, X77841.1 93 Clostridium lentocellum, X76162.1 87 "Metabacterium polyspora” , U22332.1 Epulopiscium fishelsoni str. Red Sea A1, AF067413.1 92 alkaline-enriched termite gut homogenate clone Pl-, AB189709.1 Enterococcus malodoratus str. ATCC43197, AF061012.1 75 Enterococcus sp. RfL6, AJ133478.1 Enterococcus termitis str. LMG 8895, AM039968.1 64 alkaline-enriched termite gut homogenate clone Mc-, AB189703.1 62 Enterococcus gallinarum str. NCFB 2314, Y18160.1 Hindgut homogenate Pachnoda ephippiata larva clone, AJ576347.1 79 Tetragenococcus halophilus str. DSM 20339, AJ301843.1 82 290cost002-P3L-2602 termite gut clone RsaHf388, AY571409.1 99 Clostridium acetobutylicum, U16147.1 97 Clostridium butyricum YE48, AY442812.1 Clostridium botulinum, X73844.1 67 290cost002-P3L-1599 290cost002-P3L-2244 73 termite gut homogenate clone Tc-13, AB189679.1 termite gut homogenate clone M2PB4-66, AB192035.1 89 Papillibacter cinnamivorans, AF167711.1 termite gut homogenate clone Tc-70, AB189700.1 chicken ileum/cecum clone cc184, DQ057382.1 69 human stool clone C352, AY916334.1 rumen clone F24-B10, AB185589.1 Sporobacter termitidis, Z49863.1 62 termite intestinal tract clone COB P1-19, AY160805.1 termite gut homogenate clone RPK-59, AB192279.1 99 Eubacterium siraeum, L34625.1 76 human ascending colon mucosal biopsy clone LW25, AY976205.1 termite gut homogenate clone Rs-H18 bacterium, AB088966.2 71 87 290cost002-P3L-1430 termite gut homogenate clone Tc-1, AB189675.1 Clostridium cellulosi, L09177.1 81 99 290cost002-P3L-2299 69 290cost002-P3L-568 83 termite intestinal tract clone COB P5-10, AY160797.1 termite gut homogenate clone Tc-12, AB189678.1 76 88 human cecum biopsy clone LD25, AY916202.1 rumen clone F24-H03, AB185647.1 53 56 Fecal microbial (dugong dugon) determined genes Du, AB218341.1 termite gut clone RsaHw476, AY571403.1 termite gut homogenate clone Rs-C69 bacterium, AB089047.1 Desulfitobacterium hafniense str. DCB-2, AAAW04000001.1 67 51 Syntrophobotulus glycolicus str. SlGlym, X99706.1 Thermoincola ferriacetica str. Z-0001, AY631277.1 80 88 Dehalobacter restrictus, U84497.2 Dehalobacter sp. E1, AY766465.1 290cost002-P3L-1289 Sporomusa aerivorans str. TMAM3, AJ506192.1 56 Sporomusa termitida, M61920.1 60 Sporomusa acidovorans str. DSM 3132 Type, AJ279798.1 70 52 Desulfosporomusa polytropa str. STP3, AJ006605.2 290cost002-P3L-2304 Anaerosinus glycerini str. DSM 5192(T), AJ010960.1 Acetonema longum str. DSM 6540(T), AJ010964.1 Dendrosporobacter quercicolus, M59110.1 Geosinus fermentans str. R7, DQ145536.1 74 Propionispora hippei str. KS, AJ508928.1 Selenomonas ruminantium L1, AY685143.1 Anaerovorax odorimutans str. NorPut, AJ251215.1 Eubacterium brachy, U13038.1 Mogibacterium timidum, Z36296.1 290cost002-P3L-1924 termite intestinal tract clone COB P1-16, AY160817.1 53 termite gut homogenate clone Tc-15, AB189680.1 70 termite gut homogenate clone M2PB4-24, AB192034.1 Eubacterium nodatum, Z36274.1 76 290cost002-P3L-1640 290cost002-P3L-2450 290cost002-P3L-1650 termite gut homogenate clone BCf10-24, AB062807.1 53 termite gut homogenate clone Rs-H83 bacterium, AB088976.1 52 termite gut homogenate clone Rs-K21 bacterium, AB088963.1 92 human sigmoid colon biopsy clone MH87, AY916298.1 69 termite gut clone RsaM1, AY571401.1 98 Catabacter hongkongensis str. HKU16, AY574991.1 human transverse colon biopsy clone M501, AY916160.1
0.1 Fig. S9. 16S rRNA phylogeny of termite gut clones recovered from Nasutitermes P3 lumen fluid affiliating with the phylum Firmicutes. Termite metagenome sequences are highlighted in red. Tree- Puzzle Maximum likelihood analysis was based on 875 unambiguously aligned nucleotides, HKY method for substitution across sites with uniform rate change. Cyanobacteria sequences (not shown) were used to outgroup Firmicutes. The Tree-Puzzle support values shown above nodes represent 1,000 puzzling steps. www.nature.com/nature 46 Fig. S10. Phylogenetic analysis of the glycoside hydrolase family 5 (GH5) diversity encoded by the termite gut P3 microbiota. GH5 sequences from the termite gut metagenome are colored in red, the soil metagenome in orange, human biome in cyan, and from various other sources in black. (Meta)genomic and additional public sequences are identified by their JGI Gene Object Identifier and GenBank GI number, respectively. Full-length subclone sequences recovered by database mining, activity screening, or hybridization (as indicated) are identified by their GenBank accession code. Subclones colored in green are active on phosphoric acid swollen cellulose (PASC), and subclones colored in magenta are inactive on PASC. The Pfam PF00150 (Cellulase – glycosyl hydrolase family 5) has a length of 380 residues, comprising domain sequences with an average length of 245 amino acids and 17% sequence identity. Analysis is based on a masked alignment of residues corresponding to the residues 57 to 346 of the endoglucanase from Clostridium cellulovorans (Genbank accession 98588). www.nature.com/nature 47 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Fig. S11. Phylogenetic analysis of the glycoside hydrolase family 9 (GH9) diversity encoded by the termite gut microbiota. GH9 sequences from the termite gut metagenome are colored in red, the soil metagenome in orange, and from various other sources in black. (Meta)genomic and additional public sequences are identified by their JGI Gene Object Identifier and GenBank GI number, respectively. Full-length subclone sequences recovered by database mining, activity screening, or hybridization (as indicated) are identified by their GenBank accession code. Subclones colored in green are active on phosphoric acid swollen cellulose (PASC), and subclones colored in magenta are inactive on PASC. The Pfam PF00759 (Glyco_hydro_9 – glycosyl hydrolase family 9) has a length of 510 residues, comprising domain sequences with an average length of 373 amino acids and 34% sequence identity. Analysis is based on a masked alignment of residues corresponding to positions 286 to 721 of the non-cellulosomal enzyme EngO from Clostridium cellulovorans (Genbank accession 49425363). www.nature.com/nature 48 Fig. S12. Phylogenetic analysis of the glycoside hydrolase family 10 (GH10) diversity encoded by the termite gut microbiota. GH10 xylanases from the termite gut metagenome are colored in red, the human gut microbiome in blue, the soil metagenome in orange, and from various other sources in black. (Meta)genomic and additional public sequences are identified by their JGI Gene Object Identifier and GenBank GI number, respectively. The Pfam PF00331 (Glyco_hydro_10 – glycosyl hydrolase family 10) has a length of 356 residues, comprising domain sequences with an average length of 232 amino acids and 32% sequence identity. Analysis is based on a masked alignment of 356 residues corresponding to positions 192 to 534 of xylanase B from Clostridium cellulovorans (Genbank accession 47716661).
