Much of what we know about the microbial communities colonizing animals has focused on interactions between individual hosts and their associated microorganisms. However, animals in nature exist within populations of interacting individuals, and these interactions have the potential to allow microorganisms to disperse and transmit among hosts. We conducted an experiment to determine whether inter-host dispersal influences the assembly of microbial communities associated with zebrafish (Danio rerio) intestines in a manner predicted by ecological metacommunity theory. To manipulate host factors and dispersal of microorganisms among hosts, wild type and immune-deficient zebrafish were raised in one of three housing treatments: cohoused with individuals of both genotypes, cohoused with only individuals of the same genotype, or solitary without exposure to other fish. We then compared the diversity and composition of intestinal communities to predictions from a computational metacommunity model to guide the interpretation of the results.
We observed that inter-host dispersal had a large effect on the diversity and composition of intestinal microbiomes, and these effects are largely consistent with a computational model that assumes metacommunity dynamics among hosts. Communities associated with cohoused zebrafish were more diverse and heterogeneous than those associated with solitary hosts, and inter-host dispersal was strong enough to overwhelm the effects of individual host factors, largely eliminating differences between wild-type and immune-deficient hosts. We also observed stronger relationships between community composition and host factors such as development (measured by host standard length) and innate immune activity (measured by transcript levels of host immune genes) among solitary, but not cohoused, zebrafish. These effects were similar regardless of whether dispersal occurred within or between genotypes, suggesting dispersal independently alters the ecology of host-associated communities. These results demonstrate the importance of microbial dispersal to animal microbiomes as well as the value of incorporating dispersal-based theory into the study of host-microbe systems.