Alterations in the gut microbiome of children with severe ulcerative colitis

Study information

Reviewed Marked as Reviewed by Fatima on 2022/10/20

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

22170749

DOI Digital object identifier for electronic documents.

10.1002/ibd.22860

URI

Authors

Michail S, Durbin M, Turner D, Griffiths AM, Mack DR, Hyams J, Leleiko N, Kenche H, Stolfi A, Wine E

Journal

Inflammatory bowel diseases

Year

2012

BACKGROUND: Although the role of microbes in disease pathogenesis is well established, data describing the variability of the vast microbiome in children diagnosed with ulcerative colitis (UC) are lacking. This study characterizes the gut microbiome in hospitalized children with severe UC and determines the relationship between microbiota and response to steroid therapy. METHODS: Fecal samples were collected from 26 healthy controls and 27 children hospitalized with severe UC as part of a prospective multicenter study. DNA extraction, polymerase chain reaction (PCR) amplification of bacterial 16S rRNA, and microarray hybridization were performed. Results were analyzed in GeneSpring GX 11.0 comparing healthy controls with children with UC, and steroid responsive (n = 17) with nonresponsive patients (n = 10). RESULTS: Bacterial signal strength and distribution showed differences between UC and healthy controls (adjusted P < 0.05) for Phylum, Class, Order, Family, Genus, and Phylospecies levels with reduction in Clostridia and an increase in Gamma-proteobacteria. The number of microbial phylospecies was reduced in UC (266 ± 69) vs. controls (758 ± 3, P < 0.001), as was the Shannon Diversity Index (6.1 ± 0.23 vs. 6.49 ± 0.04, respectively; P < 0.0001). Steroid nonresponders harbored fewer phylospecies than responders (142 ± 49 vs. 338 ± 62, P = 0.013). CONCLUSIONS: Richness, evenness, and biodiversity of the gut microbiome were remarkably reduced in children with UC compared with healthy controls. Children who did not respond to steroids harbored a microbiome that was even less rich than steroid responders. This study is the first to characterize the gut microbiome in a large cohort of pediatric patients with severe UC and describes changes in the gut microbiome as a potential prognostic feature.

Experiment 1

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Reviewed Marked as Reviewed by Atrayees on 2023-6-27

Curated date: 2022/10/20

Curator: Fatima

Revision editor(s): Fatima, Aiyshaaaa, WikiWorks

Subjects

Location of subjects: Canada

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

Group 0 name Corresponds to the control (unexposed) group for case-control studies: healthy controls

Group 1 name Corresponds to the case (exposed) group for case-control studies: children with ulcerative colitis

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children hospitalized for intravenous corticosteroid therapy for acute UC

Group 0 sample size Number of subjects in the control (unexposed) group: 26

Group 1 sample size Number of subjects in the case (exposed) group: 27

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 1 month

Lab analysis

Sequencing type: 16S

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: RT-qPCR

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

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

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness: decreased

Signature 1

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Curated date: 2022/10/20

Curator: Fatima

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Source: Table 2

Description: Phylum and Class comparisons for healthy children and children with ulcerative colitis (UC).

Abundance in Group 1: decreased abundance in children with ulcerative colitis

NCBI	Quality Control	Links
Actinomycetota
Actinomycetes
Alphaproteobacteria
Bacilli
Bacteroidia
Betaproteobacteria
Clostridia
Deltaproteobacteria
Campylobacterota
Erysipelotrichia
Bacillota
Fusobacteriota
Gammaproteobacteria
Lentisphaera
Pseudomonadota
Spirochaetota
Verrucomicrobiia
Coriobacteriia

Revision editor(s): Fatima, WikiWorks