Supplemental Table 1: A list of phages in the database used for BLASTx

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Supplemental Table 1: A list of phages in the database used for BLASTx

Strains Family

Genbank numbers Bdellovibrio_phage_phiMH2K Microviridae NC_002643 Cellulophaga_phage_phi12_2 Microviridae KC821606

Chlamydia_phage_1 Microviridae D00624

Enterobacteria_phage_phiX174_sensu_lato Microviridae NC_001422 Guinea_pig_Chlamydia_phage Microviridae U41758

Spiroplasma_phage_4 Microviridae M17988

Acinetobacter_phage_Ac42 Myoviridae HM032710

Geobacillus_phage_GBSV1 Caudovirales DQ340064 Nitrincola_phage_1M3-16 Caudovirales KJ534580 Acinetobacter_phage_Acj61 Caudovirales GU911519 Aeromonas_phage_vB_AsaM-56 Caudovirales JQ177063

Bacillus_phage_BCP78 Caudovirales JN797797

Bacillus_phage_BCP8-2 Caudovirales KJ081346

Bacillus_phage_Bobb Caudovirales KM051843

Bacillus_phage_CP-51 Caudovirales KF554508

Bacillus_phage_G Caudovirales JN638751

Bacillus_phage_SP10 Caudovirales AB605730

Bdellovibrio_phage_phi1422 Caudovirales JQ177062

Brochothrix_phage_A9 Caudovirales HM242243

Burkholderia_phage_BcepF1 Caudovirales EF153632 Clostridium_phage_phiCDHM14 Caudovirales LK985321

Cronobacter_phage_CR9 Caudovirales JQ691611

Cronobacter_phage_vB_CsaM_GAP32 Caudovirales JN882285 Edwardsiella_phage_GF-2 Caudovirales AP014629 Enterobacteria_phage_phi92 Caudovirales FR775895 Enterococcus_phage_EFLK1 Caudovirales KR049063 Escherichia_phage_Av-05 Caudovirales KM190144 Klebsiella_phage_0507-KN2-1 Caudovirales AB797215 Lactobacillus_phage_LfeInf Caudovirales KP054477

Ralstonia_phage_RSL1 Caudovirales AB366653

Ralstonia_phage_RSL2 Caudovirales AP014693

Rhizobium_phage_vB_RleM_P10VF Caudovirales KM199770 Salmonella_phage_Marshall Caudovirales KF669653 Shewanella_sp._phage_1/41 Caudovirales KJ018212 Staphylococcus_phage_Twort Caudovirales AY954970 Staphylococcus_phage_vB_SauM_Remus Caudovirales JX846612 Actinomyces_phage_Av-1 Caudovirales DQ123818

Bacillus_phage_B103 Caudovirales X99260

Bacillus_phage_GA-1 Caudovirales X96987

Bacillus_phage_MG-B1 Caudovirales KC685370

Bacillus_phage_phi29 Caudovirales EU771092

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Brucella_phage_Tb Caudovirales JN939331 Cellulophaga_phage_phi14_2 Caudovirales KC821624 Cellulophaga_phage_phi4_1 Caudovirales KC821632 Clostridium_phage_phiCPV4 Caudovirales JQ729991 Enterobacter_phage_phiKDA1 Caudovirales JQ267518 Enterobacteria_phage_EcoDS1 Caudovirales EU734172

Klebsiella_phage_F19 Caudovirales KF765493

Pantoea_phage_LIMElight Caudovirales FR687252 Pantoea_phage_LIMEzero Caudovirales FR751545

Ralstonia_phage_RSJ5 Caudovirales AB983711

Salmonella_phage_FSL_SP-076 Caudovirales KC139520 Staphylococcus_phage_44AHJD Caudovirales NC_004678 Streptococcus_phage_Cp-1 Caudovirales Z47794 Bacillus_phage_vB_BanS-Tsamsa Caudovirales KC481682 Bacteroides_phage_B124-14 Caudovirales HE608841 Cellulophaga_phage_phiST Caudovirales HQ634192 Clostridium_phage_phiCD146 Caudovirales LN681536 Clostridium_phage_phiCP39-O Caudovirales EU588980 Croceibacter_phage_P2559S Caudovirales JQ867099 Croceibacter_phage_P2559Y Caudovirales KC688701 Enterobacteria_phage_ES18 Caudovirales AY736146 Enterobacterial_phage_mEp213 Caudovirales JQ182733 Enterococcus_phage_IME_EF3 Caudovirales KF728385

Erwinia_phage_PhiEaH1 Caudovirales KF623294

Escherichia_phage_HK75 Caudovirales HM173637

Gordonia_phage_GTE2 Caudovirales HQ403646

Lactobacillus_phage_Lc-Nu Caudovirales AY131267 Lactobacillus_phage_LLKu Caudovirales AY739900

