A Taxonomic assignments: Discovery cohort, week 0 1 Actinobacteria Actinomyces Group Actinobacteria Propionibacterium Control Abx− Actinobacteria Rothia 0.8 CD Abx− CD Abx+ Bacteroidetes Alloprevotella Bacteroidetes Capnocytophaga 0.6 Bacteroidetes Parabacteroides Bacteroidetes Porphyromonas Bacteroidetes Prevotella 0.4 Bacteroidetes Tannerella Bacteroidetes [Weeksellaceae] 0.2 Firmicutes Abiotrophia Firmicutes Aerococcaceae Firmicutes Clostridiales 0 Firmicutes Gemella Firmicutes Gemellaceae Firmicutes Granulicatella Firmicutes Lachnospiraceae Firmicutes Selenomonas Firmicutes Staphylococcus Firmicutes Streptococcaceae Firmicutes Streptococcus Firmicutes Veillonella Fusobacteria Fusobacterium Fusobacteria Leptotrichia Fusobacteria Leptotrichiaceae Proteobacteria Actinobacillus Proteobacteria Campylobacter Proteobacteria Comamonadaceae Proteobacteria Eikenella Proteobacteria Haemophilus Proteobacteria Kingella Proteobacteria Lautropia Proteobacteria Neisseria Proteobacteria Neisseriaceae Proteobacteria Sphingomonadaceae SR1 TM7 CW040 TM7 TM7−3 HC21 HC22 HC24 HC25 HC29 HC31 HC32 HC33 HC34 HC35 HC36 HC37 HC38 HC39 HC41 HC42 HC43 HC46 HC49 HC50 HC51 HC52 HC57 HC62 HC64 HC65 HC67 HC68 HC70 ND01 ND03 R05 R07 R08 R10 R11 R12 R13 R14 R15 R16 R17 R18 R20 R21 R24 R25 R32 R36 R37 R38 ND02 ND04 ND08 R02 R09 R22 R26 R29 R30 R33 R35

B Taxonomic assignments: Validation cohort, week 0 1 Actinobacteria Actinomyces Group Actinobacteria Actinomycetaceae Control Abx− Actinobacteria Corynebacterium 0.8 CD Abx− Actinobacteria Rothia CD Abx+ Bacteroidetes Alloprevotella Bacteroidetes Capnocytophaga 0.6 Bacteroidetes Porphyromonas Bacteroidetes Prevotella Bacteroidetes S24−7 0.4 Bacteroidetes [Weeksellaceae] Firmicutes Abiotrophia 0.2 Firmicutes Aerococcaceae Firmicutes Clostridiales Firmicutes Gemella 0 Firmicutes Gemellaceae Firmicutes Granulicatella Firmicutes Lachnospiraceae Firmicutes Lactobacillus Firmicutes Oribacterium Firmicutes Ruminococcaceae Firmicutes Selenomonas Firmicutes Staphylococcus Firmicutes Streptococcaceae Firmicutes Streptococcus Firmicutes Veillonella Fusobacteria Fusobacterium Fusobacteria Leptotrichia Fusobacteria Leptotrichiaceae Proteobacteria Actinobacillus Proteobacteria Aggregatibacter Proteobacteria Campylobacter Proteobacteria Cardiobacterium Proteobacteria Comamonadaceae Proteobacteria Eikenella Proteobacteria Haemophilus Proteobacteria Kingella Proteobacteria Lautropia Proteobacteria Neisseria Proteobacteria Neisseriaceae TM7 CW040 TM7 TM7−3 HC100 HC102 HC103 HC104 HC105 HC106 HC107 HC44 HC71 HC72 HC73 HC74 HC75 HC77 HC78 HC82 HC83 HC85 HC86 HC87 HC88 HC89 HC90 HC91 HC92 HC95 HC96 HC97 HC99 ND09 ND10 ND11 ND13 ND14 ND16 ND17 ND18 ND20 ND22 ND23 ND24 ND25 ND26 ND28 ND33 ND34 ND35 ND36 ND37 ND38 ND39 ND40 R40 R41 R42 R44 R45 R46 R47 R48 R49 R50 R51 ND06 ND15 ND21 ND30 ND31 ND32 R39 R43

