title: Spatial variation of the colonic microbiota in patients with ulcerative colitis and control volunteers.
abstract: OBJECTIVE
  The relevance of spatial composition in the microbial changes associated with UC is unclear. We coupled luminal brush samples, mucosal biopsies and laser capture microdissection with deep sequencing of the gut microbiota to develop an integrated spatial assessment of the microbial community in controls and UC.
  
  
  METHODS
  A total of 98 samples were sequenced to a mean depth of 31,642 reads from nine individuals, four control volunteers undergoing routine colonoscopy and five patients undergoing surgical colectomy for medically-refractory UC. Samples were retrieved at four colorectal locations, incorporating the luminal microbiota, mucus gel layer and whole mucosal biopsies.
  
  
  RESULTS
  Interpersonal variability accounted for approximately half of the total variance. Surprisingly, within individuals, asymmetric Eigenvector map analysis demonstrated differentiation between the luminal and mucus gel microbiota, in both controls and UC, with no differentiation between colorectal regions. At a taxonomic level, differentiation was evident between both cohorts, as well as between the luminal and mucosal compartments, with a small group of taxa uniquely discriminating the luminal and mucosal microbiota in colitis. There was no correlation between regional inflammation and a breakdown in this spatial differentiation or bacterial diversity.
  
  
  CONCLUSIONS
  Our study demonstrates a conserved spatial structure to the colonic microbiota, differentiating the luminal and mucosal communities, within the context of marked interpersonal variability. While elements of this structure overlap between UC and control volunteers, there are differences between the two groups, both in terms of the overall taxonomic composition and how spatial structure is ascribable to distinct taxa.
authors.affiliation: University College Dublin, School of Medicine and Medical Science, Dublin, Ireland Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: A
authors.initials: A
authors.lastname: Lavelle
authors.affiliation: University College Dublin, School of Medicine and Medical Science, Dublin, Ireland Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: G
authors.initials: G
authors.lastname: Lennon
authors.affiliation: Teagasc, Food Research Centre, Moorepark, Fermoy, County Cork, Ireland.
authors.forename: O
authors.initials: O
authors.lastname: O'Sullivan
authors.affiliation: Department of Physiology, Trinity College Dublin, Dublin, Ireland.
authors.forename: N
authors.initials: N
authors.lastname: Docherty
authors.affiliation: University College Dublin, School of Medicine and Medical Science, Dublin, Ireland.
authors.forename: A
authors.initials: A
authors.lastname: Balfe
authors.affiliation: Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: A
authors.initials: A
authors.lastname: Maguire
authors.affiliation: Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: H E
authors.initials: HE
authors.lastname: Mulcahy
authors.affiliation: Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: G
authors.initials: G
authors.lastname: Doherty
authors.affiliation: Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: D
authors.initials: D
authors.lastname: O'Donoghue
authors.affiliation: Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: J
authors.initials: J
authors.lastname: Hyland
authors.affiliation: Teagasc, Food Research Centre, Moorepark, Fermoy, County Cork, Ireland Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: R P
authors.initials: RP
authors.lastname: Ross
authors.affiliation: 4i Centre for Interventions in Infection, Inflammation and Immunity, Graduate Entry Medical School, University of Limerick, Limerick, Ireland.
authors.forename: J C
authors.initials: JC
authors.lastname: Coffey
authors.affiliation: Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: K
authors.initials: K
authors.lastname: Sheahan
authors.affiliation: Teagasc, Food Research Centre, Moorepark, Fermoy, County Cork, Ireland Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: P D
authors.initials: PD
authors.lastname: Cotter
authors.affiliation: Alimentary Pharmabiotic Centre, University College Cork, Cork, Ireland.
authors.forename: F
authors.initials: F
authors.lastname: Shanahan
authors.affiliation: University College Dublin, School of Medicine and Medical Science, Dublin, Ireland Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: D C
authors.initials: DC
authors.lastname: Winter
authors.affiliation: University College Dublin, School of Medicine and Medical Science, Dublin, Ireland Centre for Colorectal Disease, Saint Vincent's University Hospital, Dublin, Ireland.
authors.forename: P R
authors.initials: PR
authors.lastname: O'Connell
mesh_terms: D000328:Adult; D001419:Bacteria / Q000235:genetics / Q000302:isolation & purification*; D001706:Biopsy; D003093:Colitis, Ulcerative / Q000382:microbiology* / Q000473:pathology; D003106:Colon / Q000382:microbiology* / Q000473:pathology; D003113:Colonoscopy; D005260:Female; D006801:Humans; D007413:Intestinal Mucosa / Q000382:microbiology / Q000473:pathology; D008297:Male; D064307:Microbiota / Q000502:physiology*; D008875:Middle Aged; D012329:RNA, Bacterial / Q000032:analysis; D014838:Volunteers; D055815:Young Adult
chemical_list: D012329:RNA, Bacterial
keywords: COLONIC BACTERIA; INFLAMMATORY BOWEL DISEASE; INTESTINAL MICROBIOLOGY; ULCERATIVE COLITIS