Modelling the emergent dynamics and major metabolites of the human colonic microbiota

Environ Microbiol. 2015 May;17(5):1615-30. doi: 10.1111/1462-2920.12599. Epub 2014 Oct 7.


We present here a first attempt at modelling microbial dynamics in the human colon incorporating both uncertainty and adaptation. This is based on the development of a Monod-equation based, differential equation model, which produces computer simulations of the population dynamics and major metabolites of microbial communities from the human colon. To reduce the complexity of the system, we divide the bacterial community into 10 bacterial functional groups (BFGs) each distinguished by its substrate preferences, metabolic pathways and its preferred pH range. The model simulates the growth of a large number of bacterial strains and incorporates variation in microbiota composition between people, while also allowing succession and enabling adaptation to environmental changes. The model is shown to reproduce many of the observed changes in major phylogenetic groups and key metabolites such as butyrate, acetate and propionate in response to a one unit pH shift in experimental continuous flow fermentors inoculated with human faecal microbiota. Nevertheless, it should be regarded as a learning tool to be updated as our knowledge of bacterial groups and their interactions expands. Given the difficulty of accessing the colon, modelling can play an extremely important role in interpreting experimental data and predicting the consequences of dietary modulation.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Acetates / metabolism
  • Biodiversity
  • Butyrates / metabolism
  • Colon / microbiology*
  • Computer Simulation*
  • Diet
  • Feces / microbiology
  • Humans
  • Microbiota*
  • Models, Theoretical
  • Phylogeny
  • Propionates / metabolism


  • Acetates
  • Butyrates
  • Propionates