C Taxonomic assignments: Discovery cohort, week 8 1 Actinobacteria Actinomyces Group Actinobacteria Actinomycetaceae Control Abx− Actinobacteria Corynebacterium 0.8 CD Abx− CD Abx+ Actinobacteria Rothia Bacteroidetes Alloprevotella 0.6 Bacteroidetes Bacteroides Bacteroidetes Capnocytophaga Bacteroidetes Parabacteroides 0.4 Bacteroidetes Porphyromonas Bacteroidetes Prevotella 0.2 Bacteroidetes Tannerella Bacteroidetes [Weeksellaceae] Firmicutes Abiotrophia 0 Firmicutes Aerococcaceae Firmicutes Catonella Firmicutes Clostridiales Firmicutes Gemella Firmicutes Gemellaceae Firmicutes Granulicatella Firmicutes Lachnospiraceae Firmicutes Selenomonas Firmicutes Staphylococcus Firmicutes Streptococcaceae Firmicutes Streptococcus Firmicutes Veillonella Fusobacteria Fusobacterium Fusobacteria Leptotrichia Fusobacteria Leptotrichiaceae Proteobacteria Actinobacillus Proteobacteria Campylobacter Proteobacteria Eikenella Proteobacteria Haemophilus Proteobacteria Kingella Proteobacteria Lautropia Proteobacteria Neisseria Proteobacteria Neisseriaceae Proteobacteria Pseudomonadaceae Proteobacteria Sphingomonadaceae SR1 TM7 CW040 TM7 TM7−3 HC03 HC04 HC05 HC06 HC10 HC12 HC13 HC14 HC15 HC16 HC17 HC18 HC21 HC22 HC24 HC25 HC29 HC31 HC32 HC33 HC34 HC35 HC36 HC37 HC38 HC39 HC41 HC42 HC43 HC46 HC49 HC50 HC51 HC52 HC57 HC64 HC65 HC68 HC70 ND01 ND02 ND03 ND08 R01 R02 R05 R08 R10 R11 R12 R13 R14 R15 R16 R18 R20 R21 R24 R25 R32 R33 R36 R37 R38 R09 R22 R26 R29 R31 R35

D Taxonomic assignments: Validation cohort, week 8 1 Actinobacteria Actinomyces Group Actinobacteria Actinomycetaceae Control Abx− Actinobacteria Corynebacterium 0.8 CD Abx− Actinobacteria Rothia CD Abx+ Bacteroidetes Alloprevotella Bacteroidetes Capnocytophaga 0.6 Bacteroidetes Porphyromonas Bacteroidetes Prevotella Bacteroidetes Tannerella 0.4 Bacteroidetes [Weeksellaceae] Cyanobacteria Streptophyta 0.2 Firmicutes Abiotrophia Firmicutes Aerococcaceae Firmicutes Catonella 0 Firmicutes Gemella Firmicutes Gemellaceae Firmicutes Granulicatella Firmicutes Lachnospiraceae Firmicutes Oribacterium Firmicutes Selenomonas Firmicutes Staphylococcus Firmicutes Streptococcaceae Firmicutes Streptococcus Firmicutes Veillonella Fusobacteria Fusobacterium Fusobacteria Leptotrichia Fusobacteria Leptotrichiaceae Proteobacteria Actinobacillus Proteobacteria Aggregatibacter Proteobacteria Campylobacter Proteobacteria Eikenella Proteobacteria Haemophilus Proteobacteria Kingella Proteobacteria Lautropia Proteobacteria Neisseria Proteobacteria Neisseriaceae Proteobacteria Ralstonia SR1 TM7 CW040 TM7 Rs−045 TM7 TM7−3 HC100 HC101 HC102 HC103 HC104 HC105 HC106 HC44 HC71 HC72 HC73 HC74 HC75 HC77 HC79 HC82 HC83 HC85 HC86 HC87 HC88 HC89 HC90 HC91 HC92 HC95 HC96 HC97 HC99 ND09 ND10 ND11 ND13 ND14 ND16 ND17 ND18 ND20 ND22 ND23 ND24 ND25 ND26 ND27 ND28 ND30 ND34 ND35 ND36 ND37 ND38 ND39 ND40 R40 R41 R42 R44 R45 R46 R47 R48 R49 R50 R51 ND06 ND15 ND21 ND31 ND32 ND33 R39 R43

Supplemental Digital Content 2: Bacterial taxa identified in the discovery cohort at week 0 (A), the validation cohort at week 0 (B), the discovery cohort at week 8 (C), and the validation cohort at week 8 (D).