Depth-dependent differences in community structure of the human colonic microbiota in health

PLoS One. 2013 Nov 6;8(11):e78835. doi: 10.1371/journal.pone.0078835. eCollection 2013.


Objective: The aims of this study were to develop techniques for spatial microbial assessment in humans and to establish colonic luminal and mucosal spatial ecology, encompassing longitudinal and cross-sectional axes.

Design: A microbiological protected specimen brush was used in conjunction with a biopsy forceps to sample the colon in nine healthy volunteers undergoing colonoscopy. Terminal Restriction Fragment Length Polymorphism analysis was used to determine the major variables in the spatial organization of the colonic microbiota.

Results: Protected Specimen Brush sampling retrieved region-specific, uncontaminated samples that were enriched for bacterial DNA and depleted in human DNA when compared to biopsy samples. Terminal Restriction Fragment Length Polymorphism analysis revealed a segmentation of bacterial communities between the luminal brush and biopsy-associated ecological niches with little variability across the longitudinal axis of the colon and reduced diversity in brush samples.

Conclusion: These results support the concept of a microbiota with little longitudinal variability but with some degree of segregation between luminal and mucosal communities.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Adult
  • Aged
  • Amplified Fragment Length Polymorphism Analysis / methods
  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / isolation & purification
  • Bacteriology / instrumentation
  • Biodiversity
  • Cluster Analysis
  • Colon / microbiology*
  • Colonoscopy
  • DNA, Bacterial / genetics
  • Ecosystem*
  • Female
  • Genetic Variation
  • Healthy Volunteers
  • Humans
  • Male
  • Microbiota / genetics*
  • Middle Aged
  • Mucous Membrane / microbiology*
  • RNA, Ribosomal, 16S / genetics
  • Surgical Instruments


  • DNA, Bacterial
  • RNA, Ribosomal, 16S

Grants and funding

Funding was provided by a Science Foundation Ireland grant (09/IN.1/B2606). The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.