9 8 9 1 Caenarcaniphilales 9 8 Vampirovibrionales

7 9

9 2 Gastranaerophilales 9 7 Melainabacteria 95 9 9 Obscuribacterales

100 Oxyphotobacteria

Sericytochromatia

0.05

Fig. S1. Maximum likelihood tree based on near-full length 16S rRNA genes (>1,200 bp) from the phylum Cyanobacteria. The tree was constructed using program FastTree. A total of 1,096 nucleotide positions were used with the GTR+G substitution model and 100 bootstrap resamplings. Sequences from the and gut samples fell into two orders shown in red. Samples from mammalian gastrointestinal tract

7 1 HM630178 from intestinal tract of herbivorous marine fish Naso tonganus JQ084643 from mice gut tissue CU920275 from mesophilic anaerobic digester which treats municipal wastewater sludge

6 4 GU208308 from Dongping Lake sediment 8 8 JN656845 from hypolimnion (hypoxic bottom) water from permafrost thaw pond KWK12 OTU-11710-MgMjD2 termite Macrotermes gilvus gut JPZV01257543 from whole body of Blatella germanica EF520515 from acid-impacted lake KC432436 from wetland JQ624955 from poplar biomass OTU-05081-DCn2-PRRqX from termite Dicuspiditermes nemorosus and Parrhinotermes sp. gut OTU-08574-SCaX from termite Schedorhinotermes sp. 1 gut OTU-19232-Rm from termite Reticulitermes miyatakei gut OTU-06201-Ra-Ry from termite Reticulitermes amamianus and Reticulitermes yaeyamanus gut OTU-21316-HETt from termite Heterotemes tenuior gut 8 4 OTU-18865-TcM2 from termite Termes comis gut OTU-19838-Tpq from termite Termes propinquus gut OTU-17247-LONl from termite Longitermes longipes gut OTU-21447-PRHj from termite Prorhinotermes japonicus gut OTU-08760-CKsX-PRRqX from termite Ceratokalotermes sp. and Parrhinotermes sp. gut OTU-16999-Ra from termite Reticulitermes amamianus gut OTU-19228-Rm from termite Reticulitermes miyatakei gut OTU-20701-Sv from termite Stolotermes victoriensis gut OTU-14014-SCaX from termite Schedorhinotermes sp. 2 gut OTU-12817-SCs from termite Schedorhinotermes sarawakensis gut EF453917 from termite Nasutitermes sp. gut OTU-13070-SCaX from termite Schedorhinotermes sp. 1 gut OTU-03304-NtTw from termite Nasutitermes takasagoensis gut OTU-04278-NtTw from termite Nasutitermes takasagoensis gut OTU-12118-Gf2 from termite Glyptotermes fuscus gut EF453956 from termite Nasutitermes sp. gut OTU-10360-Nl-Nl2 from termite Nasutitermes longinasus gut OTU-07803-HOSp from termite Hospitalitermes sp. gut 8 8 OTU-13805-HOSb from termite Hospitalitermes sp. 2 gut OTU-03592-Tp from termite Termitogeton planus gut OTU-12199-NtTw from termite Nasutitermes takasagoensis gut OTU-08388-PRRm2 from termite Parrhinotermes microdentiformis gut OTU-09609-HETp from termite Heterotermes paradoxus gut OTU-12792-Zn3-RsTz2 from termite Zootermopsis nevadensis and Reticulitermes speratus gut HM318898 from skin of human Homo sapiens OTU-05909-Cc3 from termite Cryptotermes cavifrons gut OTU-20951-Ntr from termite Nasutitermes toriodiae gut OTU-13172-GBg-HMe from termite Globitermes globosus and Homallotermes eleanorae gut OTU-21496-PRCx from termite Procapritermes sp. gut 7 0 AB089123 from termite Reticulitermes speratus gut JQ072402 from brewery wastewater clarifier outfall wet well

