title: pH feedback and phenotypic diversity within bacterial functional groups of the human gut.
abstract: Microbial diversity in the human colon is very high with apparently large functional redundancy such that within each bacterial functional group there are many coexisting strains. Modelling this mathematically is problematic since strains within a functional group are often competing for the same limited number of resources and therefore competitive exclusion theory predicts a loss of diversity over time. Here we investigate, through computer simulation, a fluctuation dependent mechanism for the promotion of diversity. A variable pH environment caused by acidic by-products of bacterial growth on a fluctuating substrate coupled with small differences in acid tolerance between strains promotes diversity under both equilibrium and far-from-equilibrium conditions. Under equilibrium conditions pH fluctuations and relative nonlinearity in pH limitation among strains combine to prevent complete competitive exclusion. Under far-from-equilibrium conditions, loss of diversity through extinctions is made more difficult because pH cycling leads to fluctuations in the competitive ranking of strains, thereby helping to equalise fitness. We assume a trade-off between acid tolerance and maximum growth rate so that our microbial system consists of strains ranging from specialists to generalists. By altering the magnitude of the effect of the system on its pH environment (e.g. the buffering capacity of the colon) and the pattern of incoming resource we explore the conditions that promote diversity.
authors.affiliation: Biomathematics and Statistics Scotland, Kings Buildings, Edinburgh EH9 3JZ, UK.
authors.forename: Helen
authors.initials: H
authors.lastname: Kettle
authors.affiliation: Biomathematics and Statistics Scotland, Kings Buildings, Edinburgh EH9 3JZ, UK; Department of Mathematics, Maxwell Institute for Mathematical Sciences, Heriot-Watt University, Edinburgh EH14 4AS, UK; Department of Biology, University of York, York YO10 5YW, UK. Electronic address: rd118@hw.ac.uk.
authors.forename: Ruairi
authors.initials: R
authors.lastname: Donnelly
authors.affiliation: Microbiology Group, Rowett Institute of Nutrition and Health, University of Aberdeen, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, UK.
authors.forename: Harry J
authors.initials: HJ
authors.lastname: Flint
authors.affiliation: Biomathematics and Statistics Scotland, Kings Buildings, Edinburgh EH9 3JZ, UK.
authors.forename: Glenn
authors.initials: G
authors.lastname: Marion
mesh_terms: D001419:Bacteria / Q000254:growth & development / Q000378:metabolism*; D044822:Biodiversity; D025461:Feedback, Physiological; D041981:Gastrointestinal Tract / Q000382:microbiology*; D006801:Humans; D006863:Hydrogen-Ion Concentration; D010641:Phenotype
keywords: Colon; Competitive exclusion; Diversity; Fluctuating; Microbial