Dissecting individual pathogen-commensal interactions within a complex gut microbiota community

Interactions of commensal bacteria within the gut microbiota and with invading pathogens are critical in determining the outcome of an infection. While murine studies have been valuable, we lackin vitrotools to monitor community responses to pathogens at a single-species level. We have developed a multi-species community of nine representative gut species cultured together as a mixed biofilm and tracked numbers of individual species over time using a qPCR-based approach. Introduction of the major nosocomial gut pathogen,Clostridiodes difficile, to this community resulted in increased adhesion of commensals and inhibition ofC. difficilemultiplication. Interestingly, we observed an increase in individualBacteroidesspecies accompanying the inhibition ofC. difficile. Furthermore,Bacteroides doreireducedC. difficilegrowth within biofilms, suggesting a role forBacteroides sppin prevention ofC. difficilecolonisation. We report here anin vitrotool with excellent applications for investigating bacterial interactions within a complex community.