9 6 JX095405 from descending colon ingesta of cow Bos taurus GQ449145 from feces of cow Bos taurus OTU-21389-ORi from termite Oriensubulitermes inanis gut

marine sponge 7 7 AB821786 from cattle rumen EU474510 from feces of bighorn sheep Ovis canadensis AB615061 from cattle rumen FJ680800 from MARC beef cattle fecal sample KT952876 from fish Zebrasoma xanthurum gut GQ064443 from skin of human Homo sapiens HM630179 from intestinal tract of herbivorous marine fish Naso tonganus OTU-04808-HOSm from termite Hospitalitermes medioflavus gut OTU-20000-Md2 from termite gut

8 6 OTU-05970-SCs-TGp from termite Schedorhinotermes sarawakensis and Termitogeton planus gut OTU-17104-TGp from termite Termitogeton planus gut OTU-07373-SGt-Tpq from cockroach Salganea taiwanensis and termite Termes propinquus gut

7 2 Tpq-Mel-01 (”Ca. Gastranaerophilus termiticola”) OTU-07911-HOSp from termite Hospitalitermes sp. 1 gut Detectable with OTU-14642-Pn from termite Pericapritermes nitobei gut probe MelTpq-646 9 1 OTU-19367-Tpq from termite Termes propinquus gut

8 8 AB612379 from cattle rumen EU871391 from rumen of cow Bos taurus

8 6 GQ448719 from fecal sample of cow Bos taurus 7 5 FJ684721 from MARC beef cattle fecal sample JQ084869 from NOD2 knockout mice gut tissue

9 9 OTU-00856-HOSb-HOSm from termite Hospitalitermes sp. 2 and Hospitalitermes medioflavus gut OTU-12430-Mm from termite Macrotermes malaccensis gut OTU-14997-Ra from termite Reticulitermes amamianus gut HM630217 from intestinal tract of herbivorous marine fish Naso tonganus

Samples from mammalian gastrointestinal tract OTU-06217-CKsX from termite Ceraokalotermes sp. gut OTU-10310-Gs from termite Glyptotermes satsumensis gut OTU-14961-PRRm2 from termite Parrhinotermes microdentiformis gut OTU-15827-Zn3 from termite Zootermposis nevadensis gut OTU-11542-Sv-PRRqX from termite Stolotermes victoriensis and Parrhinotermes sp. gut

OTU-12005-PRCx from termite Procapritermes sp. gut OTU-16207-Tc2 from termite Termes comis gut 8 4 OTU-20260-TcM from termite Termes comis gut AF544207 from rumen sample

9 2 AB615027 from cattle rumen 9 9 AB615027 from cattle rumen EF686586 from rumen fluid of Yunnan yellow cattle Bos taurus OTU-20360-Cp from cockroach punctulatus gut : AB824324 from rumen of swamp buffalo Bubalus bubalis : Mastotermitidae : OTU-02817-CKsX from termite Ceratokalotermes sp. gut : Stolotermitidae LC028872 from feces of Thai native cattle :

6 1 OTU-15874-Cp from cockroach Cryptocercus punctulatus gut : : Continued to OTU-11550-RsTz2 from termite Reticulitermes speratus gut Fig.S2-2 OTU-20080-Pa from cockroach Panesthia angustipennis gut Fig.S2-1 0.05 Continued 6 5 KC163104 from rumen of yak Bos grunniens from Fig.S2-1 9 6 GQ451200 from feces of Yunnan snub-nosed monkey Rhinopithecus bieti GU303703 from rumen contents of HEAN cow (Hereford x Angus) OTU-13788-DRr from termite Drepanotermes rubriceps gut OTU-02378-HOSp-HOSm from termite Hospitalitermes sp. 1 and Hospitalitermes medioflavus gut 6 9 7 3 7 6 OTU-09455-Ntr from termite Nasutitermes toriodiae gut OTU-16640-TcM from termite Termes comis gut OTU-18253-PHm from termite Prohamitermes mirabilis gut OTU-20218-SCmX from termite Schedorhinotermes medioobscurus gut 8 2 OTU-20228-SPEx from termite Speculitermes sp. gut OTU-23126-Tpq from termite Termes propinquus gut OTU-14675-Ra from termite Reticulitermes amamianus gut 7 4 OTU-23100-SCaX from termite Schedorhinotermes sp. 1 gut OTU-19474-HOSm from termite Hospitalitermes medioflavus gut GQ133151 from ASBR reactor treating swine waste KM250940 from biochemical reactor 20-30cm core

