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Phylum % Family % Genus % Supplemental Table 1 Phylum % Family % Genus % Bacteroidaceae 28.40% Bacteroides 28.40% Prevotella 9 15.50% Bacteroidetes 63.20% Prevotellaceae 25.80% Unknown Prevotellaceae 8.10% Tannerellaceae 7.50% Parabacteroides 7.50% Megamonas 7.20% Veillonellaceae 9.40% Megasphaera 2.20% Firmicutes 16.70% Acidaminococcaceae 3.80% Phascolarctobacterium 3.80% Lachnospiraceae 1.90% Blautia 1.00% Succinivibrionaceae 9.70% Anaerobiospirillum 9.60% Proteobacteria 13.80% Burkholderiaceae 1.90% Sutterella 1.90% Enterobacteriaceae 1.80% Escherichia-Shigella 1.70% Fusobacteria 4.00% Fusobacteriaceae 4.00% Fusobacterium 4.00% Actinobacteria 1.40% Bifidobacteriaceae 1.00% Bifidobacterium 1.00% Epsilonbacteraeota 0.70% Verrucomicrobia 0.10% Spirochaetes 0.00% Cyanobacteria 0.00% Deferribacteres 0.00% Supplemental Table 2. ANCOM analysis by source in healthy marmosets Phylum Class Order Family Genus W MITNE MITCL MITB MITA MIT Abundance Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella 9 136 10.64% 33.40% 9.44% 25.17% 15.40% Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Alloprevotella 136 0.00% 2.51% 0.00% 0.00% 0.38% Fusobacteria Fusobacteriia Fusobacteriales Fusobacteriaceae Fusobacterium 136 5.01% 3.96% 1.63% 8.24% 4.13% Proteobacteria Gammaproteobacteria Aeromonadales Succinivibrionaceae Anaerobiospirillum 136 13.77% 1.47% 8.50% 10.17% 9.77% Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Escherichia-Shigella 136 0.13% 3.16% 0.61% 4.92% 1.30% Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia 133 0.80% 0.65% 1.68% 0.43% 1.02% Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Unknown 131 4.78% 6.37% 13.83% 5.84% 8.07% Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium 130 0.53% 0.96% 1.42% 1.19% 0.96% Bacteroidetes Bacteroidia Bacteroidales Tannerellaceae Parabacteroides 126 6.06% 4.71% 9.61% 8.62% 7.30% Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides 126 37.37% 17.44% 29.94% 14.39% 29.27% Firmicutes Negativicutes Selenomonadales Acidaminococcaceae Phascolarctobacterium 125 4.27% 2.76% 3.85% 2.78% 3.73% Firmicutes Negativicutes Selenomonadales Veillonellaceae Megamonas 125 6.21% 9.37% 8.22% 5.62% 7.28% Firmicutes Negativicutes Selenomonadales Veillonellaceae Megasphaera 116 1.04% 2.69% 2.96% 3.96% 2.25% Bacteroidetes Bacteroidia Bacteroidales Barnesiellaceae Coprobacter 136 0.27% 0.00% 0.08% 0.00% 0.14% Bacteroidetes Bacteroidia Bacteroidales Muribaculaceae __ 136 0.15% 0.42% 0.13% 0.05% 0.17% Bacteroidetes Bacteroidia Bacteroidales Muribaculaceae uncultured bacterium 136 0.38% 0.08% 0.82% 0.36% 0.48% Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae Alistipes 136 0.18% 0.08% 0.08% 0.02% 0.11% Firmicutes Clostridia Clostridiales Lachnospiraceae __ 136 0.06% 0.01% 0.11% 0.05% 0.07% Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnoclostridium 136 0.08% 0.00% 0.22% 0.18% 0.13% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminiclostridium 5 136 0.04% 0.02% 0.01% 0.00% 0.02% Firmicutes Erysipelotrichia Erysipelotrichales Erysipelotrichaceae Asteroleplasma 136 0.20% 0.11% 0.70% 0.40% 