Lactococcus_phage_712 Caudovirales DQ227763

Lactococcus_phage_bIL67 Caudovirales L33769 Lactococcus_phage_asccphi28 Caudovirales EU438902 Lactococcus_phage_phiL47 Caudovirales KF926093 Mycobacterium_phage_Alma Caudovirales JN699005 Mycobacterium_phage_Muddy Caudovirales KF024728 Mycobacterium_phage_QuinnKiro Caudovirales KM592966 Paenibacillus_phage_PG1 Caudovirales HQ332138 Pseudoalteromonas_phage_TW1 Caudovirales KC542353 Psychrobacter_phage_Psymv2 Caudovirales JF270478 Rhodococcus_phage_ReqiPoco6 Caudovirales GU580942 Staphylococcus_phage_vB_SepS_SEP9 Caudovirales KF929199 Streptococcus_phage_5093 Caudovirales FJ965538 Streptococcus_phage_Abc2 Caudovirales FJ236310 Streptococcus_phage_phiNJ2 Caudovirales JX879087 Streptococcus_phage_Sfi19 Caudovirales AF115102 Streptococcus_phage_SM1 Caudovirales NC_004996

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Streptococcus_phage_SPQS1 Caudovirales HE962497 Caulobacter_phage_phiCb5 Leviviridae HM066936 Enterobacteria_phage_FI strain BR8 Leviviridae FJ539135 Enterobacteria_phage_Hgal1 Leviviridae JX045650 Enterobacteria phage Qbeta strain BR12 Leviviridae FJ483842 Enterobacteria phage M11 Leviviridae AF052431

Bacillus_phage_phiNIT1 Unknown AP013029

Deep-sea_thermophilic_phage_D6E Unknown GU568037 Dragonfly-associated_microphage_1 Unknown JX185431 Lactobacillus_prophage_Lj771 Unknown AF195902

Marine_RNA_phage_MB Unknown KF510034

Sodalis_phage_phiSG1 Unknown DQ785801

Streptococcus_phage_V22 Unknown FR671405

uncultured_phage Unknown EF679227

uncultured_phage_crAssphage Unknown NC_024711

unidentified_phage Unknown JQ680358

Vibrio_phage_jenny_12G5 Unknown HQ632860

Vibrio_phage_SHOU24 Unknown KF623293

Xanthomonas_phage_OP2 Unknown AP008986

Yellowstone_Lake_virophage_5 Unknown KM502589

Yersinia_phage_phiR1-37 Unknown AJ972879

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Supplemental Table 2: Subjects Crohn’s Disease

(n=7)

Ulcerative Colitis (n=5)

Control (n=12)

Male, n (%) 5(38.5) 3(23.1) 5 (38.5)

Age, mean ± SD 13.9 ± 2.7 14.6 ± 2.7 10.3 ± 2.8

BMI, mean ± SD 20.4±2.4 19.7±3.2 18.6±5.6

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Supplemental Table 3a: Enriched taxa in IBD cases.

Supplemental Table 3b. Enriched taxa in healthy controls.

OTU ID Phylum Class Family Genus

Mean

Difference P-value Q-value Model

OTU_7

Proteobacteri

a Gammaproteobacteria Pasteurellaceae Haemophilus 3658 0.02 0.09 Negative Binomial

OTU_17 Firmicutes Bacilli Streptococcaceae Streptococcus 2058 <0.001 <0.001 Negative Binomial

OTU_355 Firmicutes Bacilli Streptococcaceae Streptococcus 666 <0.001 <0.001 Negative Binomial

OTU_46 Firmicutes Clostridia Ruminococcaceae Oscillospira 352 <0.001 <0.01 Negative Binomial

OTU_65 Firmicutes Clostridia Lachnospiraceae Lachnospira 204 <0.01 0.03 Zero-inflated Negative Binomial

OTU_99 Firmicutes Clostridia Lachnospiraceae 138 <0.001 <0.01 Negative Binomial

OTU_118 Firmicutes Clostridia Lachnospiraceae 111 <0.01 0.02 Negative Binomial

OTU_162 Firmicutes Bacilli 97 <0.001 <0.001 Negative Binomial

OTU_311 Firmicutes Erysipelotrichi Erysipelotrichaceae 78 <0.001 0.01 Negative Binomial

OTU_103 Firmicutes Erysipelotrichi Erysipelotrichaceae [Eubacterium] 76 <0.01 0.02 Negative Binomial

OTU_253 Firmicutes Clostridia Lachnospiraceae Blautia 66 <0.001 0.01 Negative Binomial