9 9 AB494943 from sheep rumen KR067986 from rumen of yak Bos grunniens

7 5 OTU-05986-Gf2 from termite Glyptotermes fuscus gut 7 8 OTU-11641-CKsX from termite Ceratokalotermes sp. gut OTU-17418-PRRqX from termite Parrhinotermes sp. gut OTU-04806-Gs-NinX from termite Glyptotermes satsumensis and Neotermes sp. gut 9 0 OTU-05309-SCaX from termite Schedorhinotermes sp. 1 gut OTU-14285-PHm from termite Prohamitermes mirabilis gut OTU-08630-HOSm from termite Hospitalitermes medioflavus gut OTU-16158-RsTz2 from termite Reticulitermes speratus gut KJ874130 from equine reproductive tract JN513216 from Guerrero Negro Hypersaline Mat 08

9 6 HQ153911 from white microbial film on pebble substrate in the aphotic zone of a shallow hydrothermal vent KF758589 from ocean water JN487386 from Guerrero Negro Hypersaline Mat 06 7 3 Guerrero Negro Hypersaline Mat AB806170 from ocean drilling core sample Japan Shimokita Penninsula offshore

Guerrero Negro Hypersaline Mat

JQ611100 from biofilm near yellow vent off Kueishan Island 7 2 FR828711 from Chattam municipal waste water treatment plant 9 5 FR853013 from active hydrothermal chimney in Dudley site of Juan de Fuca Ridge 9 8 JN435590 from Guerrero Negro Hypersaline Mat 01 JN448577 from Guerrero Negro Hypersaline Mat 02 9 8 Guerrero Negro Hypersaline Mat

9 8 Guerrero Negro Hypersaline Mat

KC358057 from large-discharge carbonate springs in Mojave Desert

KC358460 from roundwater from tectonically-formed cavern in Devils Hole water column JN514452 from Guerrero Negro Hypersaline Mat 08 JQ625024 from poplar biomass

Guerrero Negro Hypersaline Mat

Guerrero Negro Hypersaline Mat

8 6 JX221840 from subsurface aquifer sediment JX223309 from subsurface aquifer sediment JN626528 from methane seep under ice cover in Lake Qalluuraq Alaska 6 5 KM410581 from biofilm in subsurface sulfidic cave stream AB240501 from root-base of phragmites at Sosei River in Sapporo, Japan JN445974 from Guerrero Negro Hypersaline Mat 02

9 9 AB240326 from rhizosphere biofilm of lab-scale reed bed reactor AF289160 from water in Parker River, USA AJ853587 from landfill leachate 9 2 JX224053 from subsurface aquifer sediment : Cockroaches JQ624966 from poplar biomass : Mastotermitidae 9 8 KJ578047 from soil in Yong Ding river : Archotermopsidae HQ178778 from sediment in Central Park, USA : Stolotermitidae : Kalotermitidae Guerrero Negro Hypersaline Mat : Rhinotermitidae : Termitidae JQ861864 from diesel-contaminated ground water OTU-14988-PRCx from termite Procapritermes sp. gut OTU-11644-CKsX-SCs from termite Ceratokalotermes sp. and Schedorhinotermes sarawakensis gut 7 4 OTU-22558-MgMjD2 from termite Macrotermes gilvus gut

0.05 Fig. S2-2. Phylogenetic positions of 16S rRNA gene sequences affiliated with “Gastranaerophilales”, obtained from termite and cockroach samples. Taxa of the host are shown in indicated colors. A neighbor-joining tree was constructed using a total of 306 nucleotide positions with the Jukes-Cantor substitution model and 100 bootstrap resamplings. Only bootstrap confidence values ≥60% are shown. Sequences of “Obscuribacterales” were used as outgroup (see Fig. S3). 9 9 CU921797 from anaerobic sludge JF266314 from white microbial mat lava tube wall

7 7 AY328748 from drinking water distribution system simulator 9 6 AY328731 from drinking water distribution system simulator FJ946529 from arctic meltwater EU134277 from soil of undisturbed mixed grass prairie preserve JN615834 from yellow microbial mat from lava cave wall HM444941 from yellow microbial mat from lava cave wall

