Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome

From BugSigDB
Reviewed Marked as Reviewed by Claregrieve1 on 2023/01/24
study design
Citation
PMID PubMed identifier for scientific articles.
DOI Digital object identifier for electronic documents.
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


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
Irritable bowel syndrome [X]Psychogenic IBS,Adaptive colitis,Colitides, Mucous,Colitis, Mucous,Colon spasm,Colon, Irritable,Functional bowel disease,IBD,IBS,IBS - Irritable bowel syndrome,IC - Irritable colon,Irritable bowel,Irritable bowel - IBS,irritable bowel syndrome,Irritable Bowel Syndromes,Irritable Colon,irritable colon,Irritable colon (disorder),Irritable colon - Irritable bowel syndrome,Irritable colon syndrome,Membranous colitis,Mucous Colitides,Mucous colitis,mucus colitis,Nervous colitis,Psychogenic IBS,psychogenic IBS,Spastic colitis,Spastic colon,spastic colon,Syndrome, Irritable Bowel,Syndromes, Irritable Bowel,Irritable bowel syndrome
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

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

Curated date: 2021/07/08

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Claregrieve1

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

Revision editor(s): Kwekuamoo, Claregrieve1

Signature 2

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

Curated date: 2021/07/08

Curator: Kwekuamoo

Revision editor(s): Kwekuamoo, Claregrieve1

Source: Figure 2; Supplementary Table 1B

Description: Differential microbial abundance between IBS patients and controls

Abundance in Group 1: decreased abundance in IBS

NCBI Quality ControlLinks
Bacteroidaceae
Cellulomonadaceae
Lachnospiraceae
Paenibacillaceae
Porphyromonadaceae
Streptococcaceae
unclassified Bacteroidota
Phocaeicola vulgatus

Revision editor(s): Kwekuamoo, Claregrieve1