0.37% Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Bilophila 136 0.01% 0.13% 0.15% 0.16% 0.09% Proteobacteria Gammaproteobacteria __ __ __ 136 0.00% 0.00% 0.00% 0.14% 0.02% Proteobacteria Gammaproteobacteria Aeromonadales Succinivibrionaceae Succinatimonas 136 0.02% 0.13% 0.05% 0.01% 0.05% Bacteroidetes Bacteroidia Bacteroidales Barnesiellaceae Barnesiella 135 0.63% 0.28% 0.06% 0.14% 0.33% Bacteroidetes Bacteroidia Bacteroidales Marinifilaceae Butyricimonas 135 0.28% 0.07% 0.02% 0.03% 0.14% Bacteroidetes Bacteroidia Bacteroidales Marinifilaceae Odoribacter 134 0.12% 0.00% 0.01% 0.00% 0.05% Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] gnavus group 134 0.05% 0.21% 0.00% 0.05% 0.06% Firmicutes Clostridia Clostridiales Lachnospiraceae Howardella 134 0.00% 0.00% 0.03% 0.01% 0.01% Firmicutes Clostridia Clostridiales Lachnospiraceae uncultured 134 0.04% 0.12% 0.19% 0.05% 0.10% Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio 134 0.12% 0.00% 0.01% 0.00% 0.05% Actinobacteria Coriobacteriia Coriobacteriales Atopobiaceae Olsenella 133 0.11% 0.05% 0.15% 0.03% 0.10% Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospiraceae UCG-004 133 0.00% 0.05% 0.00% 0.00% 0.01% Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Proteus 133 0.01% 0.00% 0.00% 0.08% 0.01% Firmicutes Clostridia Clostridiales Peptococcaceae Peptococcus 132 0.08% 0.01% 0.01% 0.01% 0.04% Firmicutes Negativicutes Selenomonadales Veillonellaceae Allisonella 132 0.00% 0.04% 0.01% 0.02% 0.01% Firmicutes Negativicutes Selenomonadales Veillonellaceae Dialister 132 0.00% 0.22% 0.01% 0.00% 0.04% Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Paraprevotella 131 0.87% 0.47% 0.79% 0.65% 0.76% Actinobacteria Coriobacteriia Coriobacteriales Atopobiaceae Libanicoccus 130 0.06% 0.02% 0.10% 0.03% 0.06% Firmicutes Clostridia Clostridiales Lachnospiraceae Oribacterium 128 0.39% 0.81% 0.62% 0.57% 0.55% Spirochaetes Spirochaetia Spirochaetales Spirochaetaceae Sphaerochaeta 127 0.05% 0.00% 0.00% 0.00% 0.02% Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Porphyromonas 126 0.00% 0.02% 0.01% 0.00% 0.01% Firmicutes Clostridia Clostridiales Lachnospiraceae GCA-900066575 126 0.04% 0.00% 0.03% 0.00% 0.02% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcaceae UCG-014 125 0.09% 0.00% 0.00% 0.00% 0.04% Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospiraceae NK4A136 group 124 0.04% 0.00% 0.00% 0.00% 0.02% Proteobacteria Alphaproteobacteria Rhodospirillales uncultured __ 124 0.09% 0.00% 0.02% 0.00% 0.04% Firmicutes Clostridia Clostridiales Ruminococcaceae Fournierella 123 0.00% 0.01% 0.00% 0.00% 0.00% Firmicutes Clostridia Clostridiales Clostridiaceae 1 Sarcina 122 0.06% 0.03% 0.04% 0.00% 0.04% Firmicutes Clostridia Clostridiales Ruminococcaceae __ 122 0.01% 0.00% 0.00% 0.00% 0.01% Bacteroidetes Bacteroidia Bacteroidales Barnesiellaceae uncultured 121 0.03% 0.00% 0.02% 0.00% 0.02% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcaceae UCG-004 121 0.02% 0.00% 0.00% 0.00% 0.01% Firmicutes Bacilli Lactobacillales Aerococcaceae Aerococcus 120 0.00% 0.00% 0.00% 0.41% 0.05% Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminiclostridium 9 120 0.05% 0.01% 0.02% 