Supplementary material for: Horizontal gene transfer as an indispensable driver for Neocallimastigomycota evolution into a distinct gut-dwelling fungal lineage

1 1 1 2 Chelsea L. Murphy ¶, Noha H. Youssef ¶, Radwa A. Hanafy , MB Couger , Jason E. Stajich3, Y. Wang3, Kristina Baker1, Sumit S. Dagar4, Gareth W. Griffith5, Ibrahim F. Farag1, TM Callaghan6, and Mostafa S. Elshahed1* Table S1. Validation of HGT-identification pipeline using previously published datasets. The frequency of HGT occurrence in the genomes of a filamentous ascomycete and a microsporidian were determined using our pipeline. The results were compared to previously published results. Organism NCBI Assembly Reference Method used Value Value accession number to original in the original reported obtained study study in this study Colletotrichum GCA_000149035.1 (1) Blast and tree 11 11 graminicola building approaches Encephalitozoon GCA_000277815.3 (2) Blast against 12-22 4 hellem custom database, AI score calculation, and tree building

Table S2. Results of transcriptomic sequencing. Accession number Genus Species Strain Number of Assembled Predicted peptides % genome Ref.

reads transcriptsa (Longest Orfs)b completenessc coveraged (%)

Anaeromyces contortus C3G 33,374,692 50,577 22,187 96.55 GGWR00000000 This study

Anaeromyces contortus C3J 54,320,879 57,658 26,052 97.24 GGWO00000000 This study

Anaeromyces contortus G3G 43,154,980 52,929 21,681 91.38 GGWP00000000 This study

Anaeromyces contortus Na 42,857,287 47,378 19,386 93.45 GGWN00000000 This study

Anaeromyces contortus O2 60,442,723 62,300 27,322 96.9 GGWQ00000000 This study Anaeromyces robustus S4 21,955,935 NA 17,127 92.41 88.7 SRX3329608 (3)

Caecomyces sp. Iso3 21,766,139 88,894 42,308 96.55 GGXE00000000 This study

Caecomyces sp. Brit4 15,199,296 59,747 24,950 92.76 GGWS00000000 This study

Feramyces austinii WSF2 23,024,082 110,716 37,114 91.03 GGWT00000000 This study

Feramyces austinii WSF3 25,911,634 155,190 42,823 91.38 GGWU00000000 This study

Neocallimastix californiae G1 36,250,970 NA 29,649 95.52 85.2 SRX2598479 (3)

Neocallimastix cf. cameroonii G3 54,184,578 98,268 35,649 96.21 GGXC00000000 This study

Neocallimastix cf. frontalis Hef5 22,033,159 95,833 47,305 96.21 GGXJ00000000 This study

Orpinomyces cf. joyonii D3A 27,863,051 36,927 17,648 91.38 GGWV00000000 This study

Orpinomyces cf. joyonii D3B 25,397,280 31,765 16,500 90.69 GGWW00000000 This study

Orpinomyces cf. joyonii D4C 25,949,247 31,155 16,756 93.45 GGWX00000000 This study

Pecoramyces ruminantium C1A 468,159,494 35,126 27,506 97.59 85.7 SRX1030108 (4)

Pecoramyces ruminantium S4B 46,78,2033 68,418 28,731 96.21 GGWY00000000 This study

Pecoramyces ruminantium FS3C 23,575,308 97,381 41,329 93.45 GGXF00000000 This study

GGWZ00000000 Pecoramyces ruminantium FX4B 25,011,052 66,074 27,589 92.07 This study

Pecoramyces ruminantium YC3 23,080,103 58,071 27,392 91.72 GGXA00000000 This study

Piromyces finnis finn 25,770,853 NA 17,008 95.17 91.4 SRX2770525 (3)

Piromyces sp. A1 39,201,276 50,514 22,628 85.52 GGXB00000000 This study

Piromyces sp. A2 50,945,955 55,306 30,581 94.83 GGXG00000000 This study

Piromyces sp. B4 104,293,067 140,717 70,061 93.1 GGXH00000000 This study

Piromyces sp. B5 110,842,283 187,158 49,460 82.76 GGXI00000000 This study Piromyces sp. E2 NA NA 17,080 81.72 70.9 (3)

a: Trinity (v 2.5.0) was used for the read assembly b: Predicted using Transdecoder using transcript orthologues (95%) clustered using CD-HIT-EST c: Calculated using BUSCO (V2) d: Percentage of genes in the strain’s genome for which a transcript was identified. Numbers were obtained from the individual genome webpages in IMG portal Tables S3-S5 are provided as separate Excel sheets.

Table S3. The identified 283 HGT events. HGT events were identified using a combination of non-fungal Blastp bit score cutoff (>100), HGT index cutoff (>30), and downstream phylogenetic analysis.

Table S4. HGT events identified with the affiliation of the donor, distribution across AGF genera studied, and specificity of gene acquisition to the Neocallimastigomycota phylum.

Table S5. Mapping HGT events to available fungal genomes (An. rob, Anaeromyces robustus; Ne. cal, Neocallimastix californiae; Pi. fin, Piromyces finnis; Pe. rum, Pecoramyces ruminantium), and general characteristics of HGT genes identified.

Supplementary Figures. Figure S1. Cartoon depicting the evolutionary history and the life cycle of the AGF in the herbivorous gut. Ancestors of the AGF have been introduced to ancient herbivores through a yet unknown mechanism, possibly ingestion. We hypothesize that the sequestration of AGF into the herbivorous gut was conducive to trait acquisition by HGT as a relatively faster strategy for niche adaptation. We further hypothesize that the donors were mostly bacterial residents of the herbivorous gut, since the life cycle of the AGF occurs entirely in the herbivorous gut, providing little opportunity for HGT acquisition from other environments. The lifecycle of AGF involves the migration of AGF zoospores towards ingested plant material (step 1), followed by the attachment and the encystment of the zoospore (Step 2). The cyst germinates (step 3), resulting in rhizoid development (Step 4) and sporangium maturation (step 5). Zoospores differentiate in the sporangia and are subsequently released to complete the life cycle (step 6).

6 Prokaryotic community 5

?* 1 4 Ancient herbivore

2

3

Unknown fungal ancestor

Figure S2. Multi-domain CAZymes. The modular nature of many CAZyme containing genes in AGF necessitates the utilization of a pfam-based rather than entire gene/transcriptome-based strategy for HGT detection. In AGF genomes, CAZyme domains of apparent different origins (fungal or non-fungal origins) are often encountered, leading to inaccurate HGT assessments when using the entire gene for similarity searches. Examples from a single (P. finnis) AGF genome are provided below. GenBank protein accession number are shown above each gene. Different domains are shown as boxes with different colors and the identity of the first hit are shown within the boxes. JGI protein ID are shown to the left.

ORX55236.1

Protein ID: GH10 GH11 581280 Fibrobacter Clostridium Blast similarity search yield GH11 domains, obscuring GH10 results

ORX49994.1

Protein ID: GH3 GH6 327415 Rhizopus (Fungal) Sorangium (DProt) Blast similarity search yield GH3 domains, obscuring GH6 results

ORX46831.1

Protein ID: GH9 GH43 98289 Actinobacteria Ruminococcus (Clostridiales) Blast similarity search yield GH43 domains, obscuring GH9 results

Figure S3. Maximum likelihood tree constructed using the D1–D2 domains of 28S rRNA gene. Isolates whose transcriptomes were sequenced in this study are shown in red, while publicly available transcriptomes included in the analysis are shown in blue. The tree was obtained using a maximum likelihood approach with Tajima-Nei model. Bootstrap values (from 100 replicates) are shown for nodes with more than 50% bootstrap support. Analysis was conducted in MEGA7 (5). Piromyces nnis LSU1 100 Piromyces nnis LSU2 Piromyces nnis LSU3 Piromyces nnis LSU4 97 Piromyces sp. A2 (MG992495) Piromyces sp. A1 (MG992496) 99 59 100 Piromyces sp. B4 (MG992497) Piromyces Piromyces sp. B5 (MG992498) Piromyces sp. Pr1 (JN939159.1) 77 Piromyces sp. 5 GRL-6 (JF974118.1) Piromyces sp. 1 BRL-3 (JF974096.1) 81 Piromyces sp. 6 GRL-7 (JF974119.1) 100 Piromyces sp. 3 BRL-5 (JF974098.1) Piromyces sp. 4 GRL-5 (JF974117.1) Piromyces sp. 10 GFM-3 (JF974127.1) 91 Cyllamyces aberensis isolate AFTOL-ID 846 (DQ273829.1) Cyllamyces Cyllamyces sp. BFK364 (KY386297.1) 76 Caecomyces sp. Iso3 (MG992499) Caecomyces sp. Brit4 (MG992500) Caecomyces sp. 2 GRL-12 (JF974124.1) Caecomyces Caecomyces communis enrichment culture clone OF1 (KM878679.1) 92 Caecomyces sp. CYR (JQ782555.1) 91 Caecomyces sp. CYF (JQ782554.1) Buwchfawromyces eastonii (KP205570.1) Buwchfawromyces 100 Oontomyces anksri strain SSD-CIB1 (JX017314.1) Oontomyces 86 Fungal sp. SSD-CIB2 (JX017315.1) 99 Anaeromyces contortus strain O2 (MF121931) Anaeromyces contortus strain Na (MF121943) 100 72 98 Anaeromyces contortus strain C3G (MF121936) Anaeromyces contortus strain G3G (MF121935) Anaeromyces contortus strain C3J (MF121942) 98 Anaeromyces cf. mucronatus LF1 (JN9391701) 89 Anaeromyces mucronatus strain 1B(KT274172.1) Anaeromyces 92 Anaeromyces cf. mucronatus BF1 (JN939169.1) Anaeromyces sp. 1A (KT274171.1) 62 Anaeromyces sp. SSD5 (HQ703470.1) Anaeromyces sp. SSD4 (HQ703469.1) 72 Anaeromyces sp. SSD1 (HQ703466.1) 64 Anaeromyces sp. SSD3 (HQ703468.1) Anaeromyces sp. SSD-BRL3 (JX017318.1) 90 Anaeromyces sp. SSD-BRL1 (JX017316.1) 100 Feramyces austinii strain F3a (MG584226) Feramyces Feramyces austinii strain F2c (MG605675) Neocallimastix cameroonii (KR920745.1) 69 Neocallimastix californiae LSU1 Neocallimastix cf. cameroonii strain G3 (MG992493) Neocallimastix californiae LSU2 94 Neocallimastix sp. 2 BRL-2 (JF974095.1) 72 72 Neocallimastix sp. 1 BRL-1 (JF974094.1) Neocallimastix Neocallimastix sp. NYF4 (JQ782545.1) 98 Neocallimastix sp. NYR3 (JQ782548.1) Neocallimastix cf. frontalis strain Hef5 (MG992494) Neocallimastix frontalis (KR920744.1) 53 Neocallimastix frontalis strain SR4 (JN939158.1) Pecoramyces ruminantium strain C1A (JN939127) 71 Pecoramyces ruminantium strain S4B (KX961618) 98 Pecoramyces ruminantium strain YC3 (MG992490) Pecoramyces Pecoramyces ruminantium strain FX4B (MG992491) 99 Pecoramyces ruminantium strain FS3C (MG992492) 85 Orpinomyces intercalaris isolate SKP2 (HQ703472.1) Orpinomyces intercalaris isolate SKP5 (HQ703475.1) 97 Orpinomyces cf. joyonii strain D3A (MG992487) Orpinomyces joyonii isolate SDP5 (HQ703480.1) 80 Orpinomyces joyonii isolate SDP6 (HQ703481.1) 99 Orpinomyces Orpinomyces joyonii isolate SDP2 (HQ703477.1) Orpinomyces sp. KF1 (JN939163.1) 72 Orpinomyces cf. joyonii strain D3B (MG992488) Orpinomyces cf. joyonii strain D4C (MG992489) Orpinomyces sp. KF5 (JN939166.1) Orpinomyces sp. OUS1 (AJ864475.1) 0.01

Figure S4. Mapping frequency of HGT events in various AGF clades and genera. The number of HGT events mapped on the nodes are in red. The majority of AGF events occurred prior to Genus level diversification, while few (51 events) appearing to be genus specific. Maximum likelihood tree constructed using the D1–D2 domains of 28S rRNA gene. Only isolates whose transcriptomes were analyzed in this study are shown. Bootstrap values (from 100 replicates) are shown for nodes with 50-70% bootstrap support as grey circles and for nodes with 70-100% bootstrap support as black circles. The size of the circle is proportional to the bootstrap value. Analysis was conducted in MEGA7 (5).

Piromyces finnis LSU1 Piromyces finnis LSU2 Piromyces finnis LSU3 Piromyces finnis LSU4 Piromyces sp. B5 LSU1 5 Piromyces sp. B4 Piromyces sp. B5 LSU2 1 Piromyces sp. A2 Piromyces sp. A1 4 Caecomyces sp. Iso3 0 Caecomyces sp. Brit4 Anaeromyces contortus strain C3J 6 Anaeromyces contortus strain G3G Anaeromyces contortus strain C3G Anaeromyces contortus strain O2 183 Anaeromyces contortus strain Na 7 Feramyces austinii strain F3a Feramyces austinii strain F2c Neocallimastix cf. cameroonii strain G3 3 11 Neocalimastix californiae LSU1 Neocalimastix californiae LSU2 Neocallimastix cf. frontalis strain Hef5 2 Orpinomyces cf. joyonii strain D3B 4 Orpinomyces cf. joyonii strain D4C Orpinomyces cf. joyonii strain D3A 2 Pecoramyces ruminantium strain C1A Pecoramyces ruminantium strain S4B 13 Pecoramyces ruminantium strain YC3 Pecoramyces ruminantium strain FX4B Pecoramyces ruminantium strain FS3C

Figures S5-S45Maximum likelihood trees showing the phylogenetic affiliation of 52 different horizontally transferred genes. The predicted function is shown in the upper left corner of each tree. AGF genes (shown in blue) are clearly nested within non-fungal clusters with strong bootstrap support reinforcing the inference of horizontal transfer. GenBank accession numbers are shown for reference sequences.

