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Spatial variation in diet-microbe associations across populations of a generalist North American carnivore


Colborn, A. Shawn; Kuntze, Corbin C.; Gadsden, Gabriel I.; Harris, Nyeema C. (2020), Spatial variation in diet-microbe associations across populations of a generalist North American carnivore, Dryad, Dataset,


1. Generalist species, by definition, exhibit variation in niche attributes that promote survival in changing environments. Increasingly, phenotypes previously associated with a species, particularly those with wide or expanding ranges, are dissolving and compelling greater emphasis on population-level characteristics. 2. In the present study, we assessed spatial variation in diet characteristics, gut microbiome, and the association between these two ecological traits across populations of coyotes (Canis latrans). We highlight the influence of the carnivore community in shaping these relationships, as the coyote varied from being an apex predator to a subordinate, mesopredator across sampled populations. 3. We implemented a scat survey across three distinct coyote populations in Michigan, USA. We used carbon (δ13C) and nitrogen (δ15N) isotopic values to reflect consumption patterns and trophic level, respectively. Corresponding samples were also paired with 16S rRNA sequencing to describe the microbial community and correlate with isotopic values. 4. Though consumption patterns were comparable, we found spatial variation in trophic level among coyote populations. Specifically, δ15N was highest where coyotes were the apex predator and lowest where coyotes co-occurred with gray wolves (Canis lupus). 5. The gut microbial community exhibited marked spatial variation across populations with the lowest OTU diversity found where coyotes occurred at their lowest trophic level. Bacteriodes and Fusobacterium dominated the microbiome and were positively correlated across all populations. We found no correlation between δ13C and microbial community attributes. However, positive associations between δ15N and specific microbial genera increased as coyotes ascended trophic levels. 6. Coyotes provide a model for exploring implications of niche plasticity because they are a highly adaptable, wide-ranging omnivore. As coyotes continue to vary in trophic position and expand their geographic range, we might expect increased divergence within their microbial community, changes in physiology, and alterations in behavior. 05-May-2020


We conducted systematic scat surveys from May-August 2016, collecting all carnivore feces found across our three study areas. Surveys occurred monthly for 7-10 days, utilizing hiking paths and wildlife trails, and usually included all available habitat types within the study area. We made concerted efforts during fieldwork to collect mostly “fresh” scat and collected from interior region to reduce contamination with collection tools cleaned with ethanol between samples. Opportunistic findings by other researchers, volunteers, and park rangers presumed to be carnivore were also included. Samples were stored in two of three liquid preservation solutions: DET, RNAlater or EtOH in 10ml sterile plastic vials as well as dry in sterile bags. However, nearly 3/4 of samples used for analysis were preserved in EtOH. All samples were stored at -20°C upon returning from the field until processed. Wet samples were used for molecular host confirmation and microbial community analysis while dry samples were processed for stable isotope analysis.