colonization is not mediated by bile salts and requires Stickland fermentation of proline in an model of infection.

Treatment with antibiotics is a major risk factor for infection, likely due to depletion of the gastrointestinal microbiota. Two microbiota-mediated mechanisms thought to limit colonization include conversion of conjugated primary bile salts into secondary bile salts toxic to growth, and competition between the microbiota and for limiting nutrients. Using a continuous flow model of the distal colon, we investigated how treatment with six clinically-used antibiotics influenced susceptibility to infection in 12 different microbial communities cultivated from healthy individuals. Antibiotic treatment reduced microbial richness; disruption varied by antibiotic class and microbiota composition, but did not correlate with susceptibility. Antibiotic treatment also disrupted microbial bile salt metabolism, increasing levels of the primary bile salt, cholate, and decreasing levels of the secondary bile salt, deoxycholate. However, decreased levels of deoxycholate did not correlate with increased susceptibility. Further, bile salts were not required to inhibit colonization. We tested whether amino acid fermentation contributed to persistence of in antibiotic-treated communities. mutants unable to use proline as an electron acceptor in Stickland fermentation due to disruption of proline reductase (Δ) had significantly lower levels of colonization than wild-type strains in four of six antibiotic-treated communities tested. This data provides further support for the importance of bile salt-independent mechanisms in regulating colonization of .