The treatment-naive microbiome in new-onset Crohn's disease

Study information

Needs review

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

24629344

DOI Digital object identifier for electronic documents.

https:/doi.org/10.1016/j.chom.2014.02.005

URI Uniform resource identifier for web resources.

https://pubmed.ncbi.nlm.nih.gov/24629344/

Authors

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ

Journal

Cell host & microbe

Year

2014

Inflammatory bowel diseases (IBDs), including Crohn's disease (CD), are genetically linked to host pathways that implicate an underlying role for aberrant immune responses to intestinal microbiota. However, patterns of gut microbiome dysbiosis in IBD patients are inconsistent among published studies. Using samples from multiple gastrointestinal locations collected prior to treatment in new-onset cases, we studied the microbiome in the largest pediatric CD cohort to date. An axis defined by an increased abundance in bacteria which include Enterobacteriaceae, Pasteurellacaea, Veillonellaceae, and Fusobacteriaceae, and decreased abundance in Erysipelotrichales, Bacteroidales, and Clostridiales, correlates strongly with disease status. Microbiome comparison between CD patients with and without antibiotic exposure indicates that antibiotic use amplifies the microbial dysbiosis associated with CD. Comparing the microbial signatures between the ileum, the rectum, and fecal samples indicates that at this early stage of disease, assessing the rectal mucosal-associated microbiome offers unique potential for convenient and early diagnosis of CD.

Experiment 1

Edit History Delete Duplicate this Experiment Add a new Signature

incomplete

Curated date: 2023/03/13

Curator: Khadeeejah

Revision editor(s): Khadeeejah, Chloe

Subjects

Location of subjects: China

Host species Species from which microbiome was sampled (if applicable): Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology: Feces , Ileum , Rectum 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,Distal intestine,Intestinum ileum,Lower intestine,Posterior intestine,Ileum,Intestinum rectum,Rectal sac,Terminal portion of intestine,Terminal portion of large intestine,Rectum

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy control
Group 1 name Corresponds to the case (exposed) group for case-control studies: Crohn's disease
Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: The treatment-naive microbiome in new-onset Crohn's disease
Group 0 sample size Number of subjects in the control (unexposed) group: 32
Group 1 sample size Number of subjects in the case (exposed) group: 33
Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 4 weeks

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance: Ion Torrent

Statistical Analysis

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

relative abundances

Statistical test

LEfSe

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)?: No
LDA Score above Threshold for the linear discriminant analysis (LDA) score for studies using the popular LEfSe tool: 3

Matched on Factors on which subjects have been matched on in a case-control study: sex

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased
Chao1 Abundance-based estimator of species richness: unchanged
Simpson Estimator of species richness and species evenness: more weight on species evenness: decreased
Richness Number of species: unchanged