49 www.nature.com/nature 49 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Fig. S13. Phylogenetic analysis of the glycoside hydrolase family 11 (GH11) diversity encoded by the termite gut microbiota. GH11 xylanases from the termite gut metagenome are colored in red, three previously discovered and characterized GH11 xylanases from insect guts (Brennan et al., 2004) are colored in blue, and GH11 xylanases from various other sources are colored in black. (Meta)genomic and additional public sequences are identified by their JGI Gene Object Identifier and GenBank GI number, respectively. The Pfam PF00457 (Glyco_hydro_11 – glycosyl hydrolase family 11) has a length of 194 residues, comprising domain sequences with an average length of 173 amino acids and 48% sequence identity. Analysis is based on a masked alignment of 194 residues corresponding to the positions 68 to 254 of the endo-1,4--xylanase from Clostridium saccharobutylicum (Genbank accession 139871).
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Contig37225_GENE_4_domain_1_of_1_Fibrobacteres tgut2fos_Contig104_GENE_18_domain_1_of_1_Treponema Contig28062_GENE_1_domain_1_of_1 BHZN34301.g1_GENE_1_domain_1_of_1 BHZN42282.g2_GENE_1_domain_1_of_1 BHZN47246.g2_GENE_1_domain_1_of_1 Contig40901_GENE_1_domain_1_of_1_Fibrobacteres Contig40825_GENE_1_domain_1_of_1_Fibrobacteres Contig37147_GENE_1_domain_1_of_1 Contig35201_GENE_1_domain_1_of_1 Contig9536_GENE_1_domain_1_of_1 BHZN19884.g1_GENE_1_domain_1_of_1 Contig4602_GENE_2_domain_1_of_1 Contig25830_GENE_2_domain_1_of_1 BHZN41157.b2_GENE_1_domain_1_of_1 BHZN890.b1_GENE_1_domain_1_of_1 BHZN7975.b2_GENE_1_domain_1_of_1 BHZN18797.g1_GENE_1_domain_1_of_ 1 Contig35224_GENE_1_domain_1_of_1_Fibrobacteres Contig32770_GENE_1_domain_2_of_2 Contig25830_GENE_1_domain_1_of_2 Contig25830_GENE_1_domain_2_of_2 Contig32442_GENE_1_domain_2_of_2 Contig32442_GENE_1_domain_1_of_2 Contig19818_GENE_1_domain_1_of_1 Contig32518_GENE_3_domain_2_of_2 Contig4328_GENE_1_domain_2_of_2 BHZN18490.g1_GENE_1_domain_1_of_1 Contig24255_GENE_1_domain_1_of_1 BHZN23981.g1_GENE_1_domain_1_of_1 Contig30071_GENE_1_domain_2_of_2 Contig41591_GENE_2_domain_2_of_2 Contig28506_GENE_1_domain_1_of_2 BHZN29886.g1_GENE_1_domain_1_of_1 Contig32770_GENE_1_domain_1_of_2 Contig32518_GENE_3_domain_1_of_2 Contig4328_GENE_1_domain_1_of_2 Contig14384_GENE_1_domain_1_of_1 Contig40987_GENE_2_domain_2_of_2_Fibrobacteres Contig22319_GENE_1_domain_1_of_1 Contig32523_GENE_2_domain_1_of_1 Contig24934_GENE_1_domain_1_of_1 Contig40987_GENE_2_domain_1_of_2_Fibrobacteres Contig27145_GENE_2_domain_1_of_1 BHZO1422.g2_GENE_1_domain_1_of_1 Contig34579_GENE_2_domain_1_of_1 BHZN43936.g2_GENE_1_domain_1_of_1 Contig24384_GENE_1_domain_1_of_1 Contig36853_GENE_1_domain_1_of_1 BHZN33129.b1_GENE_1_domain_1_of_1 Contig34892_GENE_1_domain_1_of_1 BHZN19778.b1_GENE_1_domain_1_of_1 tgut2fos_Contig97_GENE_4_domain_1_of_1_Fibrobacteres tgut2fos_Contig97_GENE_5_domain_1_of_2_Fibrobacteres tgut2fos_Contig97_GENE_5_domain_2_of_2_Fibrobacteres tgut2fos_Contig97_GENE_6_domain_1_of_1_Fibrobacteres Contig9272_GENE_1_domain_1_of_1 Contig20114_GENE_1_domain_1_of_1 Contig20100_GENE_1_domain_1_of_1 tgut2fos_Contig97_GENE_7_domain_1_of_1_Fibrobacteres Contig27933_GENE_1_domain_1_of_1 Contig2220_GENE_1_domain_1_of_1 Contig19761_GENE_1_domain_1_of_1 BHZN16344.g1_GENE_1_domain_1_of_1 Contig26308_GENE_2_domain_1_of_1 BHZN51037.g2_GENE_1_domain_1_of_1 Contig30400_GENE_1_domain_1_of_1 Contig38536_GENE_1_domain_1_of_1 Contig5278_GENE_1_domain_1_of_1 BHZN12891.g1_GENE_1_domain_1_of_1 Contig14418_GENE_1_domain_1_of_2 Contig23951_GENE_1_domain_1_of_2 Contig40870_GENE_1_domain_1_of_1 Contig27770_GENE_1_domain_1_of_1 Contig41591_GENE_2_domain_1_of_2 Contig19077_GENE_1_domain_1_of_1 Contig27341_GENE_1_domain_1_of_1 Contig28506_GENE_1_domain_2_of_2 Contig7217_GENE_1_domain_1_of_1 Contig325_GENE_1_domain_1_of_1 Contig40569_GENE_1_domain_2_of_2 Contig14054_GENE_1_domain_1_of_1 Contig25647_GENE_1_domain_1_of_1 Contig40955_GENE_1_domain_1_of_1 Contig16008_GENE_1_domain_1_of_1 Contig41634_GENE_4_domain_1_of_1 Contig38831_GENE_1_domain_1_of_1 Contig39250_GENE_1_domain_1_of_3 Contig39250_GENE_1_domain_2_of_3 Contig41565_GENE_5_domain_1_of_1 Contig41591_GENE_3_domain_1_of_1 Contig8597_GENE_2_domain_1_of_1 Contig39617_GENE_1_domain_1_of_1 Contig39949_GENE_2_domain_1_of_1 Contig34931_GENE_3_domain_1_of_1 Contig39949_GENE_1_domain_1_of_1 Contig17979_GENE_1_domain_1_of_1 Contig10217_GENE_1_domain_1_of_2 Contig10217_GENE_1_domain_2_of_2 Contig39101_GENE_3_domain_1_of_1 Contig39250_GENE_1_domain_3_of_3 Contig36660_GENE_1_domain_1_of_2 Contig36660_GENE_1_domain_2_of_2 Contig28827_GENE_1_domain_1_of_2 Contig27955_GENE_1_domain_1_of_2 Contig24649_GENE_1_domain_1_of_1 Contig39244_GENE_3_domain_1_of_1 Contig25154_GENE_1_domain_1_of_1 BHZN12947.g1_GENE_1_domain_1_of_1 Contig41485_GENE_2_domain_1_of_1 BHZN33286.b1_GENE_1_domain_1_of_1 BHZN52838.g2_GENE_1_domain_1_of_1 Contig24350_GENE_1_domain_1_of_1 Contig40569_GENE_1_domain_1_of_2 Contig14418_GENE_1_domain_2_of_2 Contig23951_GENE_1_domain_2_of_2 Contig35948_GENE_1_domain_2_of_3_Fibrobacteres Contig40858_GENE_1_domain_1_of_1 Contig27955_GENE_1_domain_2_of_2 Contig28827_GENE_1_domain_2_of_2 Fibrobacteres_succinogenes S85 Contig40625_GENE_3_domain_1_of_1