Fig S5. Aldose-1-epimerase

AWI66846.1 Piromyces sp. strain A2 OUM58917.1 Piromyces sp. E2 ORX53701.1 Piromyces finnis 99.9/100 ORY74170.1 Neocallimastix californiae

57.1/88 ORX63914.1 Anaeromyces robustus

ORY63789.1 Neocallimastix californiae Neocallimastigomycota WP_087154515.1 Lachnoclostridium sp. An196 WP_089981238.1 Lachnospiraceae bacterium NLAE-zl-G231

WP_069155075.1 Lachnospiraceae & Clostridiales WP_009254594.1 Clostridiales 100/100 WP_069158783.1 Eisenbergiella tayi 92.5/90 WP_021634803.1 Clostridiales 75.1/86 WP_025487693.1 Clostridiales bacterium VE202-27 SCI81250.1 uncultured Clostridium sp. 100 85.8/75 CCY21739.1 Firmicutes bacterium CAG 24 WP_090038195.1 Lachnospiraceae bacterium YSD2013

95.8/92 WP_103238732.1 Acetatifactor muris SCI29475.1 uncultured Clostridium sp. WP_031586045.1 Lachnospiraceae bacterium P6A3 100/100 SCH41624.1 uncultured Clostridium sp. WP_016282407.1 Lachnospiraceae bacterium A4 WP_026507088.1 Butyrivibrio sp. MC2013 WP_029233507.1 Butyrivibrio sp. VCB2006 99.4/100 89.5/70 99.7/100 WP_092250825.1 Butyrivibrio sp. INlla21 98.9/100 WP_074462841.1 Butyrivibrio hungatei WP_026513922.1 Butyrivibrio sp. LB2008 WP_026656493.1 Butyrivibrio 67.9/50 Firmicutes-Clostridiales 84.4/95 Ignavibacteriae 88.8/89 86.9/62 Acidobacteria

SPE53572.1 Verrucomicrobia bacterium

Verrucomicrobia Acidobacteria & Acidobacteria 64.3/53 95.6/90 Acidobacteria & Bacteroidetes 82.5/53 WP_012374209.1 Opitutus terrae WP_082161553.1 Rufibacter sp. DG31D WP_081867876.1 Hymenobacter sp. IS2118 OQX72098.1 Bacteroidetes bacterium 4484 249 97.5/67 WP_031553635.1 Parvularcula oceani 87.4/90 98.4/74 WP_011521128.1 Candidatus Koribacter versatilis 100/100 Verrucomicrobia 85/60 WP_060635325.1 Pyrinomonas methylaliphatogenes -/68 ODS52567.1 Acidobacteria bacterium SCN 69-37 76.5/54 Bacteroidetes OFY64353.1 Bacteroidetes bacterium RBG 13 42 15 100/100 OFY66359.1 Bacteroidetes bacterium RBG 13 43 22 OZJ03880.1 Bifiguratus adelaidae ORX52727.1 Hesseltinella vesiculosa

93.4/74 SAL96183.1 Absidia glauca 99.9/100 ORZ02524.1 Syncephalastrum racemosum Fungi CDH49380.1 Lichtheimia corymbifera JMRC FSU 9682 XP_018292236.1 Phycomyces blakesleeanus NRRL 1555 99.1/98 OBZ89595.1 Choanephora cucurbitarum CEP12957.1 Parasitella parasitica 99/100 EPB88059.1 Mucor circinelloides f. circinelloides 1006PhL 84.9/99 CEI95143.1 Rhizopus microsporus ORE07430.1 Rhizopus microsporus var. microsporus CDF30394.1 Methanoculleus sp. CAG 1088

0.3 Fig S6. Galactose-1-P uridyltransferase

GBF67802.1 Pseudoflavonifractor sp. 3BBH22

AWI66858.1 Piromyces sp. strain A1 Neocallimastigomycota OUM61859.1 Piromyces sp. E2 ORX55253.1 Piromyces finnis

ORY42098.1 Neocallimastix californiae & Clostridiales ORX75057.1 Anaeromyces robustus WP_090161937.1 Eubacterium pyruvativorans -/62 WP_090472006.1 Eubacterium pyruvativorans WP_026503816.1 Butyrivibrio sp. NC3005 WP_092995978.1 Sarcina sp. DSM 11001 WP_044973647.1 Ruminococcus sp. HUN007 WP_090017069.1 Lachnospiraceae bacterium XBB1006 WP_027868604.1 Eubacterium sp. AB3007 WP_092058397.1 Butyrivibrio sp. INlla14 WP_026658564.1 Butyrivibrio sp. AC2005 WP_027427026.1 Lachnospiraceae bacterium NC2004 WP_026491943.1 Butyrivibrio sp. XPD2002 WP_026665156.1 Butyrivibrio sp. FC2001 99.8/91 WP_026516552.1 Butyrivibrio sp. MC2021 EYF04553.1 Chondromyces apiculatus DSM 436 Delta 86.7/98 WP_081865111.1 Chondromyces apiculatus WP_103064577.1 Petrotoga sp. HWHPT.55.6.3 Proteobacteria

100/100 Candidate division Roizmanbacteria Actinobacteria Neocallimastigomycota 99.7/99 AWI66847.1 Neocallimastix cameroonii strain G3 ORY04890.1 Neocallimastix californiae WP_008678613.1 Clostridium sp. 7 2 43FAA

94.5/98 & Clostridiales WP_099346567.1 Clostridium tertium WP_057574262.1 Paeniclostridium sordellii WP_054631338.1 Paeniclostridium sordellii WP_055339562.1 Paeniclostridium sordellii WP_090014564.1 Clostridium sp. DSM 8431 71.7/90 WP_008428661.1 Clostridium sp. LS WP_077869696.1 Clostridium beijerinckii 100/100 WP_039311297.1 Clostridium baratii WP_099329493.1 Clostridium paraputrificum WP_049179441.1 Clostridium botulinum WP_055253427.1 Clostridium paraputrificum WP_005841371.1 Mitsuokella multacida WP_036374196.1 Mitsuokella jalaludinii

87.9/94 EHA18578.1 Aspergillus niger ATCC 1015 XP_001390941.1 Aspergillus niger CBS 513.88

Fungi GAQ45180.1 Aspergillus niger OJI91486.1 Aspergillus tubingensis CBS 134.48 100/100 PLB31849.1 Aspergillus ochraceoroseus IBT 24754 GAA88020.1 Aspergillus kawachii IFO 4308 98.4/99 OJJ73152.1 Aspergillus brasiliensis CBS 101740 ODQ72831.1 Lipomyces starkeyi NRRL Y-11557 WP_048162905.1 Methanosarcina sp. 1.H.A.2.2

2.0 Fig S7. Ribokinase

AWI66849.1 Piromyces sp. A1 ORX42543.1 Piromyces finnis OUM61510.1 Piromyces sp. E2 100/88 ORX77564.1 Anaeromyces robustus ORY54300.1 Neocallimastix californiae 86/74 WP_024345418.1 Clostridium methoxybenzovorans WP_024293895.1 Clostridium indolis

WP_038276986.1 Clostridium celerecrescens Neocallimastigomycota 94.4/96 WP_060930918.1 Lachnoanaerobaculum saburreum

WP_021625023.1 Atopobium sp. oral taxon 810 & Clostridiales 85.4/64 WP_101625199.1 Bifidobacterium imperatoris WP_065506916.1 Bifidobacterium breve WP_007053932.1 Bifidobacterium longum 97.3/91 WP_027441116.1 Lachnospiraceae bacterium AC2031 82.3/73 CCX66018.1 Firmicutes bacterium CAG 791 WP_087305378.1 Lachnoclostridium sp. An138

99.8/100 WP_106478221.1 Halomonadaceae bacterium R4HLG17 100/96 WP_076747974.1 Halomonas sp. 1513 WP_020409746.1 Hahella ganghwensis WP_025230980.1 Clostridium sp. ASBs410 WP_092240964.1 Desulfotomaculum guttoideum WP_100043439.1 Clostridium sphenoides 99.5/100 WP_100306356.1 Clostridium celerecrescens WP_009534770.1 Oribacterium parvum

93/100 WP_040648783.1 Oribacterium sinus EEJ50754.1 Oribacterium sinus F0268

100/100 OWB65251.1 Candida boidinii

92.8/95 OWB57413.1 Candida boidinii

XP_007375823.1 Spathaspora passalidarum NRRL Y-27907 Fungi 9 5/91 93/98 XP_001525645.1 Lodderomyces elongisporus NRRL YB-4239 AGO10885.1 Saccharomycetaceae sp. Ashbya aceri 94.9/99 90.8/90 XP_022463443.1 Kazachstania naganishii CBS 8797 ODV89933.1 Tortispora caseinolytica NRRL Y-17796 82.9/93 XP_002174339.1 Schizosaccharomyces japonicus yFS275 CCJ35835.1 Methanoculleus bourgensis MS2

1.0 Fig S8. Xylose isomerase

KGQ13041.1 Beauveria bassiana D1-5 99.9/95 AFI55138.1 Candida boidinii -/81 AFI55139.1 Candida boidinii Fungi ORY49883.1 Rhizoclosmatium globosum AWI66859.1 Piromyces sp. B4 OUM58912.1 Piromyces sp. E2 5YN3 Piromyces sp. E2 5NH4 Piromyces sp. E2 ACA65427.1 Orpinomyces sp. ukk1 ORY16061.1 Neocallimastix californiae ORY74173.1 Neocallimastix californiae ORY74169.1 Neocallimastix californiae Neocallimastigomycota ORX85088.1 Anaeromyces robustus ORX79850.1 Anaeromyces robustus & Bacteroidales ORY11475.1 Neocallimastix californiae ORY81692.1 Neocallimastix californiae ORX78688.1 Anaeromyces robustus ORX41541.1 Piromyces finnis AFG19713.1 Piromyces sp. X1 OKZ25769.1 Bacteroides sp. 43 108 PWL61794.1 Bacteroidales bacterium WP_079592857.1 Bacteroidales bacterium WCE2004 OKZ04380.1 Bacteroides sp. CAG 1060 57 27 WP_031535720.1 Bacteroides WP_090684177.1 Bacteroidales bacterium KHT7

100/92 SDG46793.1 Bacteroidales bacterium KHT7 WP_008626667.1 Paraprevotella xylaniphila WP_008618038.1 Paraprevotella clara Bacteroidales 81.3/94 Bacteroidales Bacteroidales AMM54982.1 Pyrococcus kukulkanii

1.0 Fig S9. Xylulokinase

AWI66848.1 Piromyces sp. A2 OUM70023.1 Piromyces sp. E2 ORX41540.1 Piromyces finnis ORX79851.1 Anaeromyces robustus

Neocallimastigomycota 100/100 ORY41461.1 Neocallimastix californiae -/72

WP_022933087.1 Treponema bryantii Spirochaetes & 66.1/78 WP_013701479.1 Treponema succinifaciens OJF76696.1 Treponema sp. CETP13 99.1/100 ERJ91673.1 Treponema lecithinolyticum ATCC 700332

99.8/100 WP_040847308.1 Treponema lecithinolyticum WP_016524615.1 Treponema maltophilum

-/59 WP_013970120.1 Treponema caldarium WP_015709830.1 Treponema azotonutricium 99/96 WP_013606586.1 Sphaerochaeta globosa OQY33023.1 Spirochaetaceae bacterium 4572 59 OQX29209.1 Spirochaeta sp. LUC14 002 19 P3 82.6/73 PKL27741.1 Spirochaetae bacterium HGW-Spirochaetae-2 PKL20179.1 Spirochaetae bacterium HGW-Spirochaetae-4 91.3/83 OHD32243.1 Spirochaetes bacterium GWC2 52 13 91.8/87 Gamma-Proteobacteria WP_073613400.1 Desulfopila aestuarii Proteobacteria

98.1/100 KGQ13890.1 Beauveria bassiana D1-5 KGQ13042.1 Beauveria bassiana D1-5 94/98 KGQ13015.1 Beauveria bassiana D1-5 XP_006683358.1 Batrachochytrium dendrobatidis JAM81

88.7/90 Fungi GAO48906.1 Saitoella complicata NRRL Y-17804 72.5/79 KGQ11453.1 Beauveria bassiana D1-5 67.9/80 CCA70103.1 Serendipita indica DSM 11827 KIM21242.1 Serendipita vermifera MAFF 305830 KZV91985.1 Exidia glandulosa HHB12029 KZV89436.1 Exidia glandulosa HHB12029 100/100 XP_006461815.1 Agaricus bisporus var. bisporus H97 PIA16727.1 Coemansia reversa NRRL 1564 PSC70198.1 Micractinium conductrix

2.0 Fig S10. Deoxyribose-phosphate aldolase

AWI66921.1 Piromyces sp. A1 OUM59792.1 Piromyces sp. E2 ORX43243.1 Piromyces finnis 100/100 ORX75778.1 Anaeromyces robustus Proteobacteria & Neocallimastigomycota 91.9/92 ORY73719.1 Neocallimastix californiae OKH89906.1 Thalassospira sp. TSL5-1 Alpha 90.6/76 WP_008891027.1 Thalassospira profundimaris WP_076911081.1 Burkholderia pseudomallei Beta WP_101214854.1 Alteromonadales bacterium alter-6D02 Gamma WP_021818809.1 Halomonas huangheensis 82.6/72 WP_007560353.1 Methylobacterium sp. GXF4 WP_091864015.1 Methylobacterium brachiatum WP_050734018.1 Methylobacterium sp. ARG-1 WP_009494565.1 Microvirga lotononidis