100 EU134270 from soil of undisturbed mixed grass prairie preserve EU134274 from soil of undisturbed mixed grass prairie preserve JQ769690 from biological soil crust of copper mine tailings wastelands OTU-09449-Nl2 from gut of termite Nasutitermes longinasus 81 OTU-19689-Pd from gut of termite Pericapritermes dolichocephalus 65 JF226899 from skin of Homo sapiens KC431968 from wetland HE650031 from membrane bioreactor wastewater treatment pilot plant CU926467 from mesophilic anaerobic digester of municipal wastewater sludge HE650043 from mesophilic anaerobic digester of municipal wastewater sludge EU134276 from soil of undisturbed mixed grass prairie preserve JQ624978 from poplar biomass AY957892 from drinking water biofilm 76 JF227064 from skin of Homo sapiens JN697943 from rice root endosphere 75 FJ375414 from microbial fuel cell, sheet of carbon cloth anode

100 JF922476 from drinking water pipeline FJ236043 from drinking water

AGTN01422275 from poplar biomass

100 HQ241806 from sponge Tsitsikamma favus AF280849 from bioreactors treating pharmaceutical wastewater FJ236035 from drinking water 100 HM445183 from white microbial mat lava tube wall 9 2 FJ236041 from drinking water KC432448 from wetland GU225979 from rape Brassica napus phyllosphere HM445329 from white microbial mat lava tube wall JN038282 from petroleum-contaminated soil AY775490 from sphagnum bog JF796789 from white microbial mat lava tube wall AY328704 from drinking water distribution system simulator EU134273 from soil of undisturbed mixed grass prairie preserve JN616036 from yellow microbial mat lava tube wall HM444984 from white microbial mat lava tube wall AY328596 from drinking water distribution system simulator EF516003 from grassland soil GQ487987 from soil polluted by heavy metals GU183588 from arsenic contaminated 85 m deep aquifer AY945890 from sludge-seeded bioreactor AY957889 from drinking water biofilm 70 8 4 JF500174 from terrestrial sediment Chesapeake bay impact crater KC431955 from wetland AY775491 from sphagnum bog

8 1 JQ650114 from drinking water JQ794637 from cystic fibrosis sinuses of Homo sapiens AB364841 from peat soil FJ536895 from waste-activated sludge from municipal waste water treatment plant AY328718 from drinking water distribution system simulator JN679197 from membrane bioreactor 100 KU726283 from Ann Arbor drinking water distribution system DQ376563 from aerobic sequencing batch reactor (SBR)

6 4 GU183589 from arsenic contaminated 85 m deep aquifer EU835402 from reverse osmosis membrane biofilm CU466697 from municipal wastewater treatment plant

9 8 AY375144 from deep sea sediment GQ359976 from gut of yellow catfish Pelteobagrus fulvidraco

AY328558 from drinking water distribution system simulator WWTP_8 from wastewater treatment plant : Cockroaches 100 WWTP_15 from wastewater treatment plant : Mastotermitidae : Archotermopsidae FJ375448 from microbial fuel cell, sheet of carbon cloth anode : Stolotermitidae Candidatus Obscuribacter phosphatis from wastewater treatment plant : Kalotermitidae AY328729 from drinking water distribution system simulator : Rhinotermitidae : Termitidae 0.05

Fig. S3. Phylogenetic positions of 16S rRNA gene sequences affiliated with “Obscuribacterales”, obtained from termite and cockroach samples. Sequences of “Gastranaerophilales” were used as outgroups (see Fig. S2). See the legend to Fig. S2 for explanation. a) Amino Acid Biosynthesis

tktAB rpe rpiB prsA F6P PRPP His trpF E4P Anthranilate Trp aroH trpG pheA, fbaA aroB aroD aroE aroK aroA aroC aroQ pheA2 Shikimate Chorismate Prephenate Phe

gapA sdaA tyrA2 Met Tyr

cysE cysK thrC thrB1 pgk Ser Cys Thr LL- glyA thrA Gly DAP- gpmI lysC asd dapA dapB AT dapF lysA Oxaloacetate Asp Aspartate beta- Lys semialdehyde pycB eno Asn