Reference sequences
0.10
Fig. S14. Phylogenetic analysis of overrepresented conserved hypo-thetical gene family TOG1 (TIGR02145) encoded by the P3 luminal microbiota. For the analysis the amino acid sequences of the domain were aligned and a Maximum Likelihood tree was calculated (Phylip PROML, 124 positions considered). Reference sequences comprised: Fibrobacteres succinogenes, Bacteroidetes fragilis and B. thetaiotaomicron, Chlorobium tepidum and Pelodictyon luteolum. Names are printed bold and in blue color for contigs assigned to Fibrobacteres by PhyloPythia and green for Treponema. Color-coded boxes visualize examples of the phylogenetic position of domains belonging to the same gene. Bar, 10% estimated sequence divergence. www.nature.com/nature 51 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Fig. S15. Phylogenetic diversity of iron-only Putative sensory hydrogenases hydrogenases. In the metagenomic dataset >150
genes coding for hydrogenase catalytic domains family 1 (pfam02906, large subunit, C-terminal domain) Hydrogenases with were discovered. Based on the overall protein family 5 methyl-accepting domain sequence similarity, Fe-only hydrogenase proteins were grouped into 11 families; since many family 10 sequences represented gene fragments rather than complete genes, proteins within each family family 4 were aligned and a consensus sequence for each Pelobacter carbinolicus DSM 2380 (PAS domain), ABA89074.1 family was generated, which was further used for family 8 analysis of domain composition (Fig S17). The Thermoanaerobacter tengcongensis MB4 (PAS domain), AAM23959.1 tree shows that Fe-only hydrogenases in the family 6 termite hindgut metagenome are separated into 2 Treponema denticola ATCC 35405, AAS11795.1 large groups, with one of them containing Desulfovibrio desulfuricans G20, ABB37526.1 domains typical for hydrogenases catalyzing 2004096748, Contig10773 hydrogen evolution or uptake, while in the other 2004117939, Contig25966 2004090116, Contig5808 group catalytic the domain was fused to various 2004118909, Contig26581 other conserved domains (MA – methyl-accepting 2004133409, Contig35567 chemotaxis protein signaling domain, REC – 2004142657, Contig40246 2004087291, Contig3659 response regulator receiver domain, PAS and 2004139922, Contig38965 PAS_4 – PAS/PAC sensor domain). Remarkably, 2004091513, Contig6870 most of these domains fused with Fe-only 2004142656, Contig40246 2004111139, Contig21412 hydrogenase catalytic core in the termite hindgut 2004133408, Contig35567 metagenome are known to be involved in signal 2004101268, Contig14158 transduction. Based on domain architecture of Fe- 2004086063, Contig2785 2004126522, Contig31391 only hydrogenase proteins we tentatively 2004105320, Contig17144 assigned the first group as “catalytic” 2004141757, Contig39862 hydrogenases and the second group as “sensory” 2004091623, Contig6946 2004093306, Contig8200 hydrogenases. One of the largest families of 2004083009, Contig520 “sensory” hydrogenases in termite hindgut 2004098523, Contig12149 metagenome was family 1, which represented a 2004138311, Contig38171 2004097668, Contig11484 fusion of the catalytic domain with a methyl- 2004119452, Contig26935 accepting chemotaxis protein signaling domain 2004136169, Contig37066 and response regulator receiver domain. We 2004145706, Contig41331 2004132119, Contig34839 hypothesize that the representatives of this family 2004144780, Contig41045 function as hydrogen chemoreceptors with 2004087563, Contig3857 hydrogenase domain serving as hydrogen sensor 2004128967, Contig32917 2004085995, Contig2738 rather than a catalyst of hydrogen evolution or 2004160714, BHZN39579_g2 uptake. Search for proteins with similar domain 2004128968, Contig32917 2004106470, Contig17999 architecture using CDART (Conserved Domain 2004110961, Contig21282 Architecture Retrieval Tool) retrieved no hits in 2004146072, Contig41428 any other organism, indicating that this family is 2004148312, BHZN3955_g1 unique for Treponema species inhabiting termite 2004119568, Contig27003 2004100209, Contig13393 hindguts. It has been demonstrated that strains of 2004107649, Contig18868 