99.7/100OJY37351.1 Rhizobiales bacterium 65-9 Alpha-Proteobacteria 99.6/81 WP_100963857.1 Bosea sp. FBZP-16 WP_091835540.1 Bosea lupini WP_043540358.1 Salinarimonas rosea WP_062471589.1 Rhizobium sp. WP_092985764.1 Rhizobium sp. NFR03 99.8/75 WP_092931264.1 Rhizobium sp. 9140 WP_042616130.1 Agrobacterium tumefaciens WP_006309955.1 Agrobacterium sp. ATCC 31749 WP_027674559.1 Agrobacterium larrymoorei WP_057464250.1 Pseudovibrio sp. WP_093519164.1 Pseudovibrio ascidiaceicola 100/100 WP_028481809.1 Nesiotobacter exalbescens WP_055454903.1 Pannonibacter indicus WP_058898037.1 Pannonibacter phragmitetus ORZ24020.1 Absidia repens SAM07211.1 Absidia glauca

98/100 ORX58710.1 Hesseltinella vesiculosa Fungi 99.5/95 XP_018298543.1 Phycomyces blakesleeanus NRRL 1555 - ORY93526.1 Syncephalastrum racemosum ORE14562.1 Rhizopus microsporus 99.9/100 EIE88330.1 Rhizopus delemar RA 99-880 CEP08011.1 Parasitella parasitica WP_081245943.1 Thermoproteus sp. CP80

0.9 Fig S11. Phosphoenol pyruvate synthase

AWI66855.1 Piromyces sp. A1

Neocallimastigomycota OUM59869.1 Piromyces sp. E2

ORX83933.1 Anaeromyces robustus Clostridiales & 100/100 ORX38747.1 Piromyces finnis 97.2/90 ORY11767.1 Neocallimastix californiae WP_066499475.1 Clostridiales bacterium MCWD3 WP_084053084.1 Desulfonispora thiosulfatigenes 96.7/88 KUO76075.1 Clostridia bacterium BRH c25 WP_089282543.1 Anaerovirgula multivorans WP_069975589.1 Geosporobacter ferrireducens 90.5/95 WP_047827441.1 Peptococcaceae bacterium CEB3 OXS07683.1 Aspergillus thermomutatus XP_001276450.1 Aspergillus clavatus NRRL 1 KFA70140.1 Stachybotrys chlorohalonata IBT 40285 KIL90038.1 Fusarium avenaceum

XP_018257027.1 Fusarium oxysporum f. sp. lycopersici 4287 Fungi XP_018242803.1 Fusarium oxysporum f. sp. lycopersici 4287

100/100 KFH40499.1 Acremonium chrysogenum ATCC 11550 KFH40499.1 Acremonium chrysogenum ATCC 11550 OBT44183.1 Pseudogymnoascus sp. WSF 3629 99.5/97 XP_663447.1 Aspergillus nidulans FGSC A4 KFH70864.1 Mortierella verticillata NRRL 6337 100/100 OAQ30843.1 Mortierella elongata AG-77 KFI08671.1 Massilia sp. BSC265

100/100 WP_081897384.1 Massilia sp. BSC265 WP_005662899.1 Massilia timonae Proteobacteria 84.9/85 OUS30697.1 Thalassotalea sp. 42 200 T64

94.3/84 PKL94552.1 Gammaproteobacteria bacterium HGW 52.6/72 WP_103027918.1 Salinibacter altiplanensis Bacteroidetes KHO47084.1 archaeon GW2011_AR5

0.6 Fig S12. Bisphosphoglycerate-dependent phosphoglycerate mutase

WP_068282826.1 Labrys sp. WJW 65/97 AlphaProteobacteria WP_105863042.1 Labrys okinawensis AWI66844.1 Piromyces sp. A1

ORX59121.1 Piromyces finnis Bacteria & Neocallimastigomycota ORY84039.1 Neocallimastix californiae ORX81096.1 Anaeromyces robustus OLA82000.1 Azospirillum sp. 51 20 AlphaProteobacteria WP_020716379.1 Acidobacteriaceae bacterium KBS 89 Acidobacteria WP_019000599.1 Succinimonas amylolytica GammaProteobacteria WP_010454094.1 Succinivibrionaceae bacterium WG-1 WP_005982993.1 Desulfovibrio africanus DeltaProteobacteria 87.6/93 Proteobacteria Alpha-Proteobacteria 99.8/100 PSH02848.1 Acidobacteria bacterium 93.6/100 Acidobacteria 79.3/- Cyanobacteria WP_054536533.1 Herpetosiphon geysericola Chloroflexi WP_067063137.1 Mucilaginibacter sp. L294 91.6/96 90/95 Bacteroidetes Firmicutes 99.5/100 Beta-Proteobacteria 100/98 99.7/100 Alpha-Proteobacteria XP_018746058.1 Fusarium verticillioides 7600

99.6/85 XP_013261562.1 Exophiala aquamarina CBS 119918 Fungi PNS14749.1 Elsinoe sp. CQ-2017a KLJ11610.1 Emmonsia parva UAMH 139 98.7/100 OAT13345.1 Blastomyces gilchristii SLH14081 EGE83022.1 Blastomyces dermatitidis ATCC 18188 ALV62798.1 Thermococcus sp. 2319x1

2.0 Fig S13. Bisphosphoglycerate-independent phosphoglycerate mtase

94.3/99 -/57 Firmicutes-Bacillales 100/100 76.2/51 86.7/98 Spirochaetes

-/69 Firmicutes-Clostridiales 2526283883 K341DRAFT 02165 Selenomonas artemidis DSM 19719 93.2/77 Proteobacteria

100/100 2641489376 Ga0081967 121416 Sunxiuqinia dokdonensis SK 2650498444 Ga0104931 12027 Marinifilum sp. 59.16B AWI66845.1 Piromyces sp. A2 ORX41788.1 Piromyces finnis

100/100 OUM63531.1 Piromyces sp. E2 ORY22859.1 Neocallimastix californiae ORX73484.1 Anaeromyces robustus

WP_007479213.1 Bacteroides salyersiae Neocallimastigomycota CCY51613.1 Bacteroides sp. CAG 189

WP_022390271.1 Coprobacter fastidiosus & Bacteroidales 2700127048 Ga0131254 1404 gpmI Coprobacter fastidiosus DSM 26242 2702181011 Ga0109989 100614 gpmI Bacteroides acidifaciens 1a3B 95/99 WP_024995395.1 Bacteroides graminisolvens WP_091841151.1 Prevotella sp. ne3005 WP_073210378.1 Prevotella ruminicola 2626526665 Ga0066887 0970 gpmI Prevotella sp. TC2-24 WP_092067497.1 Prevotella sp. tf2-5 WP_068854970.1 Prevotella sp. KHD1 CCZ02244.1 Paraprevotella clara CAG 116 WP_008617081.1 Paraprevotella clara 100/100 2514716085 HMPREF9441 00275 gpmI Paraprevotella clara YIT 11840 WP_008628951.1 Paraprevotella xylaniphila WP_057099600.1 Bacteroides vulgatus WP_013546135.1 Bacteroides helcogenes WP_068961342.1 Bacteroidales

0 2596294713 LY07DRAFT 01024 Parabacteroides chartae DSM 24967 2552757421 BN352DRAFT 00271 Alistipes sp. AP11 96.3/10 2515342242 ATH1DRAFT 00303 Anaerophaga thermohalophila Fru22 DSM 12881

100/100 Bacteroidetes 100/100 Fungi ADE37339.1 Methanohalophilus mahii DSM 5219

0.3 Fig S14. Bifunctional aldehyde/alcohol dehydrogenase

WP 066019972.1 Clostridium spp. 100/100 WP 010890720.1 Clostridium spp.

WP 014456464.1 Spirochaeta africana

Chlorophyta

Cyanobacteria

Cyanobacteria

Cyanobacteria

WP 039728432.1 Lyngbya confervoides

WP 008311505.1 Leptolyngbya sp. PCC 6406

WP 071516972.1 Geitlerinema sp. PCC9228

WP 015149137.1 Oscillatoria acuminata WP 017715420.1 Oscillatoria sp. PCC10802 Cyanobacteria 89.7/95 WP 015194488.1 Stanieria cyanosphaera

WP 017663281.1 Geitlerinema sp. PCC7105

PPT05648.1 Geitlerinema sp. FC II

WP 009785271.1 Lyngbya sp. PCC8106

SKB12194.1 Planktothrix sp.

WP 079678282.1 Planktothrix sp. PCC11201

WP 043997018.1 Microcystis aeruginosa

CCI04868.1 Microcystis aeruginosa

AKV67822.1 Microcystis panniformis

95.2/97 AWI66879.1 Orpinomyces joyonii

ORY20802.1 Neocallimastix californiae

AFJ73503.1 Neocallimastix frontalis

ORY86520.1 Neocallimastix californiae

100/100 AFJ73506.1 Neocallimastix frontalis Neocallimastifomycota

53.5/89 AFJ73504.1 Neocallimastix frontalis

AAQ22352.1 Piromyces sp. E2

XP 021339594.1 Mizuhopecten yessoensis

ORX79899.1 Anaeromyces robustus

Firmicutes

Fungi 99.9/100 Fungi 100/100 PMB76271.1 Fervidicoccus fontis

2.0 Fig S15. D-lactate dehydrogenase

Piromyces sp. strain A1 Clostridiales & Neocallimastigomycota OUM60465.1 Piromyces sp. strain E2 100/100 ORX76250.1 Anaeromyces robustus ORY60457.1 Neocallimastix californiae 98.3/87 ORX45574.1 Piromyces finnis CDC38802.1 Clostridium sp. CAG 352 WP 087378590.1 Anaeromassilibacillus sp. An172 94.9/99 WP 092977897.1 Ruminococcus bromii CCX81070.1 Ruminococcus sp. CAG 108 OLA50352.1 Ruminococcus sp. CAG 108-related 41 35 88.8/91 SCJ38342.1 uncultured Ruminococcus sp. 6 7 WP 015522813.1 Ruminococcus bromii WP 092968986.1 Ruminococcaceae bacterium P7 100/100 CDE33483.1 Ruminococcus sp. CAG 403 SCJ43676.1 Ruminococcus sp. WP 038670156.1 Ruminococcus bicirculans SCI59572.1 uncultured Ruminococcus sp. 52.5/68 CDC67334.1 Ruminococcus sp. CAG 57 100/100 OLA47897.1 Ruminococcus bicirculans WP 028506063.1 Ruminococcus sp. FC2018 WP 013758524.1 Treponema brennaborense WP 069643618.1 Desulfuribacillus alkaliarsenatis OLA39788.1 Firmicutes bacterium CAG 110 56 8 89.7/76 CCX93309.1 Firmicutes bacterium CAG 110 WP 016224203.1 Lachnospiraceae bacterium 3-2 WP 013605872.1 Sphaerochaeta globosa Bacteroidetes WP 076700385.1 Seonamhaeicola sp. S2-3 WP 100609931.1 Confluentibacter lentus WP 100614343.1 Confluentibacter citreus PKQ45572.1 Confluentibacter sp. 3B 8 8.6/89 GAL61504.1 Algibacter lectus WP 066223304.1 Formosa haliotis

92/70 WP 092579495.1 Hyunsoonleella jejuensis Proteobacteria WP 042245453.1 Jejuia pallidilutea WP 025488857.1 Uncultured sp. KLE 1755 OYW76467.1 Verrucomicrobia bacterium 12-59-8 PLX72538.1 Desulfuromonas sp. WP 020589967.1 Desulfobacter curvatus 50.3/76 WP_103115704 Geothermobacter sp. HR-1 XP 018274523.1 Rhodotorula graminis WP1

77.7/96 XP 007379029.1 Punctularia strigosozonata Fungi KZP16841.1 Fibularhizoctonia sp. CBS 109695 100/100 XP 007265769.1 Fomitiporia mediterranea MF3 22 OCB86128.1 Sanghuangporus baumii EJT98721.1 Dacryopinax primogenitus CCJ37096.1 Methanoculleus bourgensis

0.3 Fig S16. Fe-only hydrogenase maturation enzyme HydE

WP 008711519.1 Synergistaceae sp. 100/100 Synergistetes WP 037976693.1 Synergistes jonesii OKY90128.1 Bifidobacterium sp. 56 9 plus CDA89266.1 Ruminococcus sp. CAG 563 8 3.7/95 CDA20517.1 Ruminococcus sp. CAG 488 CDC94585.1 Firmicutes bacterium CAG 227

97.5/99 Clostridiales & Neocallimastigomycota WP_070607429.1 Anaerococcus sp. HMSC065G05 WP 006863183.1 Marvinbryantia formatexigens MH043719 Piromyces sp A1 99.5/100 OUM62451.1 Piromyces sp. E2 ORX79956.1 Anaeromyces robustus

91.5/97 ORY24735.1 Neocallimastix californiae WP 028521661.1 Ruminococcus flavefaciens WP 031561014.1 Ruminococcus flavefaciens 97.1/99 WP 074742965.1 Ruminococcus flavefaciens WP 072947979.1 Ruminococcus flavefaciens CDF00892.1 Ruminococcus sp. CAG 624 WP 055248247.1 Coprococcus comes