OTU_403 Firmicutes Clostridia Lachnospiraceae Dorea 47 <0.01 0.03 Negative Binomial

OTU_264 Firmicutes Bacilli Lactobacillaceae Pediococcus 38 <0.001 <0.01 Zero-inflated Negative Binomial

OTU_169 Actinobacteria Actinobacteria Micrococcaceae Rothia 35 <0.001 <0.01 Negative Binomial

OTU_153 Firmicutes Clostridia [Tissierellaceae] Anaerococcus 35 <0.01 0.03 Negative Binomial

OTU_273 Firmicutes Clostridia Lachnospiraceae Coprococcus 23 0.01 0.09 Negative Binomial

OTU_175 Firmicutes Bacilli Gemellaceae 20 <0.001 <0.01 Negative Binomial

OTU_207 Actinobacteria Actinobacteria Actinomycetaceae Actinomyces 17 <0.001 0.01 Negative Binomial

OTU_179 Firmicutes Clostridia Lachnospiraceae Dorea 12 <0.001 0.01 Negative Binomial

OTU_260 Firmicutes Bacilli Lactobacillaceae Lactobacillus 9 0.01 0.06 Negative Binomial

OTU_239 Firmicutes Clostridia Veillonellaceae Megasphaera 7 0.01 0.09 Negative Binomial

OTU_269 Firmicutes Clostridia Peptostreptococcacea

Peptostreptococcu

s 5 0.01 0.09 Negative Binomial

OTU_580 Firmicutes Clostridia Ruminococcaceae Faecalibacterium 3 <0.01 0.03 Negative Binomial

OTU_235 Firmicutes Erysipelotrichi Erysipelotrichaceae 1 <0.01 0.03 Zero-inflated Negative Binomial

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OTU ID Phylum Class Family Genus

Mean

Difference P-value Q-value Model OTU_14 Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 1407 <0.001 <0.01 Negative Binomial OTU_289 Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 837 <0.001 <0.01 Negative Binomial

OTU_23 Firmicutes Clostridia Ruminococcaceae 744 0.01 0.08 Negative Binomial

OTU_42 Bacteroidetes Bacteroidia Rikenellaceae 334 <0.01 0.03 Negative Binomial

OTU_52 Firmicutes Clostridia 322 <0.01 0.03 Negative Binomial

OTU_84 Firmicutes Clostridia Ruminococcaceae 181 <0.01 0.04 Negative Binomial

OTU_480 Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 135 0.01 0.08 Zero-inflated Negative Binomial

OTU_126

Proteobacteri

a Gammaproteobacteria Pseudomonadaceae Pseudomonas 87 <0.001 <0.01 Negative Binomial OTU_543 Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 62 <0.001 <0.001 Negative Binomial

OTU_116 Firmicutes Clostridia 40 <0.01 0.06 Negative Binomial

OTU_123 Firmicutes Clostridia Ruminococcaceae

Ruminococcu

s 33 <0.01 0.03 Negative Binomial

OTU_503 Bacteroidetes Bacteroidia Bacteroidaceae Bacteroides 33 <0.01 0.03 Negative Binomial

OTU_141 Firmicutes Erysipelotrichi Erysipelotrichaceae [Eubacterium] 31 <0.001 <0.001 Zero-inflated Negative Binomial

OTU_170 Firmicutes Clostridia Ruminococcaceae 28 <0.001 <0.01 Zero-inflated Negative Binomial

OTU_187 Firmicutes Clostridia Ruminococcaceae 20 <0.01 0.03 Zero-inflated Negative Binomial

OTU_552 Firmicutes Clostridia Ruminococcaceae Oscillospira 13 <0.01 0.02 Negative Binomial

OTU_185

Proteobacteri

a Betaproteobacteria Comamonadaceae Delftia 11 <0.01 0.04 Negative Binomial

OTU_317

Proteobacteri

a Betaproteobacteria Comamonadaceae 1 <0.01 0.03 Zero-inflated Negative Binomial

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Supplemental Figure 1: Diversity analyses revealed no significant difference in bacterial alpha-diversity between control and IBD groups.

P 0.14

0 100 200 300

IBD Control

Bacterial Richness

P 0.51

0.0 0.2 0.4 0.6

IBD Control

Pielou's Evenness Index

P0.31

0 2 4

IBD Control

Shannon's Diversity Index

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Supplemental Figure 2: Principal components analysis illustrating that diagnosis of IBD is significantly related to variance in gut bacterial microbiota composition.

R²0.12P0.03

−0.1 0.0 0.1 0.2

−0.2 0.0 0.2

PC1 (27.3%)

PC2 (10.4%) Diagnosis

IBD Control