title: Comprehensive analysis of the bacterial content of stool from patients with chronic pouchitis, normal pouches, or familial adenomatous polyposis pouches.
abstract: BACKGROUND
  Chronic pouchitis is an important long-term complication following ileal pouch-anal anastomosis for ulcerative colitis. Antibiotic administration reduces symptoms of pouchitis, indicating that bacteria have a role in pathogenesis. The aim of the research was to investigate the bacterial content of pouches using nucleic acid-based methods.
  
  
  METHODS
  Stool microbiota of 17 patients with normal pouches (NP), 17 patients with pouchitis (CP) utilizing samples collected from each patient when antibiotic-treated (CP-on, asymptomatic) and when untreated (CP-off, symptomatic), and 14 familial adenomatous polyposis (FAP) patients were analyzed by high-throughput sequencing, fluorescence in situ hybridization technologies, and quantitative polymerase chain reaction (qPCR).
  
  
  RESULTS
  Fluorescence in situ hybridization analysis revealed an expanded phylogenetic gap in NP and CP-off patients relative to FAP. Antibiotic treatment reduced the gap in CP stool. The phylogenetic gap of CP-off patients was due to members of the bacterial families Caulobacteriaceae, Sphingomonadaceae, Comamonadaceae, Peptostreptococcaceae, and Clostridiaceae. There was a greater diversity of phylotypes of Clostridiaceae in CP-off subjects. The phylogenetic gap of NP stool was enriched by Ruminococcaceae and Bifidobacteriaceae. CP stool microbiota had reduced diversity relative to NP and FAP stool due largely to a reduction in Lachnospiraceae/Insertae Sedis XIV/clostridial cluster IV groups.
  
  
  CONCLUSIONS
  Bacterial groups within the expanded phylogenetic gap of pouch patients may have roles in the pathogenesis of pouchitis. Further research concerning the physiology of cultured members of these groups will be necessary to explain their specific roles. Members of the Lachnospiraceae, Incertae Sedis XIV, and clostridial cluster IV could be useful biomarkers of pouch health.
authors: Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand. gerald.tannock@otago.ac.nz
authors: Gerald W
authors: GW
authors: Tannock
authors: Blair
authors: B
authors: Lawley
authors: Karen
authors: K
authors: Munro
authors: Christophe
authors: C
authors: Lay
authors: Corinda
authors: C
authors: Taylor
authors: Christopher
authors: C
authors: Daynes
authors: Lori
authors: L
authors: Baladjay
authors: Robin
authors: R
authors: Mcleod
authors: Mark
authors: M
authors: Thompson-Fawcett
mesh_terms: D011125:Adenomatous Polyposis Coli / Q000382:microbiology* / Q000473:pathology; D000293:Adolescent; D000328:Adult; D001419:Bacteria / Q000472:pathogenicity*; D002648:Child; D002675:Child, Preschool; D002908:Chronic Disease; D003093:Colitis, Ulcerative / Q000382:microbiology* / Q000473:pathology; D039021:Colonic Pouches / Q000382:microbiology* / Q000473:pathology; D004247:DNA / Q000235:genetics; D005243:Feces / Q000382:microbiology*; D005260:Female; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D007223:Infant; D007231:Infant, Newborn; D008297:Male; D019449:Pouchitis / Q000382:microbiology* / Q000473:pathology; D060888:Real-Time Polymerase Chain Reaction; D055815:Young Adult
chemical_list: D004247:DNA