Elucidating Human Gut Microbiota Interactions That Robustly Inhibit Diverse Strains Across Different Nutrient Landscapes

The human gut pathogen displays extreme genetic variability and confronts a changeable nutrient landscape in the gut. We mapped gut microbiota inter-species interactions impacting the growth and toxin production of diverse strains in different nutrient environments. Although negative interactions impacting are prevalent in environments promoting resource competition, they are sparse in an environment containing -preferred carbohydrates. strains display differences in interactions with and the ability to compete for proline. toxin production displays substantial community-context dependent variation and does not trend with growth-mediated inter-species interactions. shows substantial differences in transcriptional profiles in the presence of the closely related species or . In co-culture with , exhibits massive alterations in metabolism and other cellular processes, consistent with their high metabolic overlap. Further, inhibits the growth and toxin production of diverse strains across different nutrient environments and ameliorates the disease severity of a challenge in a murine model. In sum, strain-level variability and nutrient environments are major variables shaping gut microbiota interactions with .