0.00% 0.03% Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae __ 120 0.00% 0.00% 0.00% 0.08% 0.01% Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Collinsella 119 0.24% 0.18% 0.34% 0.09% 0.25% Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Akkermansiaceae Akkermansia 112 0.25% 0.05% 0.00% 0.00% 0.11% Firmicutes Bacilli Lactobacillales Leuconostocaceae Leuconostoc 110 0.00% 0.06% 0.00% 0.00% 0.01% Firmicutes Clostridia Clostridiales Peptostreptococcaceae Peptoclostridium 109 0.00% 0.05% 0.00% 0.00% 0.01% Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillibacter 107 0.01% 0.01% 0.00% 0.00% 0.01% Epsilonbacteraeota Campylobacteria Campylobacterales Helicobacteraceae Helicobacter 104 1.00% 0.20% 0.63% 0.65% 0.72% Firmicutes Clostridia Clostridiales Family XIII Family XIII UCG-001 103 0.00% 0.00% 0.00% 0.00% 0.00% Cyanobacteria Melainabacteria Gastranaerophilales __ __ 102 0.01% 0.00% 0.00% 0.00% 0.00% Firmicutes Clostridia Clostridiales Ruminococcaceae Subdoligranulum 102 0.00% 0.00% 0.00% 0.00% 0.00% Supplemental Table 3. Number of marmosets and associated health status for animals on study Healthy Stricture IBD MITA 8 (73%) 0 (0%) 3 (27%) MITB 27 (75%) 1 (3%) 8 (22%) MITCL 19 (43%) 1 (2%) 24 (55%) MITNE 37 (45%) 21 (26%) 24 (29%) MITALL 91 (53%) 23 (13%) 59 (34%) Supplemental Table 4. Overlap of top 25 ASVs in 4 IBD models ASVs of importance in 3+ models Family Genus ASV219 Burkholderiaceae Sutterella ASV115 Bacteroidaceae Bacteroides ASV207 Burkholderiaceae Sutterella ASV209 Burkholderiaceae Sutterella ASV346 Erysipelotrichaceae Asteroleplasma ASV779 Prevotellaceae Prevotella 9 ASV1044 Veillonellaceae Megamonas ASV1087 Veillonellaceae Megamonas Genera of importance in 3+ models with number of ASVs per model Genus MIT (all) MIT B MIT CL MIT NE Total Bacteroides 8 4 4 4 20 Sutterella 3 3 1 3 10 Megamonas 2 3 3 0 8 Bifidobacterium 1 4 2 0 7 Prevotella 9 2 0 2 3 7 Unknown Prevotellaceae 0 2 2 1 5 Parabacteroides 1 1 0 3 5 Prevotellaceae UCG-001 2 0 1 1 4 Asteroleplasma 1 1 1 0 3 Supplemental Table 5. Differentially expressed genes in the duodenum between stricture and non-stricture Supp. Table 5a. Genes upregulated in Stricture Gene name logFC logCPM F PValue FDR HYDIN -5.57275 8.235763 255.7079 9.64E-09 0.000186 FCN2 -6.2382 5.877223 181.0315 9.24E-08 0.000677 LOC100385035 -4.39198 4.35918 159.023 1.06E-07 0.000677 KIFC3 -3.72529 6.16206 147.199 1.55E-07 0.000745 FRMD1 -4.56494 4.611455 129.1226 2.96E-07 0.001139 GOLT1A -3.66778 5.210277 124.2568 3.57E-07 0.001146 LOC100415170 -4.60077 4.395378 112.2745 6.08E-07 0.001456 LOC100390425 -4.07882 7.969966 112.2804 6.21E-07 0.001456 SLC2A7 -2.82598 6.173383 104.4619 8.31E-07 0.0016 TUBAL3 -3.41415 6.772312 100.0865 1.02E-06 0.001788 LOC103792726 -3.50238 4.766558 92.43918 1.50E-06 0.001872 AQP10 -3.17156 6.834658 90.41122 1.66E-06 0.001872 ESPL1 -2.35296 7.029238 90.60278 1.65E-06 0.001872 CHAD -2.32012 6.502384 94.50606 1.35E-06 0.001872 LOC108590320 -3.69941 3.094203 81.63781 2.70E-06 0.001911 PRAP1 -3.50931 9.558516 86.09876 2.10E-06 0.001911 EPDR1 -3.28843 5.553597 85.40134 2.18E-06 0.001911
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