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

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 biofilm model for the Oligo-Mouse Microbiota 12 (OMM12) consortium, a defined community of murine gut isolates, and used it to investigate 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. Although planktonic and biofilm communities had broadly similar compositions, their response to bile acid stress were markedly distinct. Planktonic cultures, while more susceptible to bile, impaired in biomass and species associations, showed resilience by recovering biomass within 24 hours upon bile stress removal. Community biofilms, in contrast, showed greater tolerance to bile acid stress and preserved or recovered 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. ImportanceDespite decades of research, how the gut microbiota maintains diversity and persistence remains to be completely understood. Gut bacterial species must withstand harsh host-derived stresses while navigating complex interspecies interactions, many of which being highly competitive. In host-associated contexts, biofilms have largely been viewed as a detrimental trait because of their role in pathogen persistence and protection from clearance, leaving the potential contribution of commensal gut biofilms to microbiota stability underexplored. Our work establishes a simple and adaptable experimental framework to study biofilm formation in a defined multispecies gut bacterial community. We show that biofilms alter how this community responds to bile acids, host-derived molecules that can disrupt bacterial growth and community structure. Our findings support biofilm formation as a protective lifestyle that can help gut symbionts withstand bile acid stress, raising the possibility that community biofilms contribute to microbiota persistence under chemical stress encountered in the host.