PEP Ala IDH3 proB proA proC pyk 2-Oxoglutarate Glu Pro ilvB, ilvC ilvH ilvD ilvE glnA gltD, gltB Pyruvate Val leuA Gln Ornithine Arg argF Carbamoyl-P leuCD argH leuCD leuB Citruline L-Arginosuccinate ilvE leuB ilvB, Leu ilvC ilvH ilvD ilvE Ile

MEL.A1 Ca. Gastroanaerophilus termiticola

b) Vitamins and Cofactors Biosynthesis

Fatty acid biosynthesis Ca. Gastroanaerophilus phascolarctosicola

Pimeloyl [acp] bioA bioD bioB bioF Biotin Pimeloyl CoA

folE folK folP folC GTP DHF Tetrahydrofolate

rsgA nadB nadA nadC nadD nadE nadK AIR Thiamin-P Thiamine L-Asp NAD+ NADP+ Gly DOXP metK thiH Met S-adenosylmethionine (SAM) L-Tyr iscS ThiS-COOH L-Cys

ribBA ribD ribH ribE ribF ribF GTP Riboflavin FMN FAD ribBA Ru5P

ilvB, ilvH ilvC ilvD panB panC coaX coaBC coaD coaE Pyruvate [R]-Pantothenate Coenzyme A (CoA) panD L-Asp L-Cys

pdxA pdxJ Phospho-4-hydroxy-L-threonine Pyridoxine-P Pyridoxal 5-P

Fig. S4. Pathways for amino acid and cofactor biosynthesis found from the Tpq-Mel-01 genome, shown in comparison with “Ca. Gastranaerophilus phascolarctosicola” and MEL.A1. Components found in one or more genomes are highlighted with colors indicated in the top right corner. Missing pathways or components are shown in gray. FliD (filament cap)

MEL.A1 Ca. Gastroanaerophilus termiticola

FliC (filament) FlgD Hook cap FlgL Ca. Gastroanaerophilus phascolarctosicola Hook-filament FlgE FliK Hook-length control junction (hook) FlgK FlgJ Rod cap Attractant / Repellant FlgG (distal rod) FlgH FlgI (L-ring) FlgF (P-ring) Proximal rod Outer Membrane Peptidoglycan layers MotB FlgB FlgC FliE MotA Cytoplasmic membrane MCP FliF (MS ring)

Deamidation CheV FliG CheD CheA CheY FliM CheW FliN CheR FlhA FliH FlhB FliI CheB CheC CheZ CheX FliO FliQ FliP FliR

Flagellar expression regulator DNA Cytoplasmic chaperone Cytoplasmic flagellin level regulator FlhC Early gene product FlgN FliJ FliS FliT FliW CsrA FlhD DNA FlgA FlgM FliA Late gene product

Fig. S5. Genes coding for flagellar components found from the Tpq-Mel-01 genome, shown in comparison with “Ca. Gastranaerophilus phascolarctosicola” and MEL.A1. See the legend to Fig. S4 for explanation. PilQ pore OM

PilN PilO PilD PilC IM

PilM PilA

ATP PilB PilT ADP + Pi Elongation Retraction

MEL.A1 Ca. Gastroanaerophilus termiticola

Ca. Gastroanaerophilus phascolarctosicola

Fig. S6. Genes coding for pilus components found from the Tpq-Mel-01 genome, shown in comparison with “Ca. Gastranaerophilus phascolarctosicola” and MEL.A1. See the legend to Fig. S4 for explanation. Table S1. List of and cockroaches used in this study.

