title: Twin studies reveal specific imbalances in the mucosa-associated microbiota of patients with ileal Crohn's disease.
abstract: BACKGROUND
  Large interindividual variation in the composition of the intestinal microbiota between unrelated individuals has made it challenging to identify specific aspects of dysbiosis that lead to Crohn's disease (CD).
  
  
  METHODS
  To reduce variations in exposure during establishment of the gut flora and the influence of genotype, we studied the mucosa-associated microbiota of monozygotic twin pairs that were discordant (n = 6) or concordant (n = 4) for CD. DNA was extracted from biopsies collected from 5 locations between the ileum and rectum. Bacterial 16S ribosomal RNA genes were amplified and community composition assessed by terminal-restriction fragment length polymorphism, cloning and sequencing, and quantitative real-time polymerase chain reaction (PCR).
  
  
  RESULTS
  The microbial compositions at all biopsy locations for each individual were similar, regardless of disease state, but there were differences between individuals. In particular, individuals with predominantly ileal CD had a dramatically lower abundance (P < 0.001) of Faecalibacterium prausnitzii and increased abundance (P < 0.03) of Escherichia coli compared to healthy co-twins and those with CD localized in the colon. This dysbiosis was significantly correlated to the disease phenotype rather than genotype.
  
  
  CONCLUSIONS
  The reduced abundance of F. prausnitzii and increased abundance of E. coli are indicative of an ileal CD phenotype, distinct from colonic CD, and the relative abundances of these specific bacterial populations are promising biomarker candidates for differential diagnosis of CD and eventually customized treatment.
authors.affiliation: Department of Microbiology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
authors.forename: Ben
authors.initials: B
authors.lastname: Willing
authors.forename: Jonas
authors.initials: J
authors.lastname: Halfvarson
authors.forename: Johan
authors.initials: J
authors.lastname: Dicksved
authors.forename: Magnus
authors.initials: M
authors.lastname: Rosenquist
authors.forename: Gunnar
authors.initials: G
authors.lastname: Järnerot
authors.forename: Lars
authors.initials: L
authors.lastname: Engstrand
authors.forename: Curt
authors.initials: C
authors.lastname: Tysk
authors.forename: Janet K
authors.initials: JK
authors.lastname: Jansson
mesh_terms: D003106:Colon / Q000382:microbiology*; D003424:Crohn Disease / Q000235:genetics / Q000382:microbiology*; D004200:Diseases in Twins / Q000235:genetics / Q000382:microbiology*; D004926:Escherichia coli / Q000235:genetics / Q000302:isolation & purification; D004927:Escherichia coli Infections / Q000235:genetics / Q000382:microbiology; D005260:Female; D016908:Gram-Positive Bacterial Infections / Q000235:genetics / Q000382:microbiology; D006801:Humans; D007077:Ileal Diseases / Q000235:genetics / Q000382:microbiology*; D008297:Male; D008875:Middle Aged; D012150:Polymorphism, Restriction Fragment Length; D011379:Prognosis; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D045857:Ruminococcus / Q000235:genetics / Q000302:isolation & purification; D014430:Twins, Monozygotic
chemical_list: D012336:RNA, Ribosomal, 16S