78/92 WP 055260485.1 Coprococcus comes SCI11674.1 uncultured Blautia sp. 99/98 CCY96690.1 Ruminococcus sp. CAG 17 WP_006442855.1 Clostridium hylemonae WP_117598461 Dorea longicatena 79.8/- CCX75896.1 Dorea sp. CAG 105 WP 069194877.1 Clostridium sp. 100/100 WP 003513767.1 Ruminiclostridium thermocellum CRH84084.1 Chlamydia trachomatis WP 066831828.1 Collinsella ihuae 100/100 WP 087199581.1 Collinsella sp. An271 Actinobacteria 98.6/98 CDD67178.1 Eggerthella sp. CAG 368 ERK67071.1 Leptotrichia sp. oral taxon 215 str. W9775 100/100 WP 036099744.1 Leptotrichia sp. oral taxon 215 Fusobacteria WP 104434144.1 Bacteroides xylanolyticus WP 009104515.1 Treponema sp. JC4 100/100 WP 081773653.1 Treponema sp. C6A8 Bacteroidetes 100/100 WP 042372808.1 Bacteroides neonati Spirochetes WP 073350291.1 Bacteroides faecichinchillae CRZ35401.1 Herbinix hemicellulosilytica PIU21724.1 Diapherotrites archaeon CG08

1.0 Fig S17. Serine-O-acetyltransferase

Piromyces sp. strain A1

Piromyces sp. strain E2

ORX82827.1 Anaeromyces robustus 9 9.9/100 Neocallimastigomycota Delta Proteobacteria & ORY75836.1 Neocallimastix californiae

-/79 ORX55987.1 Piromyces finnis

PIU56422.1 Deltaproteobacteria bacterium CG07 land 8 20 14 0 80 38 7 93.3/97 PIR18360.1 Deltaproteobacteria bacterium CG11 big fil rev 8 21 14 0 20 49 13

OGQ49218.1 Deltaproteobacteria bacterium RIFCSPLOWO2 02 FULL 47 10

OQY68952.1 Polyangiaceae bacterium UTPRO1

WP 051129576.1 Hippea alviniae 85.7/71 99.6/98 WP 084675024.1 Hippea jasoniae

WP 013681047.1 Hippea maritima

WP 088533567.1 Geobacter sp. DSM 9736 -/61 KRT65014.1 Candidatus Dadabacteria bacterium CSP1-2

Delta Proteobacteria -/60 99.6/100 Dictyoglomus 87.9/93 OGX16565.1 Omnitrophica WOR 2 bacterium RBG 13 41 10

-/53 Firmicutes

XP 019232898.1 Nicotiana attenuata

0.9 Fig S18. O-acetylhomoserine/O-acetylserine sulfhydrylase Piromyces sp. strain A1

OUM70703.1 Piromyces sp. strain E2

ORX54686.1 Piromyces finnis

99.9/100 ORY54650.1 Neocallimastix californiae Neocallimastigomycota

ORX85231.1 Anaeromyces robustus -/63 Clostridiales & WP 015534752.1 Coprococcus eutactus

CDF45580.1 Roseburia sp. CAG 100

WP 026507687.1 Butyrivibrio sp. MC2013

WP 087171272.1 Gemmiger sp. An120 98.7/99 WP 087313000.1 Eubacterium sp. An11

WP 087276373.1 Eubacterium sp. An3

CDA91509.1 Ruminococcus sp. CAG 563

CDA19924.1 Ruminococcus sp. CAG 488 72.9/87 WP 087393486.1 Flavonifractor sp. An100

WP 093373607.1 Ruminococcaceae bacterium D5

SMC57712.1 Clostridiales bacterium 9 9.1/100 100 SNT94332.1 Clostridiales bacterium

93.8/98 WP 004632533.1 Gemella morbillorum 99.9/100 Bacteroidetes 100/100 99.8/100 Bacillales 91/97 100/100 Bacillales KXS10727.1 Gonapodya prolifera JEL478 100/100 KXS10730.1 Gonapodya prolifera JEL478

XP 018001918.1 Phialophora attae Ascomycota

XP 016223721.1 Exophiala mesophila 100 XP 016223722.1 Exophiala mesophila

100/100 Fungi EGE86523.1 Blastomyces dermatitidis ATCC 18188 100 XP 002623649.1 Blastomyces gilchristii SLH14081 Basidiomycota 99.1/100 PGH06025.1 Emmonsia parva

XP 003840463.1 Leptosphaeria maculans JN3

KIO31425.1 Tulasnella calospora MUT 4182

92.4/99 KIL59337.1 Amanita muscaria Koide BX008

XP 001887124.1 Laccaria bicolor S238N-H82

WP 091698829.1 Methanobrevibacter gottschalkii

0.3 Fig S19. Cysteine synthase

WP 072812247.1 Fibrobacter sp. UWR3 Fibrobacter WP 073188864.1 Fibrobacter sp. UWP2 WP 073115261.1 Fibrobacter sp. UWCM WP 097036834.1 Fibrobacter sp. UWT3

100/100 WP 088636991.1 Fibrobacter sp. UWR2 WP 088665546.1 Fibrobacter sp. UWH1

WP 088658658.1 Fibrobacter sp. UWH3 Bacteria & Neocallimastigomycota

-/74 WP 073282986.1 Fibrobacter sp. UWH6 Piromyces sp. strain A1 OUM64615.1 Piromyces sp. strain E2

100/100 ORX60143.1 Piromyces finnis ORX77105.1 Anaeromyces robustus ORY25599.1 Neocallimastix californiae -/68 ORY45412.1 Neocallimastix californiae WP 087189293.1 Flavonifractor sp. An52 WP 087329298.1 Flavonifractor sp. An4 WP 087398430.1 Flavonifractor sp. An9 WP 087387557.1 Flavonifractor sp. An112

100/98 WP 087269339.1 Flavonifractor sp. An91 Clostridiales 100/100 WP 065535539.1 Flavonifractor plautii WP 039996849.1 Flavonifractor plautii EHM52038.1 Flavonifractor plautii ATCC 29863 SEK27916.1 Ruminococcus flavefaciens 99.9/98 WP 074740211.1 Ruminococcus flavefaciens WP 037329187.1 Ruminococcus flavefaciens WP 003513769.1 Ruminiclostridium thermocellum 76/87 WP 003521330.1 Ruminiclostridium thermocellum WP 094550318.1 Clostridiales bacterium SK-Y3 99.9/99 OGO77758.1 Clostridiales bacterium GWB2 37 7 GBC35039.1 Rhizophagus irregularis DAOM 181602 Fungi 99/99 XP 016588383.1 Sporothrix schenckii 1099-18 CRG87478.1 Talaromyces islandicus EFP82148.2 Puccinia graminis f. sp. tritici CRL 75-36-700-3 CUA74456.1 Rhizoctonia solani XP 023907715.1 Quercus suber

0.3 Fig S20. Low-specifcity L-threonine aldolase

ATY58669.1 Cordyceps militaris

99/100 XP 008599202.1 Beauveria bassiana ARSEF 2860

XP 018701812.1 Isaria fumosorosea ARSEF 2679 100/97 XP 018757182.1 Fusarium verticillioides 7600

KPA38960.1 Fusarium langsethiae 97.6/96 Fungi XP 008098008.1 Colletotrichum graminicola M1.001

KIN03052.1 Oidiodendron maius

XP 022487641.1 Penicillium arizonense

KGO78373.1 Penicillium italicum

XP 014535981.1 Penicillium digitatum Pd1 74.8/- KUM66309.1 Penicillium freii

XP 013321892.1 Exophiala xenobiotica 93.6/92 OIW25256.1 Coniochaeta ligniaria NRRL 30616

WP 007285232.1 Intestinibacter bartlettii

CDA11518.1 Clostridium bartlettii CAG 1329 78/64 WP 053391833.1 Leptotrichia sp. oral taxon 212

WP 021766095.1 Leptotrichia sp. oral taxon 215 Neocallimastiogmycota

WP 026231297.1 Leptotrichia shahii 100 WP 015770257.1 Leptotrichia buccalis

SCJ59138.1 Uncultured Ruminococcus sp.

99.4/100 Bacteria & CDA62947.1 Firmicutes bacterium CAG 56

SCH82471.1 Uncultured Ruminococcus sp.

WP 075759251.1 Anaerostipes sp. 494a

WP 024626612.1 Bifidobacterium sp. A11

78.6/54 WP 029678621.1 Bifidobacterium sp. 7101

WP 046323154.1 Bifidobacterium asteroides

WP 015022154.1 Bifidobacterium asteroides

83.6/72 Piromyces sp. strain A1

OUM64550.1 Piromyces sp. strain E2

85/80 CDE29050.1 Catenibacterium sp. CAG 290 WP 055289551.1 Catenibacterium mitsuokai

CUO90310.1 Roseburia hominis

WP 006504962.1 Catenibacterium mitsuokai

KYK21360.1 Thermoplasmatales archaeon SG8-52-2

0.6 Fig S21. Aspartate-ammonia ligase Proteobacteria

CCX91581.1 Succinatimonas sp. CAG 777

99.6/100 WP 078929137.1 Succinivibrio dextrinosolvens WP 031579543.1 Ruminobacter sp. RM87 94/97 WP 019000506.1 Succinimonas amylolytica BBA15538.1 Petrimonas sp. IBARAKI Piromyces sp. strain A1 OUM61456.1 Piromyces sp. strain E2 Neocallimastigomycota ORX57792.1 Piromyces finnis 100/100 ORX65404.1 Anaeromyces robustus Bacteroidetes & ORY55791.1 Neocallimastix californiae 79.1/86 WP 064974459.1 Alistipes sp. Marseille-P2431 100 WP 019151169.1 Alistipes senegalensis WP 075588539.1 Tannerella forsythia OJV39032.1 Bacteroidales bacterium 36-12 WP 071134543.1 Millionella massiliensis WP 079682769.1 Parabacteroides chartae 99.9/82 WP 068185741.1 Macellibacteroides sp. HH-ZS WP 046147445.1 Parabacteroides goldsteinii

WP 048318175.1 Parabacteroides goldsteinii 94.5/99 WP 028728006.1 MULTISPECIES Parabacteroides

PCI97764.1 Flavobacteriales bacterium Spirochaetes OJF76918.1 Treponema sp. CETP13 87.6/63 WP 078930126.1 Treponema berlinense

98.6/82 WP 002698544.1 Treponema phagedenis WP 021687370.1 Treponema lecithinolyticum

OQS55141.1 Enterocytozoon hepatopenaei Microsporidia -/55 ORD93907.1 Enterospora canceri

-/63 XP 002652128.1 Enterocytozoon bieneusi H348 ELA47517.2 Vavraia culicis subsp. floridensis AHW68359.1 Nosema pernyi 97.3/85 XP 024331040.1 Nosema ceranae OIR57514.1 Amphiamblys sp. WSBS2006 AAG19311.1 Halobacterium salinarum NRC-1

1.0 Fig S22. NadA (Quinolinate synthase)

APD06958.1 Flavobacteriaceae bacterium UJ101 57/75 66/77 Proteobacteria

RJU84482.1 Marine Group II euryarchaeote 96/99 96/100 Alpha-Proteobacteria 100/100 Bacteria and Archaea -/68

PXY78178.1 Euryarchaeota archaeon 100/100 Bacillales/ Firmicutes 93/100

96/98 PTL87765.1 Candidatus Nitrosopelagicus brevis 61/98 APA97516.1 Nocardia seriolae 94/91

AEE15319.1 Thermodesulfobium narugense DSM 14796

86/66 APV44760.1 Dehalogenimonas formicexedens

PKK85174.1 Thermoplasmata archaeon HGW-Thermoplasmata-1 95/91 71/100 ACR72424.1 Eubacterium eligens ATCC 27750 86/91 99/92 Euryarchaeota Neocallimastigomycota

ORX45149.1 Piromyces finnis

97/99 AWI66860.1 Piromyces sp. A1

OUM70244.1 Piromyces sp. E2

ORY77540.1 Neocallimastix californiae 100/100 ORX87997.1 Anaeromyces robustus

97/- Myxococcales/ Delta-Proteobacteria 72/- 99/99 Viridiplantae 80/- Stramenopiles 98/100

0.9 Fig S23. Phosphomethyl pyrimidine kinase 98.3/100 Fungi 100/100 AWI66864.1 Piromyces sp. A1 75.6/35 CCX89079.1 Clostridium sp. CAG 590 WP 075819701.1 Ileibacterium valens 86.8/87 WP_090077999.1 Lachnospiraceae bacterium C7 Firmicutes WP_074719253.1 Lachnobacterium bovis WP_029067129.1 Lachnobacterium bovis & Neocallimastigomycota WP_022750516.1 Lachnobacterium bovis WP_027421563.1 Lachnobacterium bovi_ CDD64137.1 Firmicutes bacterium CAG 882 100/100 Actinobacteria CDA15382.1 Firmicutes bacterium CAG 212 85.8/99 CDE43681.1 Clostridium sp. CAG 411 93.9/93 Clostridiales 94.9/99 Clostridiales 97.1/100 Clostridiales 85.9/67 Clostridiales 74.8/84 Clostridiales WP 006860546.1 Marvinbryantia formatexigens

73.4/54 Clostridiales WP_008116653.1 Bacteroides pectinophilus 100/100 CDD56342.1 Bacteroides pectinophilus CAG 437 97.9/100 WP_092455068.1 Clostridium fimetarium WP_026504951.1 Butyrivibrio sp. NC3005 WP 069987089.1 Massilioclostridium coli 100/100 PWM98562.1 Massilioclostridium sp. 85.8/56 82/76 Clostridiales WP_093797544.1 Sporomusa acidovorans 98.9/95 Clostridiales 92.4/87 Selenomondales Clostridiales 100/100 Clostridiales 94.3/98 Clostridiales 100/100 PWL52169.1 Clostridiales bacterium Selenomonadales 96/100 Thermotogae KJS88115.1 Peptococcaceae bacterium BICA1-8 WP 101474678.1 Fusobacterium sp. 86.1/93 WP_106064609.1 Clostridium liquoris WP_035147832.1 Clostridium tetanomorphum 96.6/100 WP_006313012.1 Caldisalinibacter kiritimatiensis Clostridiales

