A mathematical model to investigate the key drivers of the biogeography of the colon microbiota

International audienceThe gut microbiota, mainly located in the colon, is engaged in a complexdialogue with the large intestinal epithelium through which important regulatoryprocesses for the health and well-being of the host take place. Imbalances ofthe microbial populations, called dysbiosis, are related to several pathologicalstatus, emphasizing the importance of understanding the gut bacterial ecology.Among the ecological drivers of the microbiota, the spatial structure of the colonis of special interest: spatio-temporal mechanisms can lead to the constitutionof spatial interactions among the bacterial populations and of environmentalniches that impact the overall colonization of the colon. In the present study, weintroduce a mathematical model of the colon microbiota in its fluid environment,based on the explicit coupling of a population dynamics model of microbialpopulations involved in fibre degradation with a fluid dynamics model of theluminal content. This modeling framework is used to study the main driversof the spatial structure of the microbiota, specially focusing on the dietaryfibre inflow, the epithelial motility, the microbial active swimming and viscositygradients in the digestive track. We found 1) that the viscosity gradients allowthe creation of favorable niches in the vicinity of the mucus layer; 2) that very lowmicrobial active swimming in the radial direction is enough to promote bacterialgrowth, which sheds a new light on microbial motility in the colon and 3) thatdietary fibres are the main driver of the spatial structure of the microbiota inthe distal bowel whereas epithelial motility is preponderant for the colonizationof the proximal colon; in the transverse colon, fibre levels and chemotaxis havethe strongest impact on the distribution of the microbial communities