Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis

ABSTRACT A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic sh...

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Autores principales:	Joseph H. Vineis, Daina L. Ringus, Hilary G. Morrison, Tom O. Delmont, Sushila Dalal, Laura H. Raffals, Dionysios A. Antonopoulos, David T. Rubin, A. Murat Eren, Eugene B. Chang, Mitchell L. Sogin
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/6415721ac44b4c63be7e9208633bd957
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spelling	oai:doaj.org-article:6415721ac44b4c63be7e9208633bd9572021-11-15T15:50:15ZPatient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis10.1128/mBio.01713-162150-7511https://doaj.org/article/6415721ac44b4c63be7e9208633bd9572016-12-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mBio.01713-16https://doaj.org/toc/2150-7511ABSTRACT A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch. IMPORTANCE This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology prior to inflammation. Because of insufficient criteria for predicting which patients will develop UC or pouchitis, the interpretation of cross-sectional study designs suffers from lack of information about the microbiome structure and host gene expression patterns that directly correlate with the onset of disease. Our unique longitudinal study design allows each patient to serve as their own control, providing information about the state of the microbiome and host prior to and during the course of disease. Of significance to the broader community, this study identifies microbial strains that may have genetic elements that trigger the onset of disease in susceptible hosts.Joseph H. VineisDaina L. RingusHilary G. MorrisonTom O. DelmontSushila DalalLaura H. RaffalsDionysios A. AntonopoulosDavid T. RubinA. Murat ErenEugene B. ChangMitchell L. SoginAmerican Society for MicrobiologyarticleMicrobiologyQR1-502ENmBio, Vol 7, Iss 6 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	Microbiology QR1-502
spellingShingle	Microbiology QR1-502 Joseph H. Vineis Daina L. Ringus Hilary G. Morrison Tom O. Delmont Sushila Dalal Laura H. Raffals Dionysios A. Antonopoulos David T. Rubin A. Murat Eren Eugene B. Chang Mitchell L. Sogin Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis
description	ABSTRACT A 2-year longitudinal microbiome study of 22 patients who underwent colectomy with an ileal pouch anal anastomosis detected significant increases in distinct populations of Bacteroides during 9 of 11 patient visits that coincided with inflammation (pouchitis). Oligotyping and metagenomic short-read annotation identified Bacteroides populations that occurred in early samples, bloomed during inflammation, and reappeared after antibiotic treatment. Targeted cultivation of Bacteroides isolates from the same individual at multiple time points and from several patients detected subtle genomic changes, including the identification of rapidly evolving genomic elements that differentiate isogenic strains of Bacteroides fragilis from the mucosa versus lumen. Each patient harbored Bacteroides spp. that are closely related to commonly occurring clinical isolates, including Bacteroides ovatus, B. thetaiotaomicron, B. vulgatus, and B. fragilis, which contained unique loci in different patients for synthesis of capsular polysaccharides. The presence of unique Bacteroides capsular polysaccharide loci within different hosts and between the lumen and mucosa may represent adaptations to stimulate, suppress, and evade host-specific immune responses at different microsites of the ileal pouch. IMPORTANCE This longitudinal study provides an opportunity to describe shifts in the microbiomes of individual patients who suffer from ulcerative colitis (UC) prior to and following inflammation. Pouchitis serves as a model for UC with a predictable incidence of disease onset and enables prospective longitudinal investigations of UC etiology prior to inflammation. Because of insufficient criteria for predicting which patients will develop UC or pouchitis, the interpretation of cross-sectional study designs suffers from lack of information about the microbiome structure and host gene expression patterns that directly correlate with the onset of disease. Our unique longitudinal study design allows each patient to serve as their own control, providing information about the state of the microbiome and host prior to and during the course of disease. Of significance to the broader community, this study identifies microbial strains that may have genetic elements that trigger the onset of disease in susceptible hosts.
format	article
author	Joseph H. Vineis Daina L. Ringus Hilary G. Morrison Tom O. Delmont Sushila Dalal Laura H. Raffals Dionysios A. Antonopoulos David T. Rubin A. Murat Eren Eugene B. Chang Mitchell L. Sogin
author_facet	Joseph H. Vineis Daina L. Ringus Hilary G. Morrison Tom O. Delmont Sushila Dalal Laura H. Raffals Dionysios A. Antonopoulos David T. Rubin A. Murat Eren Eugene B. Chang Mitchell L. Sogin
author_sort	Joseph H. Vineis
title	Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis
title_short	Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis
title_full	Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis
title_fullStr	Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis
title_full_unstemmed	Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis
title_sort	patient-specific <italic toggle="yes">bacteroides</italic> genome variants in pouchitis
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/6415721ac44b4c63be7e9208633bd957
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Patient-Specific <italic toggle="yes">Bacteroides</italic> Genome Variants in Pouchitis

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