1. Process-based modelling of microbial community dynamics in the human colon
- Author
-
Helen Kettle, Petra Louis, and Harry J. Flint
- Subjects
Biomaterials ,Biomedical Engineering ,Biophysics ,Bioengineering ,Biochemistry ,Biotechnology - Abstract
The human colon contains a dynamic microbial community whose composition has important implications for human health. In this work we build a process-based model of the colonic microbial ecosystem and compare with general empirical observations and the results of in-vivo experiments. Based our previous work (Kettle et al., 2015), the microbial model consists of 10 microbial functional groups, 4 substrates and 10 metabolites; to this we add the interaction with a human host to give simulations of the in-situ colonic microbial ecosystem. This model incorporates absorption of short chain fatty acids (SCFA) and water by the host through the gut wall, variations in incoming dietary substrates (in the form of “meals” whose composition varies in time), bowel movements, feedback on microbial growth from changes in pH resulting from SCFA production, and multiple compartments to represent the proximal, transverse and distal colon. We verify our model against a number of observed criteria, e.g. total SCFA concentrations, SCFA ratios, mass of bowel movements, pH and water absorption over the transit time; and then run simulations investigating the effect of colonic transit time, and the composition and amount of indigestible carbohydrate in the host diet, which we compare with in-vivo studies. Gut microbiota are highly complex and poory understood yet our work shows that it is nevertheless possible to develop predictive models of the key components of the dynamics of this ecological system. The code is available as an R package (microPopGut) to aid future research.Author SummaryKettle wrote the model code and led the writing of the manuscript. Louis and Flint both contributed to writing the manuscript and all aspects of microbiolgy. All authors contributed critically to the drafts and gave final approval for publication.
- Published
- 2022