Treponema isolated from the hindgut of lower 2004123602, Contig29540 termites alternatively either produce or utilize 2004113334, Contig23005 family 3 2004084376, Contig1522 molecular hydrogen. For the phylogenetic analysis Desulfovibrio vulgaris subsp. oxamicus, AAA23373.1 288 alignment positions were considered. Bar, Desulfovibrio vulgaris subsp. vulgaris, AAS96246.1 Shewanella oneidensis MR-1, NP_719451.1 10% estimated sequence divergence. Clostridium pasteurianum, AAA23248.1 Clostridium perfringens, BAA74738.1 Clostridium acetobutylicum ATCC 824, AAK78015.1 Scenedesmus obliquus, CAC34419.1 Chlamydomonas reinhardtii, CAC83731.1 Geer L. Y., Domrachev M., Lipman D. J., Bryant Megasphaera elsdenii, AAF22114.1 S. H. CDART: protein homology by domain Thermoanaerobacter tengcongensis MB4, AAM24150.1 Clostridium thermocellum, AAD33071.1 architecture. Genome Res. 2002. 12:1619-1623. Eubacterium acidaminophilum, CAC39231.1 Desulfovibrio fructosovorans, AAA87057. Graber, J.R., Leadbetter, J.R. & Breznak, J.A. Thermotoga maritima MSB8, NP_229226.1 Description of Treponema azotonutricium sp. nov. family 7 Putative and sp. nov., the first Treponema primitia catalytic hydrogenases spirochetes isolated from termite guts. Appl family 2 0.10 Environ Microbiol 70, 1315-1320 (2004).
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Fig. S16. Domain composition of iron-only hydrogenases. Conserved domains and motifs were detected in the consensus sequences of each family using InterProScan. The following domains were discovered: fer2 – pfam00111, 2Fe-2S iron-sulfur cluster binding domain; Fer4 – pfam00037, 4Fe-4S binding domain; Fe_hyd_lg_C – pfam02906, iron only hydrogenase large subunit, C-terminal domain; FeS – pfam04060, putative Fe-S cluster; MA – pfam00015, methyl-accepting chemotaxis protein (MCP) signaling domain; REC – pfam00072, response regulator receiver domain; Fe_hyd_SS – pfam02256, iron hydrogenase small subunit; PAS – pfam00989, PAS domain; PAS_4 – pfam08448, PAS_4 domain, part of the PAS domain clan; Trx-like – pfam00085, thioredoxin. Families 9 and 11 were not included in the phylogenetic analysis due to the very short sequences contained therein In the metagenomic dataset >150 genes coding for hydrogenase catalytic domains were discovered.
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Fig. S17. Three-dimensional structure of a family 2 Fe-only hydrogenase representative obtained by comparative modeling using the periplasmatic Clostridium pasteurianum enzyme Cpl as template and superimposed on its structure. The C. pasteurianum enzyme is colored cyan, family 2 protein is silver. The region in the C. pasteurianum protein that was deleted in family 2 is ice-blue. Iron-sulfur clusters in C. pasteurianum protein are presented as yellow CPK; cysteines coordinating proximal FS4A cluster are purple CPK in C. pasteurianum and green in family 2 protein. Cysteines coordinating H cluster are purple in C. pasteurianum and blue in family 2 protein, except for the subcluster-bridging cysteine, which is red in C. pasteurianum protein and pink in family 2 protein. Among the families of “catalytic” hydrogenases family 2 was the most remarkable one. Representatives of this family are very distant from any other Fe-only hydrogenase proteins and lack the C-terminal domain found in most Fe-only hydrogenases characterized so far; in addition, alignment of the catalytic domain showed that some of the cysteine residues coordinating the active-site iron-sulfur cluster may occupy different positions than in typical enzymes. The shown structure reveals that while the cysteine residues coordinating the proximal FS4A cluster align very well, cysteines coordinating the active-site iron-sulfur cluster (including the subcluster-bridging Cys) occupy different positions.
Peters J. W., Lanzilotta W. N., Lemon B. J., Seefeldt L. C. X-ray crystal structure of the Fe-only hydrogenase (CpI) from Clostridium pasteurianum to 1.8 angstrom resolution. Science. 1998. 282:1853- 1858
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Fig. S18. Predicted hydrogen diffusion channels in C. pasteurianum Fe-only hydrogenase superimposed on the predicted 3D structure of a family 2 representative. Hydrogen diffusion channel 1 in C. pasteurianum protein is ochre, residues conserved in family 2 protein are green; hydrogen diffusion channel 2 in C. pasteurianum is dark magenta, residues conserved in family 2 protein are blue. Residues conserved in family 2 protein and corresponding to the central chamber in C. pasteurianum protein are red. In conclusion, residues forming predicted hydrogen diffusion channels in C. pasteurianum enzyme are partially conserved in family 2 proteins.
