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Title: Patient-Specific Bacteroides Genome Variants in Pouchitis

Here, 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.
Authors:
 [1] ;  [2] ;  [1] ;  [2] ;  [2] ;  [3] ;  [4] ;  [2] ;  [5] ;  [2] ;  [1]
  1. Marine Biological Lab., Woods Hole, MA (United States)
  2. The Univ. of Chicago, Chicago, IL (United States)
  3. Mayo Clinic, Rochester, MN (United States)
  4. The Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
  5. Marine Biological Lab., Woods Hole, MA (United States); The Univ. of Chicago, Chicago, IL (United States)
Publication Date:
Grant/Contract Number:
AC02-06CH11357
Type:
Accepted Manuscript
Journal Name:
mBio (Online)
Additional Journal Information:
Journal Name: mBio (Online); Journal Volume: 7; Journal Issue: 6; Journal ID: ISSN 2150-7511
Publisher:
American Society for Microbiology
Research Org:
Argonne National Lab. (ANL), Argonne, IL (United States)
Sponsoring Org:
University of Chicago; USDOE
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES
OSTI Identifier:
1416005

Vineis, Joseph H., Ringus, Daina L., Morrison, Hilary G., Delmont, Tom O., Dalal, Sushila, Raffals, Laura H., Antonopoulos, Dionysios A., Rubin, David T., Eren, A. Murat, Chang, Eugene B., and Sogin, Mitchell L.. Patient-Specific Bacteroides Genome Variants in Pouchitis. United States: N. p., Web. doi:10.1128/mBio.01713-16.
Vineis, Joseph H., Ringus, Daina L., Morrison, Hilary G., Delmont, Tom O., Dalal, Sushila, Raffals, Laura H., Antonopoulos, Dionysios A., Rubin, David T., Eren, A. Murat, Chang, Eugene B., & Sogin, Mitchell L.. Patient-Specific Bacteroides Genome Variants in Pouchitis. United States. doi:10.1128/mBio.01713-16.
Vineis, Joseph H., Ringus, Daina L., Morrison, Hilary G., Delmont, Tom O., Dalal, Sushila, Raffals, Laura H., Antonopoulos, Dionysios A., Rubin, David T., Eren, A. Murat, Chang, Eugene B., and Sogin, Mitchell L.. 2016. "Patient-Specific Bacteroides Genome Variants in Pouchitis". United States. doi:10.1128/mBio.01713-16. https://www.osti.gov/servlets/purl/1416005.
@article{osti_1416005,
title = {Patient-Specific Bacteroides Genome Variants in Pouchitis},
author = {Vineis, Joseph H. and Ringus, Daina L. and Morrison, Hilary G. and Delmont, Tom O. and Dalal, Sushila and Raffals, Laura H. and Antonopoulos, Dionysios A. and Rubin, David T. and Eren, A. Murat and Chang, Eugene B. and Sogin, Mitchell L.},
abstractNote = {Here, 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.},
doi = {10.1128/mBio.01713-16},
journal = {mBio (Online)},
number = 6,
volume = 7,
place = {United States},
year = {2016},
month = {11}
}