Total Total number of Number of (Sub) family of OTU Species of host insects Origin Feeding-type number melainabacterial melainabacterial host insects code of reads reads OTUs Blatella germanica Bg Japan omnivorous 9,717 0 0 Blattellidae Symploce gigas SYg Japan omnivorous 726,304 0 0 americana PPam Japan omnivorous 17,668 0 0 Blattidae Periplaneta japonica PPja Japan omnivorous 38,006 0 0 Opisthoplatia orientalis OPo Japan omnivorous 15,254 0 0 Blaberidae Salganea taiwanensis SGt Japan wood feeder 14,639 14 1 Blaberidae Panesthia angustipennis Pa Japan wood feeder 9,340 11 1 Cryptocercidae Cryptocercus punctulatus Cp USA wood feeder 13,295 30 2 Mastotermitidae Mastotermes darwiniensis Md2 Australia wood feeder 23,141 11 1 Archotermopsidae Archotermopsis wroughtoni APK Thailand wood feeder 28,782 0 0 Archotermopsidae Hodotermopsis sjoestedti Hs3 Japan wood feeder 23,253 0 0 Archotermopsidae Hodotermopsis sp. HsK Japan wood feeder 24,306 0 0 Archotermopsidae Zootermopsis nevadensis Zn3 Japan wood feeder 31,667 42 2 Stolotermitidae Stolotermes victoriensis Sv Australia wood feeder 27,786 26 2 Kalotermitidae Ceratokalotermes sp. CKsX Australia wood feeder 27,227 312 5 Kalotermitidae Glyptotermes satsumensis Gs Japan wood feeder 24,501 62 2 Kalotermitidae Glyptotermes fuscus Gf2 Japan wood feeder 62,143 107 2 Kalotermitidae Neotermes sp. NinX Australia wood feeder 44,993 72 1 Kalotermitidae Neotermes koshunensis Nk Japan wood feeder 18,466 0 0 Kalotermitidae Neotermes koshunensis Nk2 Japan wood feeder 23,944 0 0 Kalotermitidae Neotermes koshunensis Nk3 Japan wood feeder 25,988 0 0 Kalotermitidae Cryptotermes cavifrons Cc3 USA wood feeder 36,621 76 1 Rhinotermitidae Parrhinotermes microdentiformis PRRm Malaysia wood feeder 37,584 0 0 Rhinotermitidae Parrhinotermes microdentiformis PRRm2 Malaysia wood feeder 44,523 75 2 Rhinotermitidae Parrhinotermes sp. PRRqX Australia wood feeder 42,692 121 4 Rhinotermitidae Schedorhinotermes medioobscurus SCm Thailand wood feeder 31,486 0 0 Rhinotermitidae Schedorhinotermes sp. 2 SCmX Malaysia wood feeder 36,273 11 1 Rhinotermitidae Schedorhinotermes sarawakensis SCs Malaysia wood feeder 23,946 98 3 Rhinotermitidae Schedorhinotermes sp. 1 SCaX Australia wood feeder 25,552 195 5 Rhinotermitidae Prorhinotermes japonicus PRHj Taiwan wood feeder 33,261 8 1 Rhinotermitidae Coptotermes formosanus Cf3 Japan wood feeder 34,332 0 0 Rhinotermitidae Coptotermes curvignathus COPc Malaysia wood feeder 28,349 0 0 Rhinotermitidae Heterotermes paradoxus HETp Australia wood feeder 48,162 44 1 Rhinotermitidae Heterotermes tenuior HETt Malaysia wood feeder 44,055 8 1 Rhinotermitidae Reticulitermes amamianus Ra Japan wood feeder 36,123 124 4 Rhinotermitidae Reticulitermes miyatakei Rm Japan wood feeder 36,529 26 2 Rhinotermitidae Reticulitermes sp. RPK RPK2 Thailand wood feeder 45,685 0 0 Rhinotermitidae Reticulitermes speratus RsTz2 Japan wood feeder 42,643 64 3 Rhinotermitidae