Bighorn sheep gut microbiomes associate with genetic and spatial structure across a metapopulation

Abstract

Studies in laboratory animals demonstrate important relationships between environment, host traits, and microbiome composition. However, host-microbiome relationships in natural systems are understudied. Here, we investigate metapopulation-scale microbiome variation in a wild mammalian host, the desert bighorn sheep (Ovis canadensis nelsoni). We sought to identify over-represented microbial clades and understand how landscape variables and host traits influence microbiome composition across the host metapopulation. To address these questions, we performed 16S sequencing on fecal DNA samples from thirty-nine bighorn sheep across seven loosely connected populations in the Mojave Desert and assessed relationships between microbiome composition, environmental variation, geographic distribution, and microsatellite-derived host population structure and heterozygosity. We first used a phylogenetically-informed algorithm to identify bacterial clades conserved across the metapopulation. Members of genus Ruminococcaceae, genus Lachnospiraceae, and family Christensenellaceae R7 group were among the clades over-represented across the metapopulation, consistent with their known roles as rumen symbionts in domestic livestock. Additionally, compositional variation among hosts correlated with individual-level geographic and genetic structure, and with population-level differences in genetic heterozygosity. This study identifies microbiome community variation across a mammalian metapopulation, potentially associated with genetic and geographic population structure. Our results imply that microbiome composition may diverge in accordance with landscape-scale environmental and host population characteristics.

Ecology Impacts The Decrease of Spirochaetes and Prevotella In The Fecal Gut Microbiota of Urban Humans

“…Having samples from seven different locations available for analysis we could also demonstrate that host location only has a minor in uence on the bacterial community structure. More precisely, location/geography appears to in uence only individual bacterial families in most animals, whereas the broad taxonomic levels are dictated by host phylogeny as has been shown in previous studies [34][35][36]. We could not observe any bacterial clades that were location-speci c and prevalent, most probably due to the central role of host phylogeny for bacterial prevalence patterns as well as the wellde ned and shared dietary information throughout German zoos.…”

Bacterial dispersal and drift drive microbiome diversity patterns within a population of feral hindgut fermenters

“…Evidence from captive and wild mammalian systems has shown microbiome alpha diversity to be negatively correlated with host heterozygosity (Grosser et al, 2019;Wadud Khan et al, 2019). Similarly, an effect of population-level heterozygosity has been reported on the bacterial microbiome of free-living bighorn sheep (Couch et al, 2020). The homozygosity implicit of inbred hosts might restrict their immunological complexity (Potts & Wakeland, 1993;Reid et al, 2003), thereby also restricting the dexterity with which hosts recruit and "leash" their microbial communities (Foster et al, 2017), perhaps allowing for greater stochastic variation between individuals.…”

“…Therefore, we would expect rates of bacterial dispersal to decrease as a function of the time and space separating hosts. An effect of spatial separation on the microbiome has been demonstrated at large spatial scales between (sub)populations of red squirrels (Tamiasciurus hudsonicus; ~7 km; Ren et al, 2017), bighorn sheep (~150 km; Couch et al, 2020), house mice (Mus musculus; ~1100 km; Linnenbrink et al, 2013), American pikas (Ochotona princeps; ~1400 km; Kohl et al, 2018), red colobus (Procolobus rufomitratus; ~1100 km; McCord et al, 2014), and between pairs of predator and prey species (~12,100 km; Moeller et al, 2017).…”

A rather dry subject; investigating the study of arid-associated microbial communities

“…al. in Mojave desert-dwelling Bighorn sheep [ 174 ] faecal microbiota. Other stresses found in arid environments have been examined in terms of animal-associated microbiomes, both experimentally and in observation of natural conditions.…”