The world within: Quantifying the determinants and outcomes of a host's microbiome

The fungal, bacterial, and viral microbial communities embedded as endosymbionts within all free-living organisms are extremely diverse and encode the vast majority of genes in the biosphere. Microbes in a human, for example, account for 100 times more genes than their host; similar results are emerging for virtually all free-living organisms. Disease is the best studied host-microbe interaction, but endosymbiotic microbial populations and communities also are responsible for critical functions in their hosts including nutrient uptake (plants), reduction in inflammatory responses (animals), digestion (animals), anti-herbivore defenses (plants), and pathogen resistance. In spite of the tremendous diversity and functional importance of the microbial biome to free-living organisms, we have little predictive understanding of the biotic and abiotic factors controlling within-host microbial community composition or the spatial scales at which anthropogenic changes affect host and microbial community interactions and functions. Current research suggests that anthropogenic changes to nutrient supply and food web composition can affect biological systems at scales ranging from individuals to continents. However, while current studies are clarifying the effects of some of these drivers on the structure and functioning of ecosystems, we have far less knowledge of their effects on microbial communities residing within hosts. Given the accelerating progress in metagenome studies, we are poised to make rapid advances in understanding the determinants and effects of within-host microbial communities.