Symbiotic relationships between animals and microbial communities are ubiquitous in nature. These microbes influence fitness and thus ecologically important traits of their hosts, ultimately forming a holobiont as a unit of biological organization consisting of a multicellular host and a community of associated microorganisms. The outcome of such relationships is sometimes observed as an evolutionary signal of host phylogeny and microbial community co-structuring between species – phylosymbiosis. Across models systems, investigating microbial symbionts is a complex and multifactorial issue that requires carefully constructed, hypothesis-driven experimentation. However, there are many complimentary tools available to test the mechanisms of host-association. For example, techniques like gnotobiotic, germfree, or anexic animals have made it possible to decouple the microbiota from the host and systematically reconstruct the relationships.
The aims of this research topic are to serve as a collection of research articles and reviews that will demonstrate the multidisciplinary approaches to understanding the interacting mechanisms of host-associated microbiota. Themes of the topic will address the following questions:

How do animals regulate their microbiota and what are the mechanisms involved that influence health, fitness and reproductive success of the host?

Do phylosymbiotic relationships indicate reciprocal evolutionary change between the groups of interacting species – and thereby coevolution?

How do multi-level interactions of host-microbiota-environment influence overall outcome of the biology of the system?

How does the host ‘select’ the associated microbiota and vice versa?

How stable are the ‘beneficial’ and ‘parasitic’ interactions of host and microbiota?

Important Note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.