Shades of grey: host phenotype dependent effect of urbanization on the bacterial microbiome of a wild mammal

Abstract Background Host-associated microbiota are integral to the ecology of their host and may help wildlife species cope with rapid environmental change. Urbanization is a globally replicated form severe change which we can leverage better understand microbiomes. Does colonization separate cities result in parallel changes intestinal microbiome wildlife, if so, does within-city habitat heterogeneity matter? Using 16S rRNA gene amplicon sequencing, quantified effect urbanization (across three cities) on eastern grey squirrels ( Sciurus carolinensis ). Grey ubiquitous rural urban environments throughout native range, across they display an apparent coat colour polymorphism (agouti, black, intermediate). Results squirrel microbiomes differed between city environments; however, comparable variation was explained by within cities. Our analyses suggest that operational taxonomic unit (OTU) community structure more strongly influenced local conditions (rural forests versus human built habitats) than broader landscape (city rural). The bacterial genera characterizing built-environment thought specialize host-derived products have been linked previous research low fibre diets. However, despite at fine spatial scales, phylogenetic patterns were phenotype dependent. City agouti displayed greater beta-dispersion those or forest environments, null modelling results indicated did not differ greatly from stochastic expectations. Conclusions Squirrel but differences magnitude observed land classes scale. We observe strong evidence inter-environmental disparate selective pressures. Rather, our dispersal ecological drift shaping observed. these processes partly mediated phenotype. Given well-known cline melanism, provide useful free-living system study how genetics mediate environment x interactions.