Cohen J., Kim K., Posewitz M., Ghirardi M. L., Schulten K., Seibert M., King P. Molecular dynamics and experimental investigation of H(2) and O(2) diffusion in [Fe]-hydrogenase. Biochem. Soc. Trans. 2005. 33:80-82
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CO CO 2 2 CooH-like Ion Translocating See Figure S21 Formate H2 [2] [2] NiFe Hydrogenase Dehydrogenase RnfC-like Ion Translocating Formate Oxidoreductase [30]
See Figure S22 Formyl-THF H2 [32] Synthetase ADP Carbon Monoxide Dehydrogenase ATP THF Acetyl-CoA Synthase Complex Formyl-THF CODH/ACS [21] See CooS-subunit Figure S23 Methenyl-THF Cyclohydrolase Large Subunit Fe-S-Co Protein [21] [19] Methenyl-THF Methylene-THF Small Subunit Fe-S-Co Protein [14] H2 Dehydrogenase CooC Ni-insertion Protein [23] Methylene-THF Methylene-THF H Acetyl-CoA Synthase (AcsR) [37] [15] 2 Reductase THF [CO]-X
THF: Fe-S-Co Methyl-THF CODH/ACS-associated Membrane [27] Methyl Transferase Protein with Fd Domain – Possible [32] Ion Pump (Moorella gene 63211333) ATP Acetyl-CoA ADP CoA
Acetate Acetyl-P
Fig. S19. Recovery of genes or partial genes encoding proteins relevant to the Wood-Ljungdahl pathway of CO2-reductive homoacetogenesis. Green boxes denote the number of variants for each function recovered in the metagenome dataset. Note that for all of the functions, formate dehydrogenases appears to be particularly underrepresented, suggesting that either formate is generated from a precursor other than carbon dioxide (e.g. such as pyruvate), from within another gut compartment, or by an enzyme that belongs to a not yet recognizable FDH class of proteins. The blue box encompasses 5 proteins commonly encountered as being a part of the multi-enzyme acetyl synthase complex. The red boxes denote two classes of possible ion pumps that hypothetically might be used to drive either energy consuming steps in the pathway (e.g. CO2 reduction to CO) or energy conserving steps (such as the reduction of Methylene-THF or the methyl group transfer from THF to the CODH/ACS complex).
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Yersinia bercovieri ATCC 43970 gi|77958664 54 Yersinia mollaretii ATCC 43969 gi|77961144 Yersinia intermedia ATCC 29909 gi|77978827 Yersinia frederiksenii ATCC 33641 gi|77973842 51 Rhodopseudomonas palustris BisB18 gi|90426049 57 Rhodospirillum rubrum ATCC 11170 gi|83591664 Erwinia carotovora subsp atroseptica SCRI10431 gi|49610969 99 Yersinia pestis biovar Orientalis str IP275 gi|89103974 98 Yersinia pestis biovar Microtus str 91001 gi|45440352 83 71 Yersinia pseudotuberculosis IP 31758 gi|77631397 Yersinia frederiksenii ATCC 33641 gi|77973354 82 Yersinia mollaretii ATCC 43969 gi|77960692 Erwinia carotovora subsp atroseptica SCRI1043 gi|49610715 67 99 Escherichia coli K12 gi|16131905 & 6 other strains 99 Salmonella typhimurium LT2 gi|16422846 & 2 other strains 99 Photobacterium profundum 3TCK gi|90410741 99 Psychromonas sp CNPT3 gi|90407572 99 Vibrio angustum S14 gi|90578218 100 Clostridium difficile QCD 32g58 NZ_AAML02000062 Clostridium beijerincki NCIMB 8052 gi|82745180 290cost002-P3L-BHZN13881_g1 92 Methanococcus maripaludis S2 gi|45047261 Methanococcus voltae gi|14211980 Roseobacter denitrificans OCh 114 gi|110681349 Roseovarius sp 217 gi|85703437 61 Oceanicola granulosus HTCC2516 gi|89067229 77 Sulfitobacter sp NAS 14-1 gi|83855177 67 83 Silicibacter pomeroyi DSS 3 gi|56677473i 51 Chromohalobacter salexigens DSM 3043 gi|91796215 Bradyrhizobium japonicum XSDA 110 gi|27377428 96 88 Methylobacterium extorquens gi|22652728 90 Acidovorax sp JS42 gi|110595735 57 Rhodoferax ferrireducens T118 gi|89902038 82 Methylococcus capsulatus str Bath gi|53803292 100 74 Ralstonia eutropha JMP134 gi|72121814 Sargasso Sea 1 gb|AACY01085766 Human Gut 2 gi|106747447 Methanocaldococcus jannaschii DSM 2661 gi|15669895 72 Methanococcus maripaludis S2 gi|45047727 100 Vibrio parahaemolyticus RIMD 2210633 gi|28808651 99 Vibrio sp Ex25 gi|75855374 95 Vibrio alginolyticus 12G01 gi|91226395 Vibrio splendidus 12B01 gi|84388509 87 92 Vibrio vulnificus YJ016 gi|37675860 97 Photobacterium profundum 3TCK gi|90415121 Photobacterium profundum SS9 gi|46915864 71 Sargasso Sea 5 gb|AACY01051749 67 Shewanella sp MR 7 gi|78688787 63 Sargasso Sea 3 gi|44471509 92 Shewanella sp PV 4 gi|78367417 Shewanella frigidimarina NCIMB 400 gi|69949116 80 Rhodopseudomonas palustris CGA009 gi|39933811 99 Rhodopseudomonas palustris BisB5 gi|91975103 97 Rhodopseudomonas palustris HaA2 gi|86747850 87 99 Rhodopseudomonas palustris BisA53 gi|77740102 92 Rhodopseudomonas palustris BisB18 gi|90426116 91 Sinorhizobium meliloti gi|11545455 Xanthobacter autotrophicus Py2 gi|89359739 Rhodobacterales bacterium HTCC2654 gi|84686203 Marinomonas sp MED121 gi|87120635 67 marine gamma proteobacterium HTCC2207 gi|90416712 96 Colwellia psychrerythraea 34H gi|71144732 100 Burkholderia sp 383 gi_22652728 88 78 “Sargasso Sea” 2 gb|AACY01015269 Burkholderia vietnamiensis G4 gi|67546817 90 Pseudomonas fluorescens Pf 5 gi|68348133 Pseudomonas putida F1 gi|82737790 Methylobacillus flagellatus KT gi|91775073 65 Bordetella bronchiseptica RB50 gi|33567906 Burkholderia xenovorans LB400 gi|91784828 Cupriavidus necator