Research on host-microbiome systems, particularly with an aim toward understanding the impacts of the microbiome on human health, has been a rapidly expanding field. Frustratingly, most of these studies have found that host traits explain relatively little of the variation in microbiome composition. One reason for this might be that these studies often ignore the effects of transmission between hosts. Several recent studies have shown that transmission of microbes between co-housed animals can have a large, and sometimes overwhelming effect on the composition of the gut microbiome. Ecologists working in non-host systems have long known about the importance of transmission to community composition, and have lately developed a robust set of theoretical predictions, jointly termed metacommunity theory, to understand it. Metacommunity theory as commonly employed often models local habitat patches as abiotic entities, akin to the abiotic habitats of lakes or islands, fixed in space and time. Hosts in host-microbiome systems are definitively biotic, they have population structure, move around, and evolve. It is unclear what effect this has on the composition of their microbial communities. We use a trait-based metacommunity model to explore ways in which the structure of the host population affects the outcome of community assembly.
Our model explicitly tracks both dispersal ability and niche preference of species as they compete within and disperse between hosts. In addition to giving insight into how incorporating biotic patches affects the diversity within metacommunites, it also allows us to understand the selective forces that shape microbiome composition. In a preliminary investigation, we incorporated age structure into our models of host populations by adding in processes of birth and death (i.e. host “turnover”). We found that while overall gamma diversity peaked at low host turnover, the selection for dispersal ability continued to increase monotonically with increasing turnover. We are investigating the effects of both host movement and host evolution on the composition of the microbiome community. Understanding how the biotic nature of host “patches” interacts with transmission to impact the composition of microbiomes has the potential to explain the huge amount of unexplained variation often reported in host-microbiome studies.