84.9/77 OQY38599.1 Candidatus Atribacteria bacterium 4572 76 Bacteroidetes WP 066240729.1 Anaerosporomusa subterranea 97/92 WP 088370436.1 endosymbiont TC1 of Trimyema compressum 89.2/99 WP 084233860.1 Papillibacter cinnamivorans WP 101691003.1 Clostridium sp. SN20 91.5/91 WP 040195773.1 Candidatus Soleaferrea massiliensis WP_087219295.1 Blautia sp. An249 89.8/90 WP_101550960.1 Anaerotruncus sp. AT3 98.5/89 Clostridiales Clostridiales 91.5/95 Clostridiales WP_009004642.1Clostridiales 93.6/95 WP_025653667.1Clostridiales bacterium VE202-21 WP_050639035.1Eubacterium sp. SB2 WP_055152254.1 Faecalicatena contorta ADE35895.1 Methanohalophilus mahii DSM 5219

2.0 Fig S24. GMP reductase

AWI66916.1 Piromyces sp. strain A1

ORX41889.1 Piromyces finnis

ORX77908.1 Anaeromyces robustus 98/96 Neocallimastigomycota and Eukaryotes ORY34370.1 Neocallimastix californiae

XP 005836219.1 Guillardia theta CCMP2712 Cryptophyta

XP 019399164.1 Crocodylus porosus

XP 019378533.1 Gavialis gangeticus

NP 001018448.1 Danio rerio

XP 013861323.1 Austrofundulus limnaeus

XP 015235102.1 Cyprinodon variegatus

XP 024150473.1 Oryzias melastigma

XP 004402095.1 Odobenus rosmarus divergens

XP 015347626.1 Marmota marmota marmota 100/85 XP 003474472.1 Cavia porcellus Metazoa XP 004647540.1 Octodon degus

XP 011733000.1 Macaca nemestrina

XP 006760901.1 Myotis davidii

XP 001928049.1 Sus scrofa

XP 016316291.1 Sinocyclocheilus anshuiensis

XP 016425692.1 Sinocyclocheilus rhinocerous

KTG46330.1 Cyprinus carpio

KJK68395.1 Aspergillus parasiticus SU-1

XP 023424821.1 Fusarium fujikuroi IMI 58289

PKK51264.1 Trichoderma harzianum Ascomycota 70.2/84 ATY58955.1 Cordyceps militaris Fungi

PIL36419.1 Ganoderma sinense ZZ0214-1 Basidiomycota -/66 PIL36394.1Ganoderma sinense ZZ0214-1

100/100 GBC20880.1 Rhizophagus irregularis DAOM 181602 Glomeromycota PKC64916.1 Rhizophagus irregularis

WP 011752728.1 Thermofilum pendens

2.0 Fig S25. Nucleoside/nucleotide kinase family protein Gamma Proteobacteria WP 063603866.1 Vibrio barjaei 99.9/99 WP 006071817.1 Vibrio shilonii WP 096443656.1 Vibrio mediterranei 87.7/87 WP 077651650.1 Salinivibrio kushneri WP 096632304.1 Salinivibrio sp. YCSC6 99.4/99 WP 023602715.1 Aliivibrio logei

100/98 WP 005421825.1 Aliivibrio fischeri WP 047875253.1 Photobacterium aphoticum WP 079782232.1 Salmonella enterica AWI66871.1 Piromyces sp. strain A2 ORX73518.1 Anaeromyces robustus

86.7/62 Neocallimastigomycota OUM70585.1 Piromyces sp. strain E2 ORY73706.1 Neocallimastix californiae Clostridiales & WP 090298289.1 Pseudobutyrivibrio sp. ACV-2 WP 028246225.1 Pseudobutyrivibrio ruminis 97.2/71 SDH80127.1 Pseudobutyrivibrio sp. 49 SCY36062.1 Pseudobutyrivibrio sp. AR14 WP 099392233.1 Pseudobutyrivibrio ruminis WP 091870680.1 Butyrivibrio sp. INlla16 WP 092322928.1 Butyrivibrio sp. YAB3001 WP 013280120.1 Butyrivibrio proteoclasticus 100/100 WP 026662301.1 Butyrivibrio proteoclasticus WP 049988374.1 Lachnospiraceae bacterium MA2020 OON84974.1 Oribacterium sp. C9 GAA92831.1 Aspergillus kawachii IFO 4308

PLB25748.1Aspergillus ochraceoroseus IBT 24754 Fungi OJI86035.1 Aspergillus tubingensis CBS 134.48 XP 001399233.1 Aspergillus niger CBS 513.88 89.7/95 OJJ76626.1 Aspergillus brasiliensis CBS 101740 OOF99372.1 Aspergillus carbonarius ITEM 5010 XP 013697599.1 Brassica napus

2.0 Fig S26. Cytidylate kinase

EIE88350.1 Rhizopus delemar RA 99-880 GAN07890.1 Mucor ambiguus Mucoromycota 97.5/97 CDH57756.1 Lichtheimia corymbifera JMRC FSU 9682 Fungi ORZ20529.1 Absidia repens 73.4/61 KGQ11426.1 Beauveria bassiana D1-5 Ascomycota -/55 ORY39567.1 Rhizoclosmatium globosum Chytridiomycota XP 016609940.1 Spizellomyces punctatus DAOM BR117 57.8/70 KFH72766.1 Mortierella verticillata NRRL 6337 Glomeromycota GBC24121.1 Rhizophagus irregularis DAOM 181602 AWI66917.1 Piromyces sp. strain A2 ORX49644.1 Piromyces finnis ORY23648.1 Neocallimastix californiae 100/100 OUM61155.1 Piromyces sp. E2 SCJ57491.1 Uncultured Ruminococcus sp. 98.4/99 CDC02425.1 Eubacterium sp. CAG 202

92.9/95 CDA88278.1 Clostridium sp. CAG 230 WP 078116127.1 Clostridium beijerinckii WP 087366418.1 Cloacibacillus sp. An23 OUO93026.1 Cloacibacillus sp. An23 93.3/81 WP 058985231.1 Eggerthellaceae bacterium AT8 WP 012799193.1 Slackia heliotrinireducens

CDF12714.1 Eubacterium sp. CAG 581 Neocallimastigomycota 87.9/57 CDC21494.1 Eubacterium sp. CAG 274 WP 072530659.1 Bacteroides ilei Bacteria & WP 087409695.1 Barnesiella sp. An22 Bacteroidales 75.4/89 PWM55322.1 Ruminococcaceae bacterium CCZ91887.1 Clostridium sp. CAG 167 Clostridiales Spirochaetes WP 087155595.1 Lachnoclostridium sp. An196 92.8/91 WP 086035218.1 Ruminococcaceae bacterium CPB6 PWM08400.1 Clostridiales bacterium WP 082020957.1 Candidatus Soleaferrea massiliensis WP 027399348.1 Anaerovorax odorimutans Clostridiales Clostridiales

88.2/90 WP 087198540.1 MULTISPECIES Eggerthellaceae WP 002594489.1 Clostridium clostridioforme WP 022374195.1 Anaerostipes hadrus WP 009265921.1 Anaerostipes hadrus 87.1/58 CUN18414.1 Anaerostipes hadrus 73.4/91 WP 048514896.1 Megasphaera cerevisiae 100 WP 091364550.1 Allisonella histaminiformans CCY75663.1 Brachyspira sp. CAG 700 100/100 98.6/100 Proteobacteria Bacteroidales 50.7/91 Bacteroidales 100/100 OFX54675.1 Bacteroidetes bacterium GWC2 46 850 XP 013181829.1 Papilio xuthus

2.0 Fig S27. Thymidylate synthase Bacteria, Blastocystis & Neocallimastigomycota 94.6/94 Bacteroidetes

95.4/89 Verrucomicrobia

Clostridiales 90.8/98 Clostridiales

82.4/85 XP 014525842.1 Blastocystis sp. subtype 4

WP 086350076.1 Enterococcus sp. 9E7 DIV0242 90.2/89 WP 057887609.1 Lactobacillus mindensis 78.6/58 AWI66919.1 Pecoramyces ruminantium strain C1A

WP 006038592.1 Paenibacillus curdlanolyticus

98/57 WP 068671344.1 Paenibacillus sp. 1ZS3-15 WP 095265424.1 Paenibacillus campinasensis

WP 042226964.1 Paenibacillus chitinolyticus

WP 090715307.1 Paenibacillus typhae

WP 071877932.1 Enterococcus silesiacus

WP 047374190.1 Exiguobacterium sp. ZOR0005 99/100 WP 071399001.1 Exiguobacterium sp. SH31

WP 058704045.1 Exiguobacterium indicum

PIA94946.1 Cercospora beticola

PKS04595.1 Cercospora zeina

100/100 XP 013347156.1 Aureobasidium subglaciale EXF-2481

OTA55429.1 Hypoxylon sp. EC38 75.3/91 Fungi XP 018158249.1 Colletotrichum higginsianum IMI 349063

92/97 KID84550.1 Metarhizium guizhouense ARSEF 977 XP 009221542.1 Gaeumannomyces tritici R3-111a-1

XP 008714477.1 Cyphellophora europaea CBS 101466 81.5/92 ORY68388.1 Pseudomassariella vexata

99.6/100 XP 007830131.1 Pestalotiopsis fici W106-1

PKL67126.1 Methanobacteriales archaeon HGW-Methanobacteriales-1

0.8 Fig S28. Thymidine kinase

XP 013236554.1 Mitosporidium daphniae Microsporidia EOB15520.1 Nosema bombycis CQ1 88.7/84 KCZ75122.1 Anncaliia algerae PRA109

98.4/95 KCZ81677.1 Anncaliia algerae PRA339 XP 003886666.1 Encephalitozoon hellem ATCC 50504

83.9/76 99.9/100 XP 003072286.1 Encephalitozoon intestinalis ATCC 50506

CAA07261.1 Encephalitozoon cuniculi 90.4/94 80.7/62 Verrucomicrobia

Planctomycetes

OIQ48341.1 Gammaproteobacteria bacterium MedPE

WP 061794489.1 Serratia ficaria

AWI66920.1 Piromyces sp. strain A1

OUM69121.1 Piromyces sp. strain E2

ORX44144.1 Piromyces finnis 96.7/85 PLX30526.1 Alphaproteobacteria bacterium BM001 Neocallimastigomycota OJW48086.1 Alphaproteobacteria bacterium 41-28 Proteobacteria & WP 062139289.1 Caedimonas varicaedens

OGT44043.1 Gammaproteobacteria bacterium RIFCSPHIGHO2 12 FULL 37 34

OGT35176.1 Gammaproteobacteria bacterium RIFCSPHIGHO2 12 FULL 37 14 95.7/82 OGT61398.1 Gammaproteobacteria bacterium RIFCSPHIGHO2 12 FULL 43 28

Gamma-Proteobacteria

Alpha-Proteobacteria -/73 OGO94032.1 Coxiella sp. RIFCSPHIGHO2 12 FULL 44 14

WP 010598839.1 Diplorickettsia massiliensis

AOW57987.1 Legionella pneumophila subsp. pneumophila

WP 058476260.1 Legionella steigerwaltii

WP 031566797.1 Legionella wadsworthii

WP 058519543.1 Legionella tucsonensis

KUJ99837.1 Thermococcales archaeon 44 46

2.0 Fig S29. CDP-diacylglycerol--serine-O-phosphatidyl transferase

WP 062140546.1 Caedimonas varicaedens

AIL12270.1 Candidatus Paracaedimonas acanthamoebae

99/100 Alpha-Proteobacteria & Neocallimastigomycota OJX11701.1 Caedibacter sp. 37-49

AWI66906.1 Piromyces sp. A2 100/100 72.5/73 OJW51429.1 Alphaproteobacteria bacterium 41-28 99.9/100 EKE09894.1 uncultured bacterium

94/79 Alpha-Proteobacteria

97/100 71/- Sphingomonas 93/98 82/80 WP_020399176.1 Kordiimonas gwangyangensis 89/83 88/81 Alpha-Proteobacteria 86/76 93/82 OUX92616.1 Candidatus Endolissoclinum sp. TMED26

100/100 Alpha-Proteobacteria

61.7/72 PDH65378.1 SAR116 cluster bacterium MED-G04 98/79 84.4/76 100/100 Thioclava 98.7/99 96/100 Alpha-Proteobacteria 86.1/70

Alpha-Proteobacteria -/80

WP 051908526.1 Candidatus Paracaedibacter acanthamoebae

81.3/88 Fungi

PSR87769.1 Actinidia chinensis var. chinensis

2.0 Fig S30. Methylene-fatty-acyl-phospholipid synthase WP 099292233.1 Butyricimonas sp. Marseille-P3923 WP 040371451.1 MULTISPECIES Butyricimonas WP 034503244.1 Butyricimonas virosa 82.5/94 WP 087420621.1 Butyricimonas sp. An62 OKZ17866.1 Butyricimonas synergistica KIO43496.1 Sanguibacteroides justesenii WP 041504052.1 MULTISPECIES Porphyromonadaceae WP 009136459.1 Odoribacter laneus