Reticulitermes yaeyamanus Ry Taiwan wood feeder 26,746 14 1 Rhinotermitidae Termitogeton planus TGp Malaysia wood feeder 55,608 167 3 Termitidae Macrotermitinae Macrotermes gilvus MgMjD2 Thailand fungus grower 12,902 39 2 Macrotermitinae Macrotermes malaccensis Mm Malaysia fungus grower 31,586 31 1 Macrotermitinae Odontotermes formosanus Of Japan fungus grower 26,153 0 0 Apicotermitinae Speculitermes sp. SPEx Thailand soil-grass feeder 25,021 11 1 Amitermitinae Amitermes longignathus Alo Thailand soil feeder 29,953 0 0 Amitermitinae Amitermes laurensis Ala Australia grass feeder 15,484 0 0 Amitermitinae Drepanotermes rubriceps DRr Australia grass feeder 27,366 26 1 Termitinae Microcerotermes dubius MCd Malaysia wood feeder 17,537 0 0 Termitinae Microcerotermes sp. M1NP1 M1PT4b Thailand wood feeder 24,921 0 0 Termitinae Microcerotermes crassus McPP3 Thailand wood feeder 41,609 0 0 Termitinae Globitermes globosus GBg Malaysia wood feeder 27,963 20 1 Termitinae Prohamitermes mirabilis PHm Malaysia interface feeder 24,752 40 2 Termitinae Prohamitermes mirabilis PHm2 Malaysia interface feeder 3,258 0 0 Termitinae Termes comis Tc2 Thailand interface feeder 16,746 20 1 Termitinae Termes comis TcM Malaysia interface feeder 19,226 30 2 Termitinae Termes comis TcM2 Malaysia interface feeder 11,295 14 1 Termitinae Termes propinquus Tpq Thailand interface feeder 17,190 74 4 Termitinae Macrognathotermes errator MGe Australia interface feeder 21,704 0 0 Termitinae Homallotermes eleanorae HMe Malaysia interface feeder 19,816 8 1 Termitinae Pericapritermes nitobei Pn Japan soil feeder 28,119 24 1 Termitinae Pericapritermes dolichocephalus Pd Malaysia soil feeder 11,069 12 1 Termitinae Procapritermes sp. PRCx Malaysia soil feeder 24,929 64 3 Termitinae Procapritermes setiger PRCs Malaysia soil feeder 15,793 0 0 Termitinae Dicuspiditermes nemorosus DCn Malaysia soil feeder 16,236 0 0 Termitinae Dicuspiditermes nemorosus DCn2 Malaysia soil feeder 13,104 27 1 Nasutitermitinae Nasutitermes dimorphus Nd Thailand wood feeder 37,635 0 0 Nasutitermitinae Nasutitermes longinasus Nl Malaysia wood feeder 43,659 24 1 Nasutitermitinae Nasutitermes longinasus Nl2 Malaysia wood feeder 92,889 61 2 Nasutitermitinae Nasutitermes takasagoensis NtTw Taiwan wood feeder 81,643 276 3 Nasutitermitinae Nasutitermes takasagoensis Nt2 Japan wood feeder 26,265 0 0 Nasutitermitinae Nasutitermes toriodiae Ntr Australia grass feeder 34,551 54 2 Nasutitermitinae Hospitalitermes medioflavus HOSm Malaysia lichen feeder 35,027 665 5 Nasutitermitinae Hospitalitermes sp. 1 HOSp Thailand lichen feeder 23,144 150 3 Nasutitermitinae Hospitalitermes sp. 2 HOSb Malaysia lichen feeder 23,834 147 2 Nasutitermitinae Oriensubulitermes inanis ORi Malaysia soil feeder 26,105 8 1 Nasutitermitinae Leucopitermes leucopus LEUl Malaysia wood feeder 18,486 0 0 Nasutitermitinae Longipeditermes longipes LONl Malaysia grass-leaf feeder 50,378 17 1

