Simulating distal gut mucosal and luminal communities using packed-column biofilm reactors and an in vitro chemostat model

J Microbiol Methods. 2015 Jan;108:36-44. doi: 10.1016/j.mimet.2014.11.007. Epub 2014 Nov 20.


In vivo studies of human mucosal gut microbiota are often limited to end-point analyses and confounded by bowel cleansing procedures. Therefore, we used biofilm reactors to incorporate a simulated mucosal environment into an in vitro gut chemostat model. Communities developed were complex, reproducible, distinct, and representative of in vivo communities.

Keywords: Biofilm; Chemostat; DGGE; HITChip; Human gut microbiota; Microbial ecology.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Anti-Bacterial Agents / pharmacology*
  • Bacteria / classification
  • Bacteria / drug effects
  • Bacteria / genetics
  • Bacteria / isolation & purification
  • Bacterial Physiological Phenomena* / drug effects
  • Biofilms / drug effects*
  • Clindamycin / pharmacology*
  • Gastrointestinal Tract / microbiology
  • Humans
  • Intestinal Mucosa / microbiology*
  • Microbiota / drug effects*
  • Models, Biological
  • Phylogeny


  • Anti-Bacterial Agents
  • Clindamycin