gi|3724145 98 Bacillus licheniformis ATCC 14580 gi|52003801 94 67 91 Bacillus subtilis subsp subtilis str 168 gi|2633570 Bacillus sp NRRL B 14911 gi|89098845 92 Bacillus clausii KSM K16 gi|56908912 Deinococcus geothermalis DSM 11300 gi|94554264 98 86 Staphylococcus aureus RF122 gi|82751902 100 Bacillus cereus ATCC 14579 gi|29897229 97 100 Bacillus thuringiensis serovar konkukian str 97-27 gi|49333302 97 Geobacillus kaustophilus HTA426 gi|56378836 Ferroplasma acidarmanus Fer1 gi|68139733 Sulfolobus tokodaii str 7 gi|15621042 57 290cost002-P3L-BHZN573_b1 99 Methanosarcina barkeri str fusaro gi|72396235 100 Sargasso Sea 4 gb|AACY01000779 62 99 Human Gut 1 gb|AAQL01000228.1 Human Gut 3 gi|106748230 Methanocaldococcus jannaschii gi|47132440 Uncultured methanogenic archaeon RC I gi|110622188 57 Eubacterium acidaminophilum gi|14250944 Eubacterium acidaminophilum gi|14250938 Carboxydothermus hydrogenoformans Z 2901 gi|77996762 Desulfotalea psychrophila LSv54 gi|50875370 Pelobacter propionicus DSM 2379 gi|71836213 96 Syntrophobacter fumaroxidans MPOB gi|71546007 Moorella thermoacetica gi|14717798 99 Enterococcus faecalis V583 gi|29343419 Methanoculleus marisnigri JR1 gi|110604881 Methanospirillum hungatei JF 1 gi|88603271 0.1 changes per position Methanospirillum hungatei JF 1 gi|88603273 Fig. S20. Phylogeny of the only two putative formate dehydrogenases recovered during Nasutitermes P3 Metagenomic analysis. Tree-Puzzle Maximum likelihood analysis was based on 568 unambiguously aligned amino acid positions. One formate dehydrogenase affiliates with bona fide FdhF (FDH H) type homologs from E. coli and other enteric Gammaproteobacteria, whereas the other affiliates with less well studied variants. www.nature.com/nature 57 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
Termite Treponeme Cluster A Reticulitermes Clone 144, DQ278223 Reticulitermes Clone 296, DQ278208 Zootermopsis Clone H, AY162302 Reticulitermes Clone 249, DQ278204 Zootermopsis Clone P, AY162307 Treponema primitia ZAS-2, AY162315 Zootermopsis Clone N, AY162306 Reticulitermes Clone 124, DQ278220 Treponema primitia ZAS-1, AY162313 Treponema azotonutricium ZAS-9, AY162316 Reticulitermes Clone 129, DQ278222 Reticulitermes Clone 13, DQ278232 Reticulitermes Clone 175, DQ278227 Cryptotermes Clone 27, DQ278254 290cost002-P3L-2004091492 290cost002-P3L-2004124486 290cost002-P3L-2004111036 290cost002-P3L-2004126714 Reticulitermes Clone 23, DQ278210 290cost002-P3L-2004097922 290cost002-P3L-2004144560 290cost002-P3L-2004142324 Reticulitermes Clone 183, DQ278230 Zootermopsis Clone A, AY162294 Cryptotermes Clone 56, DQ278258 Cryptotermes Clone 3, DQ278251 Zootermopsis Clone F, AY162298 Zootermopsis Clone Y, AY162311
Clostridium aceticum, AF295705 Homoacetogenic Clostridium formicaceticum, AF295702 “Classical”
Acetobacterium woodii, AF295701 Firmicutes Eubacterium limosum, AF295706 Clostridium magnum, AF295703 Thermoanaerobacter kivui, AF295704 Ruminococcus productus, AF295707 Sporomusa ovata, AF295708 Sporomusa termitida (Nasutitermes isolate), AF295709 Moorella thermoacetica, J02911
Proteus vulgaris, AF295710 0.1
Treponema primitia ZAS-1 B 290cost002-P3L-2004088671 290cost002-P3L-2004091492 290cost002-P3L-2004111036 290cost002-P3L-2004126714 290cost002-P3L-2004099364 Zootermopsis Clone H 290cost002-P3L-2004124486 T. primitia ZAS-2 Reticulitermes Clone 183 290cost002-P3L-2004083330 290cost002-P3L-2004097922 290cost002-P3L-2004107881 290cost002-P3L-2004144560 Cryptotermes Clone 56 290cost002-P3L-2004123975 290cost002-P3L-2004096868 290cost002-P3L-2004106186 290cost002-P3L-2004142324 T. azotonutricium ZAS-9 Zootermopsis Clone A Ruminococcus productus Nasutitermes 2004105509 Zootermopsis Clone Y Zootermopsis Clone F Clostridium aceticum 290cost002-P3L-2004131907 290cost002-P3L-2004093883
Fig. S21. Metagenomic formyl-tetrahydrofolate synthetases, markers of CO2-reductive homoacetogenic metabolism, affiliate with known homoacetogenic Spirochetaetes, not Firmicutes. A) Protein Maximum Likelihood phylogram of homoacetogen-like FTHFS homologs. Analysis based on 235 unambigouosly aligned amino acid positions. Short FTHFS fragments identified in Nasutitermes metagenomic libraries were not included in the phylogenetic analysis. Shaded box highlights FTHFS clade of homologs cloned from isolated termite gut homoacetogenic spirochetes and from the gut contents of species corresponding to four of the 6 major termite families. B) Variable region of FTHFS. Box highlights a short peptide region of the FTHFS protein that is unique to termite gut associated homoacetogenic spirochetes (e.g. isolated T. primitia strains ZAS-1 and ZAS-2) and gut derived PCR and metagenomic clones from Nasutitermes and termites representing an additional three termite families. A non-acetogenic gut spirochete (e.g. isolated T. azotonutricium strain ZAS-9) and “classical” firmicutes homoacetogens do not contain this character. This peptide stretch was not included in the phylogenetic analysis, thus stands in independent support of it. Note that not all of the metagenomic clones shown in B) were used in the phylogenetic analysis for A) as the gene fragments were too short to analyze fully.
