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Original article
Geographical patterns of the standing and active human gut microbiome in health and IBD
  1. Ateequr Rehman1,
  2. Philipp Rausch2,3,
  3. Jun Wang2,3,
  4. Jurgita Skieceviciene1,4,
  5. Gediminas Kiudelis5,
  6. Ketan Bhagalia6,
  7. Deepak Amarapurkar6,
  8. Limas Kupcinskas4,5,
  9. Stefan Schreiber1,7,
  10. Philip Rosenstiel1,
  11. John F Baines2,3,
  12. Stephan Ott7
  1. 1Institute of Clinical Molecular Biology, Christian-Albrechts-University of Kiel, Kiel, Germany
  2. 2Max Planck Institute for Evolutionary Biology, Plön, Germany
  3. 3Institute for Experimental Medicine, Christian-Albrechts-University of Kiel, Kiel, Germany
  4. 4Institute for Digestive Research, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
  5. 5Department of Gastroenterology, Medical Academy, Lithuanian University of Health Sciences, Kaunas, Lithuania
  6. 6Bombay Hospital and Medical Research Center, Mumbai, India
  7. 7Department of General Internal Medicine, Christian-Albrechts-University of Kiel, University Hospital Schleswig-Holstein, Kiel, Germany
  1. Correspondence to Professor Philip Rosenstiel; Schittenhelmstr. 12, Institut für Klinische Molekular Biologie Kiel D-24105, Germany; p.rosenstiel{at}mucosa.de Professor John F Baines; Arnold-Heller-Str. 3, Haus 17, Institut für Experimentelle Medizin, Kiel D- 24105, Germany; j.baines{at}iem.uni-kiel.de Dr. Stephan Ott; Arnold-Heller-Str. 3, Haus 6, Klinik für Innere Medizin I Kiel D-24105, Germany; s.ott{at}mucosa.de

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.

Design 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.

  • COLONIC MICROFLORA
  • INFLAMMATORY BOWEL DISEASE
  • ULCERATIVE COLITIS
  • IBD BASIC RESEARCH
  • CROHN'S DISEASE

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