Applying the core microbiome to understand host–microbe systems

Summary

The host-associated core microbiome was originally coined to refer to common groups of microbes or genes that were likely to be particularly important for host biological function. However, the term has evolved to encompass variable definitions across studies, often identifying key microbes with respect to their spatial distribution, temporal stability or ecological influence, as well as their contribution to host function and fitness. A major barrier to reaching a consensus over how to define the core microbiome and its relevance to biological, ecological and evolutionary theory is a lack of precise terminology and associated definitions, as well the persistent association of the core microbiome with host function. Common, temporal and ecological core microbiomes can together generate ins