Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome

Study information

Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/24

study design

case-control

Citation

PMID PubMed identifier for scientific articles.

21741921

DOI Digital object identifier for electronic documents.

10.1053/j.gastro.2011.06.072

URI

Authors

Saulnier DM, Riehle K, Mistretta TA, Diaz MA, Mandal D, Raza S, Weidler EM, Qin X, Coarfa C, Milosavljevic A, Petrosino JF, Highlander S, Gibbs R, Lynch SV, Shulman RJ, Versalovic J

Journal

Gastroenterology

Year

2011

BACKGROUND & AIMS: The intestinal microbiomes of healthy children and pediatric patients with irritable bowel syndrome (IBS) are not well defined. Studies in adults have indicated that the gastrointestinal microbiota could be involved in IBS. METHODS: We analyzed 71 samples from 22 children with IBS (pediatric Rome III criteria) and 22 healthy children, ages 7-12 years, by 16S ribosomal RNA gene sequencing, with an average of 54,287 reads/stool sample (average 454 read length = 503 bases). Data were analyzed using phylogenetic-based clustering (Unifrac), or an operational taxonomic unit (OTU) approach using a supervised machine learning tool (randomForest). Most samples were also hybridized to a microarray that can detect 8741 bacterial taxa (16S rRNA PhyloChip). RESULTS: Microbiomes associated with pediatric IBS were characterized by a significantly greater percentage of the class γ-proteobacteria (0.07% vs 0.89% of total bacteria, respectively; P < .05); 1 prominent component of this group was Haemophilus parainfluenzae. Differences highlighted by 454 sequencing were confirmed by high-resolution PhyloChip analysis. Using supervised learning techniques, we were able to classify different subtypes of IBS with a success rate of 98.5%, using limited sets of discriminant bacterial species. A novel Ruminococcus-like microbe was associated with IBS, indicating the potential utility of microbe discovery for gastrointestinal disorders. A greater frequency of pain correlated with an increased abundance of several bacterial taxa from the genus Alistipes. CONCLUSIONS: Using 16S metagenomics by PhyloChip DNA hybridization and deep 454 pyrosequencing, we associated specific microbiome signatures with pediatric IBS. These findings indicate the important association between gastrointestinal microbes and IBS in children; these approaches might be used in diagnosis of functional bowel disorders in pediatric patients.

Experiment 1

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Reviewed Marked as Reviewed by Claregrieve1 on 2023-5-30

Curated date: 2021/07/04

Curator: Kwekuamoo

Revision editor(s): WikiWorks, LGeistlinger, Claregrieve1, Kwekuamoo, Peace Sandy

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

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: IBS

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group: Children ages 7-12 who met the Pediatric Rome III criteria for IBS (Table 1). Subtyping of IBS was based on previous recommendations for IBS in adults because no Pediatric Rome subtype criteria exist for children.

Group 0 sample size Number of subjects in the control (unexposed) group: 27

Group 1 sample size Number of subjects in the case (exposed) group: 28

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any): 6 months

Lab analysis

Sequencing type: 16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene: V1-V3

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

Statistical Analysis

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

Statistical test: Mann-Whitney (Wilcoxon)

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

Alpha Diversity

Richness Number of species: unchanged

Signature 1

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Curated date: 2021/07/08

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Claregrieve1, WikiWorks

Source: Figure 2; Supplementary Table 1A

Description: Differential microbial abundance between IBS patients and controls

Abundance in Group 1: increased abundance in IBS

NCBI	Quality Control	Links
Acidobacteriaceae
Aeromonadaceae
Alteromonadaceae
Bacillaceae
Cellulomonadaceae
Clostridiaceae
Coxiellaceae
Desulfobacteraceae
Desulfovibrionaceae
Enterobacteriaceae
Escherichia coli
Eubacteriaceae
Lachnospiraceae
Nitrospiraceae
Pasteurellaceae
Peptococcus
Peptostreptococcaceae
Polyangiaceae
Prevotellaceae
Promicromonosporaceae
Streptococcaceae
Syntrophobacteraceae
Thiotrichaceae