Table S2. PCR primers and FISH probes used in this study.

Primer/Probe ID Sequence Reference COII-FW-A-tLeu 5ʹ-CAGATAAGTGCATTGGATTT-3ʹ 4 COII-RV-B-tLys 5ʹ-GTTTAAGAGACCAGTACTTG-3ʹ 4 27F-mix 5ʹ-AGRGTTTGATYMTGGCTCAG-3ʹ 2 1390R 5ʹ-ACGGGCGGTGTGTACAA-3ʹ 2 341F 5ʹ-AATGATACGGCGACCACCGAGATCTACAC-3ʹ 3 806R 5ʹ-AGTCAGTCAGCCGGACTACHVGGGTWTCTAAT-3ʹ 3 341F-read1 5ʹ-TATGGTAATTGGCCTACGGGAGGCAGCAG-3ʹ 3 806R-read2 5ʹ-AGTCAGTCAGCCGGACTACHVGGGTWTCTAAT-3ʹ 3 MelTpq-646 (Texas Red) 5ʹ-TACCACATTCTAGTTTAT-3ʹ present study EUB338 (6FAM Green) 5ʹ-GCTGCCTCCCGTAGGAGT-3ʹ 1

Table S3. List of bacteria used in the phylogenomic tree shown in Fig. 2 and their genomic distance (nucleotide sequence dissimilarity of aligned genome regions) to phylotype Tpq- Mel-01 (“Ca. Gastranaerophilales termiticola”) based on calculation using Genome-to- Genome Distance Calculator. Genome Class Strain Accession number distance Oxyphotobacteria Gloeobacter violaceus PCC 7421 0.18 GCF_000011385.1 Calothrix sp. PCC 7507 0.20 GCA_000316575.1 Leptolyngbya sp. PCC 7376 0.19 GCA_000316605.1 Synechococcus elongatus PCC 7942 0.23 GCA_000012525.1 Prochlorococcus sp. MIT 0801 0.23 GCA_000757865.1 Melainabacteria Vampirovibrio chlorellavorus 0.17 GCA_001858525 ACD20 0.11 GCA_000299275 Candidatus Melainabacteria bacterium MEL.A1 0.11 GCA_001765415 Candidatus Melainabacteria bacterium MEL.B2 0.10 *MEL.B2 Candidatus Melainabacteria bacterium MEL.C1 0.11 *MEL.C1 Candidatus Gastranaerophilales bacterium MH_37 0.12 GCA_001899425 Candidatus Gastranaerophilus phascolarctosicola 0.07 GCA_001899335 Candidatus Gastranaerophilales bacterium Zag_1 0.13 GCA_001899365 Candidatus Gastranaerophilales bacterium Zag_111 0.14 GCA_001899395 Candidatus Gastranaerophilales bacterium HUM_1 0.07 GCA_002103105 Candidatus Gastranaerophilales bacterium HUM_2 0.14 GCA_002103055 Candidatus Gastranaerophilales bacterium HUM_3 0.11 GCA_002102975 Candidatus Gastranaerophilales bacterium HUM_4 0.12 GCA_002102985 Candidatus Gastranaerophilales bacterium HUM_5 0.12 GCA_002103085 Candidatus Gastranaerophilales bacterium HUM_6 0.10 GCA_002102805 Candidatus Gastranaerophilales bacterium HUM_7 0.08 GCA_002102735 Candidatus Gastranaerophilales bacterium HUM_8 0.08 GCA_002102725 Candidatus Gastranaerophilales bacterium HUM_9 0.15 GCA_002103075 Candidatus Gastranaerophilales bacterium HUM_10 0.12 GCA_002102745 Candidatus Gastranaerophilales bacterium HUM_11 0.11 GCA_002102995 Candidatus Gastranaerophilales bacterium HUM_12 0.12 GCA_002102825 Candidatus Gastranaerophilales bacterium HUM_13 0.14 GCA_002102875 Candidatus Gastranaerophilales bacterium HUM_15 0.11 GCA_002102815 Candidatus Gastranaerophilales bacterium HUM_16 0.09 GCA_002102885 Candidatus Gastranaerophilales bacterium HUM_17 0.08 GCA_002102905 Candidatus Gastranaerophilales bacterium HUM_18 0.11 GCA_002102715 Candidatus Gastranaerophilales bacterium HUM_21 0.09 GCA_002103135 Candidatus Gastranaerophilales bacterium HUM_22 0.07 GCA_002103035 Candidatus Gastranaerophilales bacterium HUM_23 0.12 GCA_002102895 CAG_196 0.11 GCA_000433235 CAG_306 0.11 GCA_000431555 CAG_439 0.18 GCA_000438175 CAG_484 0.12 GCA_000431315 CAG_715 0.11 GCA_000431115 CAG_815 0.08 GCA_000437775 Candidatus Obscuribacter phosphatis 0.19 GCA_001899315 WWTP_8 0.17 **3300003765 WWTP_15 0.17 **3300003764 Candidatus Caenarcanum bioreactoricola 0.23 GCA_001899385 SSGW_16 0.22 **3300000574 Sericytochromatia CBMW_12 0.17 GCA_002083825 RAAC_196 0.09 GCA_002083785 LSPB_72 1.00 GCA_002083815 *) ggkBase accession names not deposited in Genbank. **) IMG accession numbers not deposited in Genbank.

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