The role of animal hosts in shaping gut microbiome variation

Abstract

Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host–microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue ‘Sculpting the microbiome: how host factors determine and respond to microbial colonization’.

Sculpting the microbiome

“…Reflecting this view, Maritan et al . [ 10 ] provide a comprehensive review of how host factors shape and adapt to the presence of the microbiome across organisms. Their extensive discussion spans multiple animal phyla, existing in widely varying ecologies and reflects on the processes that are common or distinct to different lineages and different systems.…”

Caenorhabditis elegans as a Convenient Animal Model for Microbiome Studies

“…C. elegans has been used to screen and study the effects of gut microbiota [ 24 ]. Because of genetic similarities between mammals and the worm, C. elegans ’ reaction to different environments can resemble its effect on mammals.…”