Salmassi, T. M., and J. R. Leadbetter. 2003. Analysis of genes of tetrahydrofolate-dependent metabolism from cultivated spirochaetes and the gut community of the termite Zootermopsis angusticollis. Microbiology 149:2529-2537. www.nature.com/nature 58 doi: 10.1038/nature06269 SUPPLEMENTARY INFORMATION
95 Alkaliphilus metalliredigenes, 77685053 100 Clostridium difficile QCD-32g5, 90575780 A 100 290cost002-P3L-Contig10353, 2004096177 100 290cost002-P3L-Contig23438, 2004113965 290cost002-P3L-Contig25237, 2004116794 Syntrophobacter fumaroxidans MPOB, 71544930 Candidatus Kuenenia stuttgartiensis, 91202652 B 96 delta proteobacterium MLMS-1, 93451867 100 290cost002-P3L-Contig23031, 2004113367 290cost002-P3L-Contig36877, 2004135826 100 290cost002-P3L-Contig40494, 2004143255 99 290cost002-P3L-Contig29326, 2004123265 290cost002-P3L-Contig41666, 2004147053 290cost002-P3L-Contig41758, 2004147523 100 Pelobacter carbinolicus DSM 2380, 77917675 100 Geobacter sulfurreducens PCA, 39984086 Geobacter uraniumreducens Rf4, 88934697 99 Methanosaeta thermophila PT, 88951575 100 Methanosarcina mazei Go1, 21226223 Methanosarcina acetivorans C2A, 19917315 Methanosarcina barkeri str. fusaro, 72398121 Methanospirillum hungatei JF-1, 88602556 Syntrophobacter fumaroxidans MPOB, 71543677 82 74 Desulfovibrio vulgaris subsp.vulgaris, 46449922 91 Desulfovibrio desulfuricans G2, 78220473 delta proteobacterium MLMS-1, 93451388
78 Azotobacter vinelandii AvOP, 67154767 Carboxydothermus hydrogenoformans Z2901, 77996167 Desulfitobacterium hafniense Y51, 89897188 91 100 Moorella thermoacetica ATCC 39073, 83590051 73 Desulfitobacterium hafniense Y51, 89894399 Carboxydothermus hydrogenoform Z2901, CHY1221 100 Thermoanaerobacter tengcongensis MB4, 20516721 Carboxydothermus hydrogenoform Z2901, 77996689 Alkaliphilus metalliredigenes GS-15 , 77685868 Candidatus Kuenenia stuttgartiensis, 91202312 Carboxydothermus hydrogenoformans Z2901, 77995533 86 Desulfitobacterium hafniense Y51, 89895376 100 Rhodospirillum rubrum ATCC 11170, 83592763 Rhodopseudomonas palustris BisB18, 90425970 Moorella thermoacetica ATCC 39073, 83590804 86 87 Chlorobium phaeobacteroides DSM 266, 67935114 100 Geobacter metallireducens GS-15, 78194364 100 Campylobacter concisus 13826, 109672145 Campylobacter curvus 525.92, 109673545 Methanocaldococcus jannaschii DSM 2661 , 2826314 82 92 100 Methanopyrus kandleri AV19, 19886936 C 100 Methanopyrus kandleri AV19, 9247062 Pelobacter carbinolicus DSM 2380, 77918498 91 Clostridium acetobutylicum ATCC 824, 15022942 97 Clostridium beijerincki NCIMB 8052, 82748981 100 Caldicellulosiruptor saccharolyticus DSM 8903, 82501374 Clostridium difficile QCD-32g5, 90576262 Clostridium tetani E88, 28210849 91 94 Carboxydothermus hydrogenoformans Z2901, 77995321 99 Desulfitobacterium hafniense Y51, 89896919 71 84 Clostridium acetobutylicum ATCC 824, 15025519 Clostridium beijerincki NCIMB 8052 , 82746157 64 Archaeoglobus fulgidus DSM 430, 11499434 100 Methanosaeta thermophila PT, 88950484 0.1 100 Methanosarcina mazei Go1, 21228403i Methanosarcina acetivorans C2A, 19915158 Methanosarcina barkeri str. fusaro, 72398307
Fig. S22. Phylogeny of Carbon Monoxide Dehydrogenase Catalytic Subunits (CooS) recovered during Nasutitermes P3 Metagenomic analysis. The enzymatic activity catalyzed by CooS homologs can be used in either the oxidative or reducitive direction, and in either anabolism or energy metabolism, depending on the Bacteria or Archaea in question, or their mode of growth. In CO2-reducing homoacetogens, the enzyme operates in the reductive direction (see Fig. S20). Maximum likelihood analysis was based on 245 unambigouosly aligned amino acid positions. Full length or near full length CooS are highlighted in blue and fell within two clusters, colored boxes A and B. Partial CooS fragments from the metagenomic dataset (not included in this phylogram) affiliated with either cluster A (1 sequence), B (9 sequences) or grouped within colored box C (4 sequences). One short CooS fragment affiliated with the two CooS homologs present in Campylobacter genomes (not shown). Values are given for a 1000 bootstrap analysis of the dataset. Bar represents evolutionary distance given as 0.1 changes per amino acid position.