CCZ80021.1 Odoribacter laneus CAG 561 Neocallimastigomycota 73.2/64 WP 009130711.1 Bacteroides oleiciplenus WP 073314440.1 Bacteroides stercorirosoris Bacteroidales & OKZ07253.1 Bacteroides oleiciplenus WP 025726054.1 MULTISPECIES Bacteroides WP 007482206.1 Bacteroides salyersiae WP 005933422.1 Bacteroides salyersiae CCY47609.1 Bacteroides sp. CAG 189 85.2/69 WP 025074521.1 Bacteroides faecichinchillae CDA22231.1 Bacteroides sp. CAG 144 WP 032945812.1 Bacteroides vulgatus

83.8/92 OKZ42881.1 Bacteroides vulgatus EEO62880.2 Bacteroides sp. 9 1 42FAA WP 007845841.1 Bacteroides dorei WP 005941007.1 Bacteroides massiliensis WP 081415378.1 Parabacteroides sp. SN4 EEC95760.1 Parabacteroides johnsonii DSM 18315 OKZ33002.1 Parabacteroides sp. merdae-related 45 40 WP 005647927.1 Parabacteroides merdae WP 005651222.1 Parabacteroides merdae EDN84565.1 Parabacteroides merdae ATCC 43184 99.9/100 WP 081693309.1 Parabacteroides gordonii AWI66899.1 Caecomyces sp. strain Iso3 100/100 Spirochaetes CCX57268.1 Bacteroides sp. CAG 1060 OKZ34939.1 Bacteroidales bacterium 43 8 87.3/99 WP 008862727.1 Barnesiella intestinihominis OAD04637.1 Mucor circinelloides f. lusitanicus CBS 277.49 GAN01815.1 Mucor ambiguus ORE08734.1 Rhizopus microsporus var. microsporus

90.5/93 ORZ03224.1 Syncephalastrum racemosum CDS09987.1 Lichtheimia ramosa Fungi 64/81 XP 018287303.1 Phycomyces blakesleeanus NRRL 1555 - -/84 OZJ03579.1 Bifiguratus adelaidae XP 006959108.1 Wallemia mellicola CBS 633.66 100/100 KDQ20756.1 Botryobasidium botryosum FD-172 SS1 ORX96727.1 Basidiobolus meristosporus CBS 931.73 100 ORX96666.1 Basidiobolus meristosporus CBS 931.73 -/69 PIA18158.1 Coemansia reversa NRRL 1564 ORX69936.1 Linderina pennispora OUV26396.1 Euryarchaeota archaeon TMED97

2.0 Fig S31. Glyoxalase I

KXS12765.1 Gonapodya prolifera JEL478 67.9/78 EGF76134.1 Batrachochytrium dendrobatidis JAM81

XP 002175809.1 Schizosaccharomyces japonicus yFS275 Fungi

XP 013022715.1 Schizosaccharomyces cryophilus OY26

ABB89044.1 Verticillium dahliae

AAP03992.1 Paracoccidioides brasiliensis

97.4/88 EER41380.1 Histoplasma capsulatum H143

XP 016602628.1 Penicillium expansum

KXG48217.1 Penicillium griseofulvum

ADG03436.1 Candida magnoliae

WP 097959663.1 Bacillus toyonensis Firmicutes

WP 097854997.1 Bacillus toyonensis

99.5/100 WP 001217525.1 MULTISPECIES Bacillus cereus group Bacteria & Neocallimastigomycota

WP 098954781.1 Bacillus toyonensis Bacteroidetes

WP_079688196 Ohtaekwangia koreensis -/64 WP 091544774.1 Thermoflexibacter ruber

WP 076671071.1 Vibrio lentus

WP 065104381.1 Vibrio tasmaniensis Proteobacteria

WP 017102273.1 MULTISPECIES Vibrio

WP 017108861.1 Vibrio tasmaniensis 99.9/96 WP 099167080.1 Vibrio splendidus

WP 034872303.1 Endozoicomonas montiporae

WP 013044419.1 Coraliomargarita akajimensis

AWI66929.1 Piromyces sp. strain A2 65.6/53 OUM56568.1 Piromyces sp. strain E2

ORX59193.1 Piromyces finnis

ORY24273.1 Neocallimastix californiae Fibrobacteres 79.6/76 WP 088658090.1 Fibrobacter sp. UWB1

WP 072980181.1 Fibrobacter sp. UWH4

WP 073323489.1 Fibrobacter sp. UWOV1 94.1/97 WP 088641573.1 Fibrobacter sp. UWB4

WP 072800657.1 Fibrobacter sp. UWT2

OLD12073.1 Crenarchaeota archaeon 13 1 40CM 3 52 10

2.0 AWI66851.1 Piromyces sp. Neocallimastigomycota & Blastocystis 100/100 ORY23520.1 Neocallimastix californiae Fig S32. Glyoxalase II ORX76839.1 Anaeromyces robustus OUM65043.1 Piromyces sp. E2 ORY36974.1 Neocallimastix californiae 87.2/99 ORX60215.1 Piromyces finnis XP_012896903.1 Blastocystis hominis XP_014527157.1 Blastocystis sp. subtype 4 89.4/94 OAO17957.1 Blastocystis sp. ATCC 50177 Nand II 86.6/99 OAO14550.1 Blastocystis sp. ATCC 50177 Nand II 100/100 76.9/66 XP_014530143.1 Blastocystis sp. subtype 4 XP_012894888.1 Blastocystis hominis 86.5/58 XP_014153786.1 Sphaeroforma arctica JP610 93.7/97 Alpha-Proteobacteria WP_031500411.1 Bryobacter aggregatus 76.8/55 WP_014394137.1 Corallococcus coralloides OFW53332.1 Actinobacteria bacterium RBG 16 70 17 KRT64006.1 Chloroflexi bacterium CSP1-4 92.8/100 Acidobacteria OLS19007.1 Candidatus Heimdallarchaeota archaeon LC 2 97.5/98 Acidobacteria GBC95524.1 bacterium HR16 OYT69889.1 Armatimonadetes bacterium CP1 7O WP_072260851.1 unclassified Armatimonadetes WP_072266524.1 Armatimonadetes bacterium DC 67.5/56 GBC91821.1 bacterium HR15 PYU13731.1 Acidobacteria bacterium OLD79801.1 Ignavibacteria bacterium 13 1 40CM 2 61 4 PYU32787.1 Acidobacteria bacterium OGQ06264.1 Deltaproteobacteria bacterium RIFCSPHIGHO2 01 FULL 43 49 OFV94073.1 Acidobacteria bacterium RIFCSPLOWO2 12 FULL 54 10 PYQ62858.1 Acidobacteria bacterium OLB95044.1 Actinobacteria bacterium 13 2 20CM 2 66 6 81.8/72 OLC19565.1 Chloroflexi bacterium 13 1 40CM 66 19 OLB90024.1 Actinobacteria bacterium 13 2 20CM 2 66 6 OLB99415.1 Actinobacteria bacterium 13 2 20CM 2 66 6 89.8/60 PYT06486.1 Acidobacteria bacterium 100/99 Acidobacteria

WP_111318031.1 Thermosporothrix hazakensis & ArchaeaBacteria 100/100 Acidobacteria PIW28877.1 Rhodospirillales bacterium CG15 BIG FIL POST REV 8 21 14 020 66 15 100/100 Verrucomicrobia 97.4/72 Delta-Proteobacteria 87.1/83 Euryarchaeota WP_088334687.1 Methanopyrus sp. KOL6 Q8TV58.1 Methanopyrus kandleri AV19 OYT63302.1 Candidatus Bathyarchaeota archaeon ex4484 205 100/100 Euryarchaeota 72.8/95 Crenarchaeota PNV77108.1 Candidatus Korarchaeota archaeon 100/100 Thermodesulfobacteria 95.3/100 Clostridiales EJY73435.1 Oxytricha trifallax 100/100 CDW90903.1 Stylonychia lemnae CDW88408.1 Stylonychia lemnae 93.4/- EJY86878.1 Oxytricha trifallax 99.2/100 Chloroflexi OLE29755.1 Actinobacteria bacterium 13 1 20CM 3 68 10 OLD97927.1 Actinobacteria bacterium 13 1 20CM 4 69 9 WP_114796675.1 Gaiella occulta 89.8/90 WP_115603206.1 Bradymonadaceae bacterium TMQ3 WP_111728677.1 Bradymonadales bacterium B210 PHX81893.1 Thermoleophilia bacterium 97.8/99 Acidobacteria 79/- OUU33180.1 Deltaproteobacteria bacterium TMED58 WP_075162420.1 Chthonomonas calidirosea WP_016481851.1 Chthonomonas calidirosea WP_012874712.1 Thermobaculum terrenum OUU24347.1 Planctomycetia bacterium TMED53 100/99 OUW44706.1 bacterium TMED181 PCJ14546.1 Planctomycetes bacterium 55.8/51 63.9/- WP_011564242.1 Rubrobacter xylanophilus WP_038681412.1 Rubrobacter radiotolerans GBD30836.1 bacterium HR32 PZN38436.1 Firmicutes bacterium WP_054493931.1 Ardenticatena maritima 90.2/90 WP_068139762.1 Limnochorda pilosa PZR63515.1 candidate division WPS-2 bacterium PZS08481.1 Chloroflexi bacterium GBC84230.1 bacterium HR11 XP_023917608.1 Quercus suber

0.7 Fig S33. Squalene-hopene cyclase Neocallimastigomycota

AWI66911.1 Piromyces sp. A2

OUM63777.1 Piromyces sp. E2 and Ciliophora ORX59851.1 Piromyces finnis ORY20771.1 Neocallimastix californiae 100/100 ORX80478.1 Anaeromyces robustus

92.1/100 ORY20687.1 Neocallimastix californiae KRX02665.1 Pseudocohnilembus persalinus -/83 XP 001026696.2 Tetrahymena thermophila SB210 XP 001456822.1 Paramecium tetraurelia strain d4-2 99.3/100 BAL50000.1 Stygiella incarcerata 81.1/99 BAL49999.1 Paratrimastix pyriformis 99.3/99 OFY99200.1 Bdellovibrionales bacterium GWB1 52 6 OQW54542.1 Proteobacteria bacterium SG bin7 Gamma-Proteobacteria 93.3/100 Delta-Proteobacteria Gamma-Proteobacteria 98.9/100 Alpha-Proteobacteria Bacteria Bacillales Actinobacteria 100/100 OGT81973.1 Gammaproteobacteria bacterium RIFCSPLOWO2 02 FULL 61 13 95/100 96.5/100 Delta-Proteobacteria XP 002174512.1 Schizosaccharomyces japonicus yFS275 WP 107561886.1 Candidatus Methylomirabilis sp. Zug 100/100 Planctomycetes WP 089937337.1 Candidatus Entotheonella palauensis 97.9/98 ETX06844.1 Candidatus Entotheonella gemina WP 012774567.1 Geobacter sp. M21 WP 012531788.1 Geobacter bemidjiensis Fungi 96/98 Fungi AKB35867.1 Methanosarcina siciliae C2J

2.0 AWI66893.1 Caecomyces sp. 77.3/92 Fig S34. Superoxide dismutase Fe/Mn type GAE78413.1 Cutibacterium acnes JCM 18918

GAE67569.1 Cutibacterium acnes JCM 18909

WP_100973958.1 Cutibacterium acnes

EFS81529.1 Cutibacterium acnes HL050PA1

WP_002517672.1 MULTISPECIES Propionibacteriaceae

WP_002543987.1 Cutibacterium acnes

KFC16292.1 Cutibacterium acnes HL201PA1

KPG64674.1 Cutibacterium acnes

WP_070652626.1 Propionibacterium sp. HMSC065F07

RFS98982.1 Cutibacterium acnes Neocallimastigomycota

84.8/97 WP_002514823.1 MULTISPECIES Propionibacteriaceae Actinobacteria &

WP_023033057.1 Propionibacterium sp. KPL1854

WP_032506043.1 Cutibacterium acnes 99.6/100 WP_002516078.1 MULTISPECIES Propionibacteriaceae

98.4/95 AAU04426.1 Rhizopus stolonifer 83.3/98 Propionibacteriaceae

66.2/92 82.5/97 Cutibacterium

WP_015071201.1 Acidipropionibacterium acidipropionici 94.8/94

WP_028700962.1 Acidipropionibacterium acidipropionici

96.2/97 WP_114044218.1 Acidipropionibacterium sp. JS278

WP_028702581.1 Acidipropionibacterium jensenii

WP_027587887.1 Acidipropionibacterium thoenii 91.6/83 52.4/36 Actinobacteria

WP_040157786.1 Nigerium massiliense

WP_114929169.1 Ornithinimicrobium sp. AMA3305

99.2/100 WP_022920977.1 Ornithinimicrobium pekingense 96.4/97

KZM27685.1 Ascochyta rabiei

90.3/98 Actinobacteria

78.6/97 Fungi

WP_101477254.1 Nitrosotalea sp. SbT1

0.5 Fig S35. Glutathione peroxidase

WP 093043159.1 Ruminococcaceae bacterium FB2012

97.7/100 WP 092967635.1 Ruminococcaceae bacterium P7

WP 002851555.1 Ruminococcus albus Neocallimastigomycota

WP 074829413.1 Ruminococcus albus

80/95 Clostridiales & WP 074962451.1 Ruminococcus albus

EXM38962.1 Ruminococcus albus SY3

WP 037288326.1 Ruminococcus albus 99.3/99 WP 013499741.1 Ruminococcus albus

AWI66900.1 Piromyces sp. strain A1

OUM60383.1 Piromyces sp. strain E2

69.6/87 ORX77814.1 Anaeromyces robustus

99.1/100 ORX46367.1 Piromyces finnis

81.7/90 ORY24622.1 Neocallimastix californiae 90.2/98 Spirochaetes 99.7/100 93.8/96 Bacteroidetes Fusobacteria 96.2/98 WP 024470165.1 Treponema pedis

