Control Abx− CD Abx− CD Abx+ Group 1 0.8 0.6 0.4 0.2 0 Control Abx− CD Abx− CD Abx+ Control Abx− CD Abx− CD Abx+ Group Group 1 0.8 0.6 0.4 0.2 0 Control Abx− CD Abx− CD Abx+ 1 0.8 0.6 0.4 0.2 0 Group 1 0.8 0.6 0.4 0.2 0 Actinobacteria Actinomyces Actinobacteria Actinomycetaceae Actinobacteria Corynebacterium Actinobacteria Rothia Bacteroidetes Alloprevotella Bacteroidetes Bacteroides Bacteroidetes Capnocytophaga Bacteroidetes Parabacteroides Bacteroidetes Porphyromonas Bacteroidetes Prevotella Bacteroidetes Tannerella Bacteroidetes [Weeksellaceae] Firmicutes Abiotrophia 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 R35 R31 R29 R26 Actinobacteria Actinomyces Actinobacteria Actinomycetaceae Actinobacteria Corynebacterium Actinobacteria Rothia Bacteroidetes Alloprevotella Bacteroidetes Capnocytophaga Bacteroidetes Porphyromonas Bacteroidetes Prevotella Bacteroidetes Tannerella Bacteroidetes [Weeksellaceae] Streptophyta Cyanobacteria Firmicutes Abiotrophia Firmicutes Aerococcaceae Firmicutes Catonella 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 Actinobacteria Actinomyces Actinobacteria Actinomycetaceae Actinobacteria Corynebacterium Actinobacteria Rothia Bacteroidetes Alloprevotella Bacteroidetes Capnocytophaga Bacteroidetes Porphyromonas Bacteroidetes Prevotella Bacteroidetes S24−7 Bacteroidetes [Weeksellaceae] Firmicutes Abiotrophia Firmicutes Aerococcaceae Firmicutes Clostridiales Firmicutes Gemella 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 R22 R43 R43 R09 R39 R39 R38 ND33 Actinobacteria Actinomyces Actinobacteria Propionibacterium Actinobacteria Rothia Bacteroidetes Alloprevotella Bacteroidetes Capnocytophaga Bacteroidetes Parabacteroides Bacteroidetes Porphyromonas Bacteroidetes Prevotella Bacteroidetes Tannerella Bacteroidetes [Weeksellaceae] Firmicutes Abiotrophia Firmicutes Aerococcaceae 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 Comamonadaceae Proteobacteria Eikenella Proteobacteria Haemophilus Proteobacteria Kingella Proteobacteria Lautropia Proteobacteria Neisseria Proteobacteria Neisseriaceae Proteobacteria Sphingomonadaceae SR1 TM7 CW040 TM7 TM7−3 ND32 R37 ND32 R35 ND31 R36 ND31 ND30 ND21 R33 R33 ND21 ND15 R30 ND15 R32 ND06 R29 ND06 R25 R51 R26 R51 R24 R50 R22 R50 R21 R49 R09 R49 R20 R48 R02 R48 R18 R47 ND08 R47 R16 R46 ND04 R46 R15 R45 ND02 R45 R14 R44 R38 R44 R13 R42 R42 R41 R37 R12 R41 R40 R36 R40 R11 ND40 R32 ND40 R10 ND39 R25 ND39 R08 ND38 R24 ND38 R05 ND37 R21 ND37 R02 ND36 R20 ND36 R01 ND35 R18 ND35 ND08 ND34 R17 ND34 ND03 ND30 R16 ND33 ND02 ND28 R15 ND28 ND01 ND27 ND26 ND26 R14 HC70 ND25 ND25 R13 ND24 HC68 ND24 R12 ND23 HC65 ND23 R11 ND22 HC64 ND22 R10 ND20 HC57 ND20 R08 ND18 HC52 ND18 R07 ND17 HC51 ND17 R05 ND16 HC50 ND16 ND03 ND14 HC49 ND14 ND01 ND13 HC46 ND13 HC70 ND11 HC43 ND11 ND10 ND10 HC68 HC42 ND09 ND09 HC67 HC99 HC41 HC99 HC65 HC97 HC39 HC97 HC64 HC96 HC38 HC96 HC62 HC95 HC37 HC95 HC57 HC92 HC36 HC92 Taxonomic assignments: Discovery cohort, assignments: Discovery week 8 Taxonomic HC52 HC91 HC35 HC91 HC51 HC90 HC34 HC90 Taxonomic assignments: Validation cohort, week 8 assignments: Validation Taxonomic HC50 cohort, week 0 assignments: Validation Taxonomic HC89 HC33 HC89 HC49 HC88 HC32 HC88 Taxonomic assignments: Discovery cohort, assignments: Discovery week 0 Taxonomic HC46 HC87 HC31 HC87 HC86 HC86 HC43 HC29 HC85 HC85 HC42 HC83 HC25 HC83 HC41 HC82 HC24 HC82 HC39 HC78 HC22 HC79 HC38 HC77 HC21 HC77 HC37 HC75 HC18 HC75 HC36 HC74 HC17 HC74 HC35 HC73 HC16 HC73 HC34 HC72 HC15 HC72 HC33 HC71 HC14 HC71 HC32 HC44 HC13 HC44 HC107 HC106 HC31 HC12 HC106 HC105 HC29 HC105 HC10 HC104 HC25 HC104 HC06 HC103 HC24 HC103 HC05 HC102 HC22 HC102 HC04 HC101 cohort at week 0 (B), the discovery cohort at week 8 (C), and the validation cohort at week 8 (D). HC21 HC100 HC03 HC100 Supplemental Digital Content 2: Bacterial taxa identified in the discovery cohort at week 0 (A), the validation D C B A.