Maintaining phenotypic diversity in a mechanistic model of gut bacteria

The principle of competitive exclusion states that two species can not co-exist if they occupy the same niche. In reality we see many species co-existing - particularly in the case of human gut microbiota.


Through a long term collaboration with the Rowett Institute we have developed a detailed mechanistic model of human gut microbiota which simulates the interactions of many functionally-distinct groups of gut bacteria. To simulate adaptation to a changing environment, we have taken a complex systems style approach whereby the model is seeded with hundreds of bacterial strains with stochastically-generated traits. However, due to the competitive exclusion principle, in a resource competition model with a constant environment, each functional group will eventually become completely dominated by the strain with the characteristics most suited to that environment. However, in reality phenotypic diversity is high in the colon with many functionally similar strains co-existing.


We have found that diversity can be maintained in our model by including a feedback from the microbial system to the environment through changes in pH caused by the acidic metabolites produced during bacterial growth. In conjunction with a trade-off between acid tolerance and maximum bacterial growth rate, this feedback allows many strains to co-exist. Our methods are transferable to many analogous ecosystems featuring resource competition.

maintain diversity

Figure shows time evolution of the concentration of 30 bacterial strains in the Bacteroides group with a sinusoidal resource input representing food consumption during the day. Left panels show results when there is no feedback; right panels show results when there is a pH feedback from bacterial growth.


Kettle H, R. Donnelly, HJ Flint, G. Marion. 2014. pH feedback and phenotypic diversity within bacterial functional groups of the human gut. Journal of Theoretical Biology 342: 62-69. doi:10.1016/j.jtbi.2013.10.015

Kettle H, P Louis, G Holtrop, S. Duncan, HJ Flint. 2015. Modelling the Emergent Dynamics and Major Metabolites of the Human Colonic Microbiota. Environmental Microbiology.DOI: 10.1111/1462-2920.12599.

Kettle H, G Holtrop, P Louis, HJ Flint. 2018. microPop: Modelling microbial populations and communities in R. Methods in Ecology and Evolution, 9(2), p399-409. doi: 10.1111/2041-210X.12873

H Kettle, P Louis, HJ Flint. 2022 Process-based modelling of microbial community dynamics in the human colon Journal of the Royal Society Interface 19 (195), 20220489


This work was done in collaboration with Harry Flint and Petra Louis at the Rowett Institute. It was funded under the Scottish Government's Strategic Research Programme for environment, agriculture and food.



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