title: Geographical patterns of the standing and active human gut microbiome in health and IBD.
abstract: OBJECTIVE
  A global increase of IBD has been reported, especially in countries that previously had low incidence rates. Also, the knowledge of the human gut microbiome is steadily increasing, however, limited information regarding its variation on a global scale is available. In the light of the microbial involvement in IBDs, we aimed to (1) identify shared and distinct IBD-associated mucosal microbiota patterns from different geographical regions including Europe (Germany, Lithuania) and South Asia (India) and (2) determine whether profiling based on 16S rRNA transcripts provides additional resolution, both of which may hold important clinical relevance.
  
  
  METHODS
  In this study, we analyse a set of 89 mucosal biopsies sampled from individuals of German, Lithuanian and Indian origins, using bacterial community profiling of a roughly equal number of healthy controls, patients with Crohn's disease and UC from each location, and analyse 16S rDNA and rRNA as proxies for standing and active microbial community structure, respectively.
  
  
  RESULTS
  We find pronounced population-specific as well as general disease patterns in the major phyla and patterns of diversity, which differ between the standing and active communities. The geographical origin of samples dominates the patterns of β diversity with locally restricted disease clusters and more pronounced effects in the active microbial communities. However, two genera belonging to the Clostridium leptum subgroup, Faecalibacteria and Papillibacter, display consistent patterns with respect to disease status and may thus serve as reliable 'microbiomarkers'.
  
  
  CONCLUSIONS
  These analyses reveal important interactions of patients' geographical origin and disease in the interpretation of disease-associated changes in microbial communities and highlight the added value of analysing communities on both the 16S rRNA gene (DNA) and transcript (RNA) level.
authors.affiliation: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.
authors.forename: Ateequr
authors.initials: A
authors.lastname: Rehman
authors.affiliation: Max Planck Institute for Evolutionary Biology, Plön, Germany Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany.
authors.forename: Philipp
authors.initials: P
authors.lastname: Rausch
authors.affiliation: Max Planck Institute for Evolutionary Biology, Plön, Germany Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
authors.forename: Jurgita
authors.initials: J
authors.lastname: Skieceviciene
authors.affiliation: Department of Gastroenterology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
authors.forename: Gediminas
authors.initials: G
authors.lastname: Kiudelis
authors.affiliation: Bombay Hospital and Medical Research Center, Mumbai, India.
authors.forename: Ketan
authors.initials: K
authors.lastname: Bhagalia
authors.affiliation: Bombay Hospital and Medical Research Center, Mumbai, India.
authors.forename: Deepak
authors.initials: D
authors.lastname: Amarapurkar
authors.affiliation: Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania Department of Gastroenterology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania.
authors.forename: Limas
authors.initials: L
authors.lastname: Kupcinskas
authors.affiliation: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany Department of General Internal Medicine, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Schreiber
authors.affiliation: Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany.
authors.forename: Philip
authors.initials: P
authors.lastname: Rosenstiel
authors.affiliation: Max Planck Institute for Evolutionary Biology, Plön, Germany Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany.
authors.forename: John F
authors.initials: JF
authors.lastname: Baines
authors.affiliation: Department of General Internal Medicine, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany.
authors.forename: Stephan
authors.initials: S
authors.lastname: Ott
mesh_terms: D000293:Adolescent; D000328:Adult; D000368:Aged; D000369:Aged, 80 and over; D003013:Clostridium / Q000302:isolation & purification; D005260:Female; D005858:Germany; D006801:Humans; D007194:India; D015212:Inflammatory Bowel Diseases / Q000382:microbiology*; D007413:Intestinal Mucosa / Q000382:microbiology*; D008097:Lithuania; D008297:Male; D064307:Microbiota; D008875:Middle Aged; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S / Q000032:analysis; D055815:Young Adult
chemical_list: D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S
keywords: COLONIC MICROFLORA; CROHN'S DISEASE; IBD BASIC RESEARCH; INFLAMMATORY BOWEL DISEASE; ULCERATIVE COLITIS