Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases

Study information

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

study design

prospective cohort

Citation

PMID PubMed identifier for scientific articles.

28494241

DOI Digital object identifier for electronic documents.

10.1016/j.chom.2017.04.010

URI Uniform resource identifier for web resources.

Authors

Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ

Journal

Cell host & microbe

Year

2017

Keywords:

Microbiome, butyrate, remission, roseburia, treatment response, vedolizumab

The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation. To determine whether the gut microbiome may predict responses to IBD therapy, we conducted a prospective study with Crohn's disease (CD) or ulcerative colitis (UC) patients initiating anti-integrin therapy (vedolizumab). Disease activity and stool metagenomes at baseline, and weeks 14, 30, and 54 after therapy initiation were assessed. Community α-diversity was significantly higher, and Roseburia inulinivorans and a Burkholderiales species were more abundant at baseline among CD patients achieving week 14 remission. Several significant associations were identified with microbial function; 13 pathways including branched chain amino acid synthesis were significantly enriched in baseline samples from CD patients achieving remission. A neural network algorithm, vedoNet, incorporating microbiome and clinical data, provided highest classifying power for clinical remission. We hypothesize that the trajectory of early microbiome changes may be a marker of response to IBD treatment.

Experiment 1

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

Curated date: 2025/04/24

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, UtibeIta, Victoria

Subjects

Location of subjects: United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.: Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces Cow dung,Cow pat,Droppings,Dung,Excrement,Excreta,Faeces,Fecal material,Fecal matter,Fewmet,Frass,Guano,Matières fécales@fr,Merde@fr,Ordure,Partie de la merde@fr,Piece of shit,Porción de mierda@es,Portion of dung,Portion of excrement,Portion of faeces,Portion of fecal material,Portion of fecal matter,Portion of feces,Portion of guano,Portion of scat,Portionem cacas,Scat,Spoor,Spraint,Stool,Teil der fäkalien@de,Feces,feces

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Crohn's disease Colitis, Granulomatous,CROHN DIS,Crohn Disease,Crohn disease,Crohn's associated gastritis,Crohn's disease,Crohn's disease of colon,Crohn's disease of large bowel,CROHNS DIS,Crohns Disease,Enteritis, Granulomatous,Enteritis, Regional,Gastritis Associated with Crohn Disease,Gastritis Associated with Crohn's Disease,granulomatous colitis,Ileitis, Regional,Ileitis, Terminal,Ileocolitis,pediatric Crohn's disease,regional enteritis,crohn disease,crohn's disease

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-remitters at Baseline (Crohn's disease)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Remitters at Baseline (Crohn's disease)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Crohn's Disease patients whose baseline samples were collected before treatment and who later achieved clinical remission at week 14

Lab analysis

Sequencing type: WMS

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: Not specified

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).: relative abundances

Statistical test: T-Test

Significance threshold p-value or FDR threshold used for differential abundance testing (if any): 0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?: Yes

Alpha Diversity

Richness Number of species: increased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

Curated date: 2025/04/26

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa

Source: Fig-2a

Description: The Significantly Differentiated Taxa between Remission and Non-remission Groups in Baseline Samples

Abundance in Group 1: increased abundance in Remitters at Baseline (Crohn's disease)

NCBI	Quality Control	Links
Roseburia inulinivorans
Burkholderiales

Revision editor(s): Aiyshaaaa

Experiment 2

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

Curated date: 2025/04/26

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, UtibeIta, Victoria

Differences from previous experiment shown

Subjects

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non Remitters Crohn's disease (CD)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Remitters Crohn's disease (CD)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Comparison of Crohn's Disease (CD) patients who did not achieve remission and Crohn's Disease (CD) patients who achieved remission between baseline and follow-up of week 14

Group 0 sample size Number of subjects in the control (unexposed) group: 24

Group 1 sample size Number of subjects in the case (exposed) group: 10

Alpha Diversity

Richness Number of species: increased

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

Curated date: 2025/04/26

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, UtibeIta

Source: Fig-3c

Description: Log2FC of species that represented significant change at week 14 follow-up in comparison with baseline sample of CD divided into remission and non-remission groups

Abundance in Group 1: decreased abundance in Remitters Crohn's disease (CD)

NCBI	Quality Control	Links
Bifidobacterium longum
Eggerthella
Mediterraneibacter gnavus
Roseburia inulinivorans
Veillonella parvula

Revision editor(s): Aiyshaaaa, UtibeIta

Experiment 3

Edit History Delete

Flag for review

Your review change was submittedDuplicate this Experiment Add a new Signature

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

Curated date: 2025/04/26

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, UtibeIta, Victoria

Differences from previous experiment shown

Subjects

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology: Ulcerative colitis colitis ulcerative,Colitis, Ulcerative,Left-sided ulcerative (chronic) colitis,Left-sided ulcerative colitis,left-sided ulcerative colitis,Other ulcerative colitis,Other ulcerative colitis (disorder),UC - ulcerative colitis,ulcerative colitis,ulcerative colitis (disease),ulcerative colitis (disorder),Ulcerative colitis, unspecified,ULCERATVE COLITIS UNSPCF,Ulcerative colitis

Group 0 name Corresponds to the control (unexposed) group for case-control studies: Non-Remitters Ulcerative Colitis (UC)

Group 1 name Corresponds to the case (exposed) group for case-control studies: Remitters Ulcerative Colitis (UC)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Comparison of Ulcerative Colitis (UC) patients who achieved remission and Ulcerative Colitis (UC) patients who did not achieve remission between baseline and follow-up of week 14

Group 0 sample size Number of subjects in the control (unexposed) group: 17

Group 1 sample size Number of subjects in the case (exposed) group: 11

Alpha Diversity

Richness Number of species: unchanged

Signature 1

Edit History Delete

Flag for review

Your review change was submitted

Reviewed Marked as Reviewed by KateRasheed on 2025-6-25

Curated date: 2025/04/26

Curator: Aiyshaaaa

Revision editor(s): Aiyshaaaa, UtibeIta

Source: Fig-3c

Description: Log2FC of species that represented significant change at week 14 follow-up in comparison with baseline sample of UC divided into remission and non-remission groups

Abundance in Group 1: decreased abundance in Remitters Ulcerative Colitis (UC)

NCBI	Quality Control	Links
Streptococcus salivarius

Revision editor(s): Aiyshaaaa, UtibeIta