Incorporating functional trade-offs into studies of the gut microbiota

Trade-offs constrain evolution through genetic linkages and environmental limitations, impacting organismal physiology, morphology, and behavior. They are likely to also play a role in modulating functions of the microbiota, but previous research has not included tests of trade-off theory. Here, we review broadly how gut microbial functions are typically studied and outline evolutionarily-informed mechanisms to improve such research. These include measuring a diverse set of functions, with a focus on changes in host phenotype; more explicitly articulating the selective forces relevant to the microbiota; and using functionally relevant models. We present dietary intervention as a case study where trade-offs are likely to be relevant and discuss how the health effects of the modern human diet could be better understood in light of trade-offs. Appreciating microbial functional trade-offs as well as host trade-offs will be necessary to design effective interventions targeting the microbiota and, more generally, to understand the evolution of host-microbe interactions.