WP 020964653.1 Treponema pedis

PHH83303.1 Ophiocordyceps australis

75/88 PHH63394.1 Ophiocordyceps australis

PHH85631.1 Cordyceps sp. RAO-2017

XP 001598652.1 Sclerotinia sclerotiorum 1980 UF-70 89.2/75 ESZ89701.1 Sclerotinia borealis F-4128 Fungi XP 007917656.1 Phaeoacremonium minimum UCRPA7

-/67 XP 003711364.1 Magnaporthe oryzae 70-15

KXH46191.1 Colletotrichum nymphaeae SA-01

83/85 XP 007591118.1 Colletotrichum fioriniae PJ7

KHO00340.1 Metarhizium album ARSEF 1941 85.8/93 KDB18850.1 Ustilaginoidea virens

XP 003661572.1 Thermothelomyces thermophila ATCC 42464

OUX49290.1 Euryarchaeota archaeon TMED279

0.4 Fig S36. Rubrerythrin

XP 014563517.1 Ordospora colligata OC4

KHN69475.1 Ordospora colligata OC4

KRH93215.1 Pseudoloma neurophilia Microsporidia 91/74 ELQ76215.1 Trachipleistophora hominis 97.4/55 KXN72257.1 Conidiobolus coronatus NRRL 28638

PHZ16653.1 Rhizopus microsporus ATCC 52813

77.4/52 KMV66034.1 Encephalitozoon cuniculi

CAD25498.1 Encephalitozoon cuniculi GB-M1

69.5/59 AFM98505.1 Encephalitozoon hellem ATCC 50504

XP 003887486.1 Encephalitozoon hellem ATCC 50504 -/51 XP 003073099.1 Encephalitozoon intestinalis ATCC 50506

WP 013739571.1 Sphaerochaeta coccoides

PKL12358.1 Spirochaetae bacterium HGW-Spirochaetae-8 Spirochaetes 83.3/95 WP 009164380.1 Pyramidobacter piscolens Synergistetes CDF22420.1 Prevotella sp. CAG 617

WP 027450343.1 Prevotella brevis Bacteroidetes

82.9/50 WP 006849366.1 Prevotella copri

AWI66881.1 Piromyces sp. strain A1 Neocallimastigomycota

ORX80610.1 Anaeromyces robustus

100 Clostridiales & ORY49678.1 Neocallimastix californiae 91.2/52 ORX54283.1 Piromyces finnis 95.3/55 WP 093369423.1 Ruminococcaceae bacterium D5

WP 004617814.1 Clostridium papyrosolvens

WP 014313755.1 Clostridium sp. BNL1100

WP 024834200.1 Clostridium josui 84.7/- WP 080066605.1 Clostridium hungatei

CDD68090.1 Eggerthella sp. CAG 368 WP 102378396.1 Raoultibacter timonensis Actinobacteria WP 087195977.1 Gordonibacter sp. An232A 9 2.1/91 DAA85259.1 TPA Candidatus Gastranaerophilales bacterium HUM 3 Melainabacteria 85.8/91 WP 023050766.1 Cetobacterium somerae Fusobacteria ADE03169.1 Haloferax volcanii DS2

0.8 Fig S37. Alkyl hydroperoxidase

AWI67041.1 Piromyces sp. strain A2 ORX49361.1 Piromyces finnis 97.5/100 OUM64903.1 Piromyces sp. strain E2 ORX68444.1 Anaeromyces robustus ORY05194.1 Neocallimastix californiae

CDE12196.1 Ruminococcus sp. CAG 330 Bacteria & Neocallimastigomycota SCI81011.1 Uncultured Ruminococcus sp. WP 074802076.1 Enterococcus mundtii Firmicutes WP 059348726.1 Aerococcus urinaeequi

83/95 KGJ33966.1 Enterococcus faecalis WP 080280423.1 Enterococcus faecalis OFR18417.1 Enterococcus sp. HMSC073E09 KII49995.1 Enterococcus faecalis WP 087306567.1 Lachnoclostridium sp. An138 WP 087165900.1 Lachnoclostridium sp. An131 Bacteroidetes CCY73532.1 Eubacterium sp. CAG 115

85.5/75 WP 005641731.1 Parabacteroides merdae EKN34985.1 Parabacteroides merdae CL09T00C40 WP 081446910.1 Bacteroides coprophilus 84/96 CDC58186.1 Bacteroides coprophilus CAG 333 WP 101452134.1 Bifidobacterium thermophilum Actinobacteria AGH41265.1 Bifidobacterium thermophilum RBL67 WP 026650504.1 Bifidobacterium thermophilum WP 033492584.1 Bifidobacterium thermophilum WP 026502950.1 Bifidobacterium boum WP 033505554.1 Bifidobacterium thermacidophilum 100/100 WP 094660945.1 Pseudoscardovia radai WP 101455096.1 Bifidobacterium thermophilum WP 087205053.1 Collinsella sp. An268 KFX44364.1 Talaromyces marneffei PM1 PCH07113.1 Penicillium occitanis KZL83275.1 Colletotrichum incanum OHW99640.1 Colletotrichum incanum 61.6/76

KZL77890.1 Colletotrichum tofieldiae Fungi 81.9/87 PKX96918.1 Aspergillus novofumigatus IBT 16806 OOF91502.1 Aspergillus carbonarius ITEM 5010 97.3/98 PMD46526.1 Meliniomyces variabilis 87.5/96 XP 007280127.1 Colletotrichum gloeosporioides Nara gc5 XP 016233038.1 Exophiala spinifera 82.1/89 9 8 XP 022514156.1 Fonsecaea monophora XP 003857437.1 Zymoseptoria tritici IPO323 ABW01315.1 Caldivirga maquilingensis IC-167

0.6 Fig S38. Phosphoglycolate phosphatase

EEQ31488.1 Microsporum canis CBS 113480 EGD94684.1 Trichophyton tonsurans CBS 112818 88.3/99 KNB19613.1 Fusarium oxysporum f. sp. lycopersici 4287 Fungi KMK55785.1 Aspergillus fumigatus Z5 -/89 GAT22605.1 Aspergillus luchuensis EHY58433.1Exophiala dermatitidis 100/100 ONH67268.1 Cyberlindnera fabianii XP 020546796.1 Pichia kudriavzevii AWI66882.1 Piromyces sp. strain A1 OUM62093.1 Piromyces sp. strain E2 ORX50326.1 Piromyces finnis 100/100 ORY41169.1 Neocallimastix californiae ORX85333.1 Anaeromyces robustus WP 024855983.1 Ruminococcus albus

WP 037286844.1 Ruminococcus albus Neocallimastigomycota WP 074963433.1 Ruminococcus albus

WP 074835262.1 Ruminococcus albus Clostridiales & WP 013497965.1 Ruminococcus albus WP 002849799.1 Ruminococcus albus

91.6/93 Firmicutes WP 041337309.1 Ruminococcus bicirculans SCJ53443.1 Uncultured Ruminococcus sp. SCI26219.1 Uncultured Ruminococcus sp. CDC67016.1 Ruminococcus sp. CAG 57 WP 072418482.1 Ruminococcus WP 093039679.1 Ruminococcaceae bacterium FB2012 WP 044976757.1 Ruminococcus sp. HUN007 CDA74570.1 Ruminococcus sp. CAG:579 84.9/80 WP 084194320.1 Ruminococcus callidus ERJ90142.1 Ruminococcus callidus ATCC 27760 WP 031561505.1 Ruminococcus flavefaciens WP 074740195.1 Ruminococcus flavefaciens WP 009987652.1 Ruminococcus flavefaciens WP 109727098.1 Ruminococcus flavefaciens CDF01014.1 Ruminococcus sp. CAG:624 91.2/78 Clostridiales WP 040196400.1 Candidatus Soleaferrea massiliensis 77.8/53 WP 034840515.1 Clostridium cellulosi PZM89746.1 Clostridium cellulosi 96/60 Erysipelotrichales Clostridiales 88.4/64 Clostridiales 92.3/63

WP 053984172.1 Niameybacter massiliensis Bacteroidetes 96.1/63 WP 059026370.1 Gabonibacter massiliensis WP 041504461.1 Sanguibacteroides justesenii -/56 -/55 Bacteroidetes 85.7/59 CDA76918.1 Bacteroides sp. CAG 530 WP 022383932.1 Bacteroides sp. Marseille-P3684 WP 006744109.1 Bacteroides coprosuis 98.1/88 WP 018108927.1 Bacteroides propionicifaciens WP 009131697.1 Bacteroides oleiciplenus WP 069572641.1 Methanobrevibacter sp.

2.0 Fig S39. Chloramphenicol acetyltransferase Gamma Proteobacteria WP 061064244.1 Providencia stuartii

-/55 WP 023593083.1 Zymomonas mobilis

KLE49552.1 Enterobacter aerogenes

77.2/54 KLF67370.1 Enterobacter aerogenes

WP 087857849.1 Klebsiella aerogenes 99.7/68 WP 087849279.1 Klebsiella quasipneumoniae

WP 094334037.1 Klebsiella quasipneumoniae

WP 042708353.1 Methanobrevibacter wolinii

AWI67026.1 Piromyces sp. strain A2 85.9/83

ORX52254.1 Piromyces finnis Neocallimastigomycota Methanobacterales &

ORX72527.1 Anaeromyces robustus 94.1/94 ORY61983.1 Neocallimastix californiae 54.5/68 WP 042704586.1 Methanobrevibacter arboriphilus

WP 012955224.1 Methanobrevibacter ruminantium

90.7/76 WP 019263977.1 Methanobrevibacter smithii

WP 094516465.1 Methanobrevibacter smithii 98.8/88 WP 004033915.1 Methanobrevibacter sp.

EEE41442.1 Methanobrevibacter smithii DSM 2375 85.3/87 WP 069574745.1 Methanobrevibacter sp. A27

99.8/100 WP 091699573.1 Methanobrevibacter gottschalkii

PRQ21109.1 Rosa chinensis

0.9 Fig S40. Aminoglycoside Phosphotransferase

XP 003852326.1 Zymoseptoria tritici IPO323 73.8/91 Fungi POR39377.1 Tolypocladium paradoxum 99/100 9 9.1/100 XP 018139758.2 Pochonia chlamydosporia 170

PCH05393.1 Penicillium occitanis

WP 073370396.1 Flavobacterium fluvii

AWI67072.1 Piromyces sp. strain A2 Bacteroidetes & Neocallimastigomycota ORY74174.1 Neocallimastix californiae

OUM63705.1 Piromyces sp. E2 9 9.8/97 ORX64887.1 Anaeromyces robustus

CCX62427.1 Bacteroides sp. CAG 598

95.6/93 WP 075318185.1 Bacteroides sp. Marseille-P3166

WP 022021599.1 Mediterranea massiliensis

CDB11482.1 Bacteroides sp. CAG 633

WP 044468620.1 Bacteroides uniformis

WP 042371718.1 Bacteroides neonati 100/86 WP 004308565.1 Bacteroides ovatus

WP 027324816.1 Bacteroides pyogenes

WP 013816394.1 Porphyromonas gingivalis

WP 077084550.1 Porphyromonas gingivalis

Clostridiales 99.2/76

OMO98542.1 Corchorus olitorius

3.0 Fig S41. DNA-3-methyl adenine glycosylase I

ORY40523.1 Rhizoclosmatium globosum 90.5/80

KGQ13028.1 Beauveria bassiana D1-5 Fungi & Gamma Proteobacteria OJV96253.1 Gammaproteobacteria bacterium 39-13 97.4/96 WP 057624663.1 Candidatus Berkiella cookevillensis

KRG18360.1 Candidatus Berkiella cookevillensis

WP 021267900.1 Bacteriovorax sp. BAL6 X 99.9/100 84.8/- WP 103218080.1 Halobacteriovorax sp. DA5

WP 083482815.1 Candidatus Berkiella aquae

KXS22408.1 Gonapodya prolifera JEL478 Spirochaetes

WP 069731545.1 Brachyspira hampsonii

WP 020003595.1 Brachyspira innocens

100/100 WP 013115074.1 Brachyspira murdochii

WP 028328647.1 Brachyspira alvinipulli

AWI66814.1 Piromyces sp. strain A1

OUM67291.1 Piromyces sp. E2 Neocallimastigomycota -/55 -/61 ORX43831.1 Piromyces finnis Actinobacteria & 91.6/98 ORY34144.1 Neocallimastix californiae

ORX63978.1 Anaeromyces robustus

WP 006292831.1 Scardovia inopinata 91.6/94 99.8/100 85.8/92 EFG26847.2 Scardovia inopinata F0304

WP 012799482.1 Slackia heliotrinireducens

92.8/97 WP 028263840.1 Atopobium fossor

97/94 99.9/100 ERL15305.1 Atopobium sp. BV3Ac4 WP 002563252.1 MULTISPECIES Atopobium

KRN55437.1 Atopobium minutum

WP 096368448.1 Lactococcus garvieae

WP 003135720.1 Lactococcus garvieae 99.9/100

WP 081168247.1 Lactococcus garvieae Firmicutes

KZK53376.1 Lactococcus lactis subsp. cremoris

80/76 WP 048704557.1 Lactobacillus ginsenosidimutans WP 036089560.1 Leuconostoc mesenteroides

60.8/82 WP 047340910.1 Enterococcus cecorum WP 047242186.1 Enterococcus cecorum 96.3/99 WP 016183564.1 Enterococcus columbae

XP 017253811.1 Daucus carota subsp. sativus

0.3 99.8/100 Bacteroidetes

Fig S42. Methylated DNA protein-cysteine methyl transferase 86.8/99 XP_006683143.1 Batrachochytrium dendrobatidis JAM81 99.6/100 77.6/97 Bacillales

