Medlock, G. L. et al. Cell Sys. 7, 245–257 (2018).

Gut microbes have a profound effect on human metabolism, but the complexity of interactions among microbial species and metabolites makes it extremely challenging to extract mechanistic insights. Medlock et al. took a synthetic approach to the problem, by culturing six bacterial strains from the well-characterized altered Schaedler flora (ASF). The researchers first measured growth rates and profiled the metabolomes of ASF monocultures and co-cultured strain pairs. They then fed these data into their constant yield expectation (ConYE) analytical model, which identifies potential metabolic interactions that contribute to growth modulation in co-culture. They validated one predicted cross-feeding interaction between Clostridium and Parabacteroides strains, based on Stickland fermentation of amino acids, with in vitro supplementation experiments.