Understanding Competition and Cooperation within the Mammalian Gut Microbiome

The mammalian gut harbors a vast community of microorganisms — termed the microbiota — whose composition and dynamics are considered to be critical drivers of host health. These factors depend, in part, upon the manner in which microbes interact with one another. Microbes are known to engage in a myriad of different ways, ranging from unprovoked aggression to actively feeding each other. However, the relative extent to which these different interactions occur between microbes within the gut is unclear. In this minireview we assess our current knowledge of microbe–microbe interactions within the mammalian gut microbiota, and the array of methods used to uncover them. In particular, we highlight the discrepancies between different methodologies: some studies have revealed rich networks of cross-feeding interactions between microbes, whereas others suggest that microbes are more typically locked in conflict and actively cooperate only rarely. We argue that to reconcile these contradictions we must recognize that interactions between members of the microbiota can vary across condition, space, and time — and that only through embracing this dynamism will we be able to comprehensively understand the ecology of our gut communities. Microbe–microbe interactions are the key drivers that determine the composition and function of the gut microbiome. Here, Coyte and Rakoff-Nahoum discuss how we interrogate microbe–microbe interactions, what we have learned, and what we still need to learn about the nature of competition and cooperation in this critical ecosystem.