94.5/92 WP_100361299.1 Bacillus sp. FJAT-45505

WP_005212715.1 Clostridium celatum

ORX78673.1 Anaeromyces robustus

ORX51113.1 Piromyces finnis

OUM63864.1 Piromyces sp. E2 99.5/100 ORY55016.1 Neocallimastix californiae

WP_009558064.1 Lactobacillus equicursoris Neocallimastigomycota

WP_008463145.1 Lactobacillus equicursoris 87.1/96 75.9/59 WP_019554584.1 Propionispira raffinosivorans Bacteria & WP_091834122.1 Propionispira arboris 96.7/100 Clostridiales

WP_103981826.1 Helcococcus massiliensis 98.9/100 Lactobacillales 99.1/100 Bacillales

WP_073996457.1 Arcanobacterium urinimassiliense 68.3/72 WP_071132125.1 Ileibacterium massiliense

PWM66490.1 Clostridiales Family XIII bacterium 100/100 Clostridiales 100/100 -/81 Lactobacillales

WP_092561300.1 Clostridium populeti

WP_024993483.1 Bacteroides paurosaccharolyticus 67.9/77 90.5/75 Clostridiales 87/86 100/99 Clostridiales 96.4/94 Clostridiales -/61 WP_006440636.1 Clostridium hiranonis 98/100 Fungi 57/- XP_003684789.1 Tetrapisispora phaffii CBS 4417 90.9/75 XP_003958714.1 Kazachstania africana CBS 2517 71.5/50 99.5/55 Fungi Fungi 96.3/52 Fungi

SCU89337.1 Lachancea dasiensis CBS 10888

SCU86955.1 Lachancea nothofagi CBS 11611

90.2/96 SCV02424.1 Lachancea meyersii CBS 8951

XP_022631247.1 Lachancea lanzarotensis

XP_022631190.1 Lachancea lanzarotensis 91/99 Fungi

WP_008161840.1 Natronorubrum sulfidifaciens

2.0 Fig S43. Galactoside-O-acetyl transferase

XP 016604442.1 Spizellomyces punctatus DAOM BR117 91.1/99 ELR06899.1 Pseudogymnoascus destructans 20631-21 Fungi 100/100 OBT68163.1 Pseudogymnoascus sp. 23342-1-I1 Neocallimastigomycota Methanobacterales & AWI67040.1 Feramyces austinii strain F2c ORX85535.1 Anaeromyces robustus ORX41865.1 Piromyces finnis 75.4/73 OUM70024.1 Piromyces sp. strain E2 WP 042692364.1 Methanobrevibacter oralis WP 058738854.1 Methanobrevibacter millerae 95.9/89 WP 067147293.1 Methanobrevibacter olleyae WP 012956556.1 Methanobrevibacter ruminantium WP 087380595.1 Flavonifractor sp. An135

-/78 WP 087259710.1 Flavonifractor sp. An92 Firmicutes 93.4/97 WP 101693198.1 Clostridium sp. SN20 WP 087370869.1 Butyricicoccus pullicaecorum WP 016146777.1 Butyricicoccus pullicaecorum 9 9.9/99 WP 029565832.1 Bacillus indicus WP 003443439.1 Clostridium pasteurianum 9 2.1/96 99.4/100 WP 070370764.1 Acetobacterium wieringae

WP 048595146.1 Brachyspira suanatina Spirochaetes 98.8/100 WP 014487594.1 Brachyspira intermedia WP 028331263.1 Brachyspira hyodysenteriae WP 047108858.1 Brachyspira hyodysenteriae WP 012670196.1 Brachyspira hyodysenteriae WP 047116178.1 Brachyspira hyodysenteriae WP 047108353.1 Brachyspira hyodysenteriae WP 047109888.1 Brachyspira hyodysenteriae WP 063285551.1 Lactobacillus collinoides Firmicutes KRM77947.1 Lactobacillus collinoides DSM 20515 95.7/97 98.7/99 WP 054762556.1 Lactobacillus collinoides 75.5/87 KRL79259.1 Lactobacillus paracollinoides DSM 15502 WP 054710993.1 Lactobacillus paracollinoides WP 054762648.1 Lactobacillus collinoides AWI67039.1 Feramyces austinii strain F2c ORX52201.1 Piromyces finnis 89.6/62 ORY70579.1 Neocallimastix californiae Neocallimastigomycota 97.6/100 ORX53783.1 Piromyces finnis WP 007562291.1 MULTISPECIES Bacteroides WP 087360677.1 Alistipes sp. An31A Bacteroidales & SCJ99022.1 uncultured Bacteroides sp. WP 046149281.1 Parabacteroides sp. HGS0025 91.4/95 WP 007485549.1 Bacteroides nordii EKU87702.1 Bacteroides oleiciplenus YIT 12058 WP 044138738.1 Bacteroides oleiciplenus 9 6.2/97 OKZ10407.1 Bacteroides oleiciplenus WP 025830573.1 Bacteroides stercorirosoris WP 044263630.1 Bacteroides timonensis 97.5/98 WP 007219538.1 Bacteroides cellulosilyticus WP 100263075.1 Bacteroides vulgatus WP 084274225.1 MULTISPECIES Bacteroidales 93.7/99 CCX48225.1 Bacteroides sp. CAG 927 PSC67235.1 Micractinium conductrix

0.4 Fig S44. Maltose acetyl transferase

XP 015468761.1 Debaryomyces fabryi 99/100 Fungi XP 460495.2 Debaryomyces hansenii CBS767 82.7/89 XP 002619058.1 Clavispora lusitaniae ATCC 42720 98.1/100 OVF08337.1 Clavispora lusitaniae

WP 007125695.1 Lactobacillus ultunensis

87.8/84 Neocallimastiogmycota SCJ55822.1 uncultured Ruminococcus sp. 85.9/87

WP 071866221.1 Enterococcus mundtii Firmicutes & 89.7/95 WP 010624152.1 Lactobacillus versmoldensis

AWI67038.1 Caecomyces sp. strain Iso3

WP 076339069.1 Paenibacillus sp. FSL H8-0548 99.1/99 WP 068606009.1 Paenibacillus swuensis

99.9/100 72.3/78 WP 040193747.1 Clostridium sp. CL-6

WP 013291584.1 Clostridium cellulovorans

WP 003841531.1 Bifidobacterium dentium Actinobacteria 68/74 WP 080822628.1 Bifidobacterium dentium

OQM55277.1 Bifidobacterium dentium 100/100 94.5/94 WP 003839751.1 MULTISPECIES Bifidobacterium

SEC88896.1 Bifidobacterium dentium JCM 1195

WP 054672414.1 Photobacterium sp. JCM 19050

KPL95103.1 Vibrio splendidus

97.2/98 Proteobacteria WP 086713304.1 Vibrio gigantis

WP 029225060.1 Vibrio splendidus 99.9/100 EDK26201.1 Vibrionales bacterium SWAT-3

WP 032498803.1 Vibrionales bacterium SWAT-3

WP 065675209.1 Vibrio celticus

WP 082082765.1 Vibrio sp. ECSMB14106

WP 053949277.1 Halolamina sediminis

0.3 Fig S45. Methionine-R-sulfoxide reductase

KFH63459.1 GAF Mortierella verticillata NRRL 6337 99.1/100 XP 021875985.1 Lobosporangium transversale OAQ28617.1 Mortierella elongata AG-77 83.7/84 CDS04513.1 Lichtheimia ramosa

ORE05512.1 Rhizopus microsporus var. microsporus Fungi ORE16763.1 Rhizopus microsporus 87.3/79 EIE87869.1 Rhizopus delemar RA 99-880 94.9/88 ORX51614.1 Hesseltinella vesiculosa 79/86 ORY96717.1 Syncephalastrum racemosum OAL44572.1 Pyrenochaeta sp. DS3sAY3a 88.3/93 ORY13191.1 Clohesyomyces aquaticus 93.9/81 XP 016213392.1 Verruconis gallopava 98.4/100 CEP20253.1 Cyberlindnera jadinii Proteobacteria WP 036357268.1 Microvirga sp. BSC39 99/100 WP 027315405.1 Microvirga flocculans

93.3/98 WP 047191487.1 Microvirga vignae WP 093460454.1 Pseudomonas sp. NFR16

92.7/100 WP 028764933.1 Shewanella colwelliana Actinobacteria WP 069669996.1 Shewanella colwelliana WP 062530637.1 Olsenella sp. DNF00959 9 1/94 CDD85537.1 Collinsella sp. CAG 289 WP 003150078.1 MULTISPECIES Atopobium WP 022772289.1 Butyrivibrio sp. AE2015 WP 074888019.1 Butyrivibrio proteoclasticus 90.6/92 WP 071177288.1 Butyrivibrio hungatei

WP 072911413.1 Pseudobutyrivibrio xylanivorans Neocallimastigomycota WP 090168840.1 Pseudobutyrivibrio sp. 49

WP 090527227.1 Pseudobutyrivibrio sp. UC1225 Clostridiales & 94/88 WP 099391856.1 Pseudobutyrivibrio ruminis WP 035768636.1 Butyrivibrio sp. NC2002 WP 026517512.1 Butyrivibrio sp. MC2021 AWI66787.1 Piromyces sp. strain A2 79.3/86 ORX77568.1 Anaeromyces robustus WP 044937593.1 Pseudobutyrivibrio sp. LB2011 73.9/- WP 028243451.1 Pseudobutyrivibrio ruminis WP 090550042.1 Pseudobutyrivibrio sp. OR37 98.4/96 CBK74954.1 GAF Butyrivibrio fibrisolvens 16 4 WP 033154412.1 Pseudobutyrivibrio ruminis WP 090482503.1 Pseudobutyrivibrio sp. JW11 WP 090395482.1 Pseudobutyrivibrio sp. C4 OUV40827.1 Euryarchaeota archaeon TMED103

0.6 Figure S46. Cartoon depicting the impact HGT had on the ability of AGF to degrade several plant polysaccharides including (A) cellulose, (B) glucoarabinoxylans/ glucuronoarabinoxylan,

(C) galactoglucomannan, (D) xyloglucan, (E) lichenesin ( -1,3 and -1,4), (F) laminarin ( -1,3 and -1,6), (G) starch ( -1,4 and -1,6), (H) chitin, (I) trehalose, (J) poly-N-acetyl- -D- galactosamine, (K) peptidoglycan, (L) rhamnogalactouronan, and (M) homogalactouronan. The major CAZymes identified in the transcriptomes studied are shown, with the highlight color indicating the extent of HGT in that CAZy family as follows; (1) 100% of transcripts identified belonging to families highlighted in red were horizontally transferred, (2) the majority (>50%) of transcripts identified belonging to families highlighted in orange were horizontally transferred, (3) a small fraction (< 50%) of transcripts identified belonging to families highlighted in light blue were horizontally transferred, and (4) 100% of transcripts identified belonging to families highlighted in dark blue were of fungal origin. GH GH GH GH GH GH A GH GH Cellulose 45 9 8 5 48 6 3 1

B Glucoarabinoxylans/Glucuronoarabinoxylan GH67 GH115 GH2, GH3 GH GH 1 10 1 30 43 39 CE1 GH GH GH CE2, CE3,CE4, CE6, CE7

C Galactoglucomanan GH GH 26 26

D Xyloglucan GH95 GH2, GH35 67 GH31 GH

E Lichenesin GH16, β-1,3 and GH17 β-1,4

F Starch α-1,4 and α-1,6 GH GH GH13, 57 13 GH57

G Laminarin GH64 β-1,3 and β-1,6 H Chitin I Trehalose CE4 N N GH 3 7

N GH GH GH N 19 18 2 0 , , GH J Poly-N-acetyl-α-D-galactosamine K GH Peptidoglycan GH 2 2 4 5 5 ,

N 7 N N N

N N N N GH GH GH P P P L

L Rhamnogalactour- L CE12 L 2 1 7 28 1 4 8 1 8

, onan

CE13

GH 8 CE1 8 GH53 GH43 GH43 GH2, GH35 P P L M Homogalacturonan L 3 9 , P L !GH"#$28 CE8 1

N D-xylose L-fucose Ferulic acid Glucosamine L-arabinose D-glucose D-glucuronate Acetyl D-galactose D-Galactouronate Muramate N L-rhamnose Methyl

References: 1. Jaramillo VDA, Sukno SA, Thon MR. 2015. Identification of horizontally transferred genes in the genus Colletotrichum reveals a steady tempo of bacterial to fungal gene transfer. BMC Genomics 16:2. 2. Alexander WG, Wisecaver JH, Rokas A, Httinger CT. 2016. Horizontally aquired gene in early-diverging pathogenic fungi enable the use of host nucleosides and nucleotides. Proc Nat Acad Sci USA 113:4116-4121. 3. Haitjema CH, Gilmore SP, Henske JK, Solomon KV, Groot Rd, Kuo A, Mondo SJ, Salamov AA, LaButti K, Zhao Z, Chiniquy J, Barry K, Brewer HM, Purvine SO, Wright AT, Hainaut M, Boxma B, Alen Tv, Hackstein JHP, Henrissat B, Baker SE, Grigoriev IV, O'Malley MA. 2017. A parts list for fungal cellulosomes revealed by comparative genomics. Nature Microbiol 2:17087. 4. Couger MB, Youssef NH, Struchtemeyer CG, Liggenstoffer AS, Elshahed MS. 2015. Transcriptomic analysis of lignocellulosic biomass degradation by the anaerobic fungal isolate Orpinomyces sp. strain C1A. Bitechnol Biofuels 8:208. 5. Kumar S, Stecher G, Tamura K. 2016. MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets. Mol Biol Evol 33:1870-4.