Biofilms promote tolerance and stability in gut bacterial communities during bile acid stress

Abstract

Several mechanisms have been described to explain how bacterial species colonize and persist in the mammalian gut. However, biofilm formation remains underexplored as a mechanism for gut microbiota symbiont persistence. While evidence of biofilm formation by individual gut symbionts is beginning to emerge, its occurrence and relevance in multispecies gut microbiota communities remain poorly studied. Here, we established an in vitro model to study multispecies gut microbiota biofilms using the Oligo-Mouse Microbiota 12 (OMM12) consortium, a defined community of murine gut isolates. We investigated community biofilm formation and responses to bile acids, host-derived detergent-like molecules released into the gut that can perturb bacterial growth and community structure. We identified distinct contributions of two OMM12 members: removal of Enterococcus faecalis strongly reduced community biofilm biomass, whereas removal of Bacteroides caecimuris had limited effect on biomass but strongly altered species associations. These results, together with monoculture assays, show that individual biofilm capacity does not directly predict community-level contribution. Moreover, planktonic and biofilm communities had markedly distinct responses to bile acid stress. Planktonic cultures, while more susceptible to bile acids, showed resilience by recovering growth yield within 24 hours upon bile stress removal. Community biofilms, in contrast, showed greater tolerance to bile acid stress and more species associations. Overall, our findings support biofilms as a community-level lifestyle that can buffer defined gut microbiota communities against host-associated chemical perturbations.