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Small molecules produced and modified by gut microorganisms can influence human physiology. An atlas of metabolic outputs of diverse gut microbes offers new ways to decipher the microbial mechanisms behind their production.
The microorganisms in our gut can have far-reaching effects — on our liver1, arteries2 and potentially even on our behaviour3. One way these microbes exert their effects is through the generation or consumption of small molecules, termed metabolites. Measuring metabolite levels, an approach called metabolomics, has led to ever-increasing recognition of their importance. And yet only rarely do we understand the underlying mechanisms driving these levels: namely, which microbes, enzymes and interactions are involved in the production and uptake of a specific metabolite. This task is further hindered by the complexity of microbial communities such as the gut microbiome, studies of which have to take into account the large number of microbes, the interactions between them, their diverse metabolic capabilities and several hard-to-measure non-microbial factors, such as host diet4. Writing in Nature, Han et al.5 present a comprehensive approach to addressing this major challenge, by carrying out metabolic and genetic analyses of a broad set of microbes commonly found in the human gut.