Fluid flow structures gut microbiota biofilm communities by distributing public goods.

Abstract

Bacterial gut commensals experience a biologically and physically complex mucosal environment. While many chemical factors mediate the composition and structure of these microbial communities, less is known about the role of mechanics. Here, we demonstrate that fluid flow impacts the spatial organization and composition of gut biofilm communities by shaping how different species interact metabolically. We first demonstrate that a model community composed of <i>Bacteroides thetaiotaomicron</i> (<i>Bt</i>) and <i>Bacteroides fragilis</i> (<i>Bf</i>), two representative human commensals, can form robust biofilms in flow. We identified dextran as a polysaccharide readily metabolized by <i>Bt</i> but not <i>Bf</i>, but whose fermentation generates a public good enabling <i>Bf</i> growth. By combining simulations with experiments, we demonstrate that in flow, <i>Bt</i> biofilms share dextran metabolic by-products, promoting <i>Bf</i> biofilm formation. By transporting this public good, flow structures the spatial organization of the community, positioning the <i>Bf</i> population downstream from <i>Bt</i>. We show that sufficiently strong flows abolish <i>Bf</i> biofilm formation by limiting the effective public good concentration at the surface. Physical factors such as flow may therefore contribute to the composition of intestinal microbial communities, potentially impacting host health.