Gastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.

TitleGastrointestinal microbiome signatures of pediatric patients with irritable bowel syndrome.
Publication TypeJournal Article
Year of Publication2011
AuthorsSaulnier, DM, Riehle, K, Mistretta, T-A, Diaz, M-A, Mandal, D, Raza, S, Weidler, EM, Qin, X, Coarfa, C, Milosavljevic, A, Petrosino, JF, Highlander, S, Gibbs, RA, Lynch, SV, Shulman, RJ, Versalovic, J
JournalGastroenterology
Volume141
Issue5
Pagination1782-91
Date Published2011 Nov
ISSN1528-0012
KeywordsAbdominal Pain, Case-Control Studies, Child, DNA Probes, Female, Gastrointestinal Tract, Haemophilus parainfluenzae, Humans, Incidence, Irritable Bowel Syndrome, Male, Metagenome, Phenotype, Phylogeny, RNA, Ribosomal, 16S, Ruminococcus
Abstract

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.

DOI10.1053/j.gastro.2011.06.072
Alternate JournalGastroenterology
PubMed ID21741921
PubMed Central IDPMC3417828
Grant ListUH2 DK083990-01 / DK / NIDDK NIH HHS / United States
UH3 DK083990 / DK / NIDDK NIH HHS / United States
P30 DK56338 / DK / NIDDK NIH HHS / United States
U54 HG003273 / HG / NHGRI NIH HHS / United States
R01 AT004326-04 / AT / NCCIH NIH HHS / United States
R01 DK065075 / DK / NIDDK NIH HHS / United States
U54 HG003273-08 / HG / NHGRI NIH HHS / United States
UH3 DK083990-02 / DK / NIDDK NIH HHS / United States
P30 DK056338 / DK / NIDDK NIH HHS / United States
R01 DK065075-04 / DK / NIDDK NIH HHS / United States
R21 AT003102 / AT / NCCIH NIH HHS / United States
P30 DK056338-09 / DK / NIDDK NIH HHS / United States
R01 AT004326 / AT / NCCIH NIH HHS / United States
UH2 DK083990 / DK / NIDDK NIH HHS / United States
5U54 HG003273-08 / HG / NHGRI NIH HHS / United States