Intrinsic and extrinsic factors influence on an omnivore’s gut microbiome

Abstract

Gut microbiomes (GMBs), complex communities of microorganisms inhabiting the gastrointestinal tracts of their hosts, perform countless micro-ecosystem services such as facilitating energy uptake and modulating immune responses. While scientists increasingly recognize the role GMBs play in host health, the role of GMBs in wildlife ecology and conservation has yet to be realized fully. Here, we use brown bears (Ursus arctos) as an ecological model to (1) characterize GMB community composition associated with location, season, and reproductive condition of a large omnivore; (2) investigate how both extrinsic and intrinsic factors influence GMB community membership and structure; and (3) quantify differences in GMB communities among different locations, seasons, sex, and reproductive conditions. To achieve these aims, we subsampled brown bear fecal samples collected during United States National Park Service research activities at three National Parks and Preserves (Katmai, Lake Clark, and Gates of the Arctic) and extracted microbial DNA for 16S rRNA amplicon sequencing and microbial taxonomic classification. We analyzed GMB communities using alpha and beta diversity indices, subsequently using linear mixed models to examine relationships between alpha diversity and extrinsic and intrinsic factors. Katmai brown bears hosted the greatest alpha diversity, whereas Gates brown bears hosted the least alpha diversity. Our results indicate that location and diet drive GMB variation, with bears hosting less phylogenetic diversity as park distance inland increases. Monitoring brown bear GMBs could enable managers to quickly detect and assess the impact of environmental perturbations on brown bear health. By integrating macro and micro-ecological perspectives we aim to inform local and landscape-level management decisions to promote long-term brown bear conservation and management.

The gut microbiome of wild American marten in the Upper Peninsula of Michigan

“…Given the high level of among-individual variation detected in the bacterial communities of marten in this study, as well as the findings from other studies of carnivore gut microbiomes (e.g., mink [ 84 ], Ursus spp. [ 41 , 85 ]), it is not surprising that we detected statistically significant differences in unweighted UniFrac between live-trapped and harvested marten. As a metric, unweighted UniFriac disproportionately weights taxa that are present at low relative abundances.…”

“…PLOS ONE (e.g., mink [84], Ursus spp. [41,85]), it is not surprising that we detected statistically significant differences in unweighted UniFrac between live-trapped and harvested marten. As a metric, unweighted UniFriac disproportionately weights taxa that are present at low relative abundances.…”

“…Recent studies have demonstrated that the gut microbiome can be used as an indicator of food resource use. For instance, black bear consuming processed anthropogenic foods host significantly degraded gut microbiomes [ 90 ], whereas brown bears with access to salmon host gut microbial communities that are distinguishable from populations limited to terrestrial food sources [ 85 ]. Given that marten consume a variety of prey across trophic levels, from terrestrial and aquatic environments and from both natural and anthropogenic sources, the gut microbiome of marten may be used to distinguish among animals consuming food items across a variety of sources and land covers with variable human influences.…”

Correlating gut microbial membership to brown bear health metrics

“…In congruence with the NVH, brown bears exhibit the ability to achieve similar body conditions across substantial range of among-individual dietary niche variation [7][8][9] . In a previous study, we characterized brown bear GMB bacterial community composition associated with location, season, and reproductive condition with taxa relative abundance 44 . We found that brown bear GMBs vary in membership and overall composition, complementary to the nutritional landscape of each location and that GMB composition presents similarly high levels of among-individual variation as diet.…”

Conservation Innovations and Future Directions for the Study of Rhinoceros Gut Microbiome

“…The study of the gut microbiome in wildlife elicits particular challenges. Interindividual variation may mask the effects of geographic location, diet, reproductive groups [91], or body condition [92], making it difficult to identify what constitutes a "typical" or core microbiome for a given host species, much less to detect statistically significant differences among populations [93]. Limited populations and low sample sizes inherent to endangered and elusive species further compound these issues.…”