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.
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Nawy, T. Mechanistic microbiota models. Nat Methods 15, 860 (2018). https://doi.org/10.1038/s41592-018-0202-0
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DOI: https://doi.org/10.1038/s41592-018-0202-0