The Effects of Spatial Organization and Fluid Flow on the Social Interactions in Microbial Communities

Bacteria often engage in social interactions with neighbouring bacteria. Ecosystems which are subjected to social interactions have been widely studied in well mixed settings such as test tubes, allowing us to identify the cellular components contributing to fitness. However, such growth condition does not resemble conditions in nature as bacteria often co-exist with defined spatial organizations. Furthermore, influences from common environmental forces such as fluid flow on bacteria growth is also neglected. For example, fluid flow may modulate the concentration landscape of public goods, limiting its dispersal to surrounding bacterial communities. Our aim is to systematically examine the impacts of fluid flow, relative spatial arrangement and biofilm morphologies on the fitness, metabolic activity, and organization of surface-associated bacterial communities. We chose to focus our work on the microbial communities found in human gut microbiota as the organization and abundance of member species can have a major impact on host health. To achieve this, we first developed a novel technique combining anaerobic microfluidics and fluorescence confocal microscopy which allowed us to identify that the Bacteroides, a common class of bacteria found within the gut microbiota, forms robust biofilms in flow. We then characterized the nutrient sharing capabilities of gut microbes by utilizing a model gut microbiota consisting of two species: Bacteroides thetaiotaomicron (Bt) and Bacteroides fragilis (Bf), where Bt metabolizes the polysaccharide dextran and cross-feeds its metabolic by-product glucose to Bf, which promotes Bf biofilm formation. By transporting this public good, flow structures the spatial organization of the community, positioning the Bf population downstream from Bt. We show that sufficiently strong flows abolish Bf 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. Finally, we also demonstrated that intrinsic properties of polysaccharides such as molecular weight impacts the rate of sugar metabolism by microbes and the extent of nutrient sharing within the community, which may lead to overall changes in community composition.