www.nature.com/nature 59 n s o s r e m e c
Metagenomes n u i l n s l e
e n m e g t s a i g a a c l l o u 2 t m o g o o a n x g 1 o s i u n i
i o c v i o l i i c r m K i d a e t c r i r t t c g i l g i m l n l c e e e u n t a i a o e a u 1 2 3 h m r 7 8 h s O D l n t f t g c n i r d p s i F F F G G n M M o e T H H A A W W W A S T. T. L. B. B. P. F. C. W. E. COG0840 Methyl-accepting chemotaxis protein (MCP) COG2201 CheB, chemotaxis response regulator w/ CheY-like receiver and methylesterase domain COG1871 CheD, chemotaxis protein; stimulates methylation of MCP proteins COG1352 CheR, methylase of chemotaxis methyl-accepting proteins COG0643 CheA, chemotaxis protein histidine kinase and related kinases COG0835 CheW, chemotaxis coupling protein COG0784 CheY-like receiver, response regulator
Chemotaxis COG3143 CheZ, chemotaxis protein COG1776 CheC, inhibitor of MCP methylation COG0642 ST histidine kinase OmpR COG0745 Response regulators w/ a CheY-like receiver domain and a winged-helix DNA-bd COG3850 Signal transduction (ST) histidine kinase, nitrate/nitrite-specific COG3851 ST histidine kinase, glucose-6-phosphate specific NtrC COG4585 ST histidine kinase COG2197 Response regulator w/ CheY-like receiver domain and an HTH DNA-bd COG3852 ST histidine kinase, nitrogen metabolism specific NarL COG0642 ST histidine kinase COG2204 Response regulator containing CheY-like receiver, AAA-type ATPase, and DNA-bd COG3290 ST histidine kinase regulating citrate/malate metabolism CitB COG4565 Response regulator of citrate/malate metabolism COG2972 Predicted ST protein with a C-terminal ATPase domain LytT/ COG3275 Putative regulator of cell autolysis AgrA COG3279 Response regulator of the LytR/AlgR family COG2205 Osmosensitive K+ channel histidine kinase COG3920 ST histidine kinase COG4191 ST histidine kinase regulating C4-dicarboxylate transport system COG4192 ST histidine kinase regulating phosphoglycerate transport system COG4251 Bacteriophytochrome (light-regulated ST histidine kinase) COG4564 ST histidine kinase COG5000 ST histidine kinase involved in nitrogen fixation and metabolism COG5002 ST histidine kinase COG0478 RIO-like serine/threonine protein kinase fused to N-terminal HTH domain COG0515 Serine/threonine protein kinase COG0317 Guanosine polyphosphate pyrophosphohydrolases/synthetases COG0394 Protein-tyrosine-phosphatase
other kinases, phosphatasea COG0467 RecA-superfamily ATPases implicated in ST COG0631 Serine/threonine protein phosphatase COG1762 Phosphotransferase system mannitol/fructose-specific IIA domain (Ntr-type) COG2062 Phosphohistidine phosphatase SixA COG2114 Adenylate cyclase, family 3 (some proteins contain HAMP domain) COG2365 Protein tyrosine/serine phosphatase COG2453 Predicted protein-tyrosine phosphatase COG1551 Carbon storage regulator (could also regulate swarming and quorum sensing) COG1639 Predicted ST protein COG1702 Phosphate starvation-inducible protein PhoH, predicted ATPase COG1956 GAF domain-containing protein COG1974 SOS-response transcriptional repressors (RecA-mediated autopeptidases) COG2172 Anti-sigma regulatory factor (Ser/Thr protein kinase) COG1716 FHA domain COG2198 HPt domain (Histidine containing phosphotransfer domain, in phosphorelay proteins) COG2199 GGDEF domain COG2200 EAL domain COG2203 GAF domain (cGMP, cAMP binding) COG2206 HD-GYP domain COG2770 HAMP domain COG2905 Predicted ST protein containing cAMP-binding and CBS domains COG3434 Predicted ST protein containing EAL and modified HD-GYP domains COG3437 Response regulator w/ CheY-like receiver domain and an HD-GYP domain COG3456 Uncharacterized conserved protein, contains FHA domain COG3480 Predicted secreted protein w/ PDZ domain COG3604 Transcriptional regulator containing GAF, AAA-type ATPase, and DNA bd COG3605 ST protein containing GAF and PtsI domains COG3629 DNA-binding transcriptional activator of the SARP family COG3706 Response regulator w/ CheY-like receiver domain and a GGDEF domain other regulators, domains COG3707 Response regulator with putative antiterminator output domain COG3830 ACT domain-containing protein COG3887 Predicted signaling protein w/ a modified GGDEF and a DHH domain COG3947 Response regulator containing CheY-like receiver and SARP domains COG4566 Response regulator COG4567 Response regulator w/ CheY-like receiver and Fis-type HTH domains COG4725 Transcriptional activator, adenine-specific DNA methyltransferase COG4753 Response regulator w/ CheY-like receiver and AraC-type DNA-bd COG4978 Transcriptional regulator, effector-bd/component COG1966 Carbon starvation protein, predicted membrane protein COG2202 PAS/PAC domain COG3292 Predicted periplasmic ligand-binding sensor domain COG3300 MHYT domain (predicted integral membrane sensor domain) COG3322 Predicted periplasmic ligand-binding sensor domain COG3447 Predicted integral membrane sensor domain COG3448 CBS-domain-containing membrane protein COG3452 Predicted periplasmic ligand-binding sensor domain COG3614 Predicted periplasmic ligand-binding sensor domain COG4219 Antirepressor for drug resistance, predicted ST N-terminal membrane component COG4250 Predicted sensor protein/domain COG4252 Predicted transmembrane sensor domain COG4936 Predicted sensor domain sensors, domains COG4943 Predicted ST protein containing sensor and EAL domains COG5001 Predicted ST protein w/ membrane domain, EAL and GGDEF domains COG5278 Predicted periplasmic ligand-binding sensor domain
Fig. S23. Abundance distribution of “Signal Transduction Mechanism COG” genes and functional domains among metagenomic datasets and representative single bacterial genomes. To account for the differences in size between the different datasets and genomes, the frequencies were normalized according to a Z-score method in IMG/M. The resulting normalized abundance frequencies were represented as gray scale intensities using Genesis software. Blue rectangles indicate COG categories having a high abundance within the termite gut metagenomic dataset, red rectangles indicate the highest abundance among the analyzed metabiomes and individual genomes. www.nature.com/nature 60