Seasonal dynamics in the mammalian microbiome between disparate environments

Host-associated bacterial microbiomes can facilitate host acclimation to seasonal environmental change and are hypothesized to help hosts cope with recent anthropogenic environmental perturbations (e.g., landscape modification). However, it is unclear how recurrent and recent forms of environmental change interact to shape variation in the microbiome. The majority of wildlife microbiome research occurs within a single seasonal context. Meanwhile, the few studies of seasonal variation in the microbiome often restrict focus to a single environmental context. By sampling urban and exurban eastern grey squirrel populations in the spring, summer, autumn, and winter, we explored whether seasonal rhythms in the grey squirrel gut microbiome differed across environments using a 16S amplicon sequencing approach. Differences in the microbiome between urban and exurban squirrels persisted across most of the year, which we hypothesize is linked to anthropogenic food consumption; but we also observed..., Sampling Protocol Adult eastern grey squirrels were trapped from 2016–2018 (Animal Utilization Protocol no. 3506, Wildlife Scientific Collectors Authorization no. 1087323). The main campus of the University of Guelph (43°31052.3300 N, 80°13036.8000 W, Guelph, Ontario, Canada) was used as our urban site, while the deciduous forests of the ‘rare Charitable Research Reserve’ (43°22052.1700 N, 80°20052.4600 W, Cambridge, Ontario, Canada) served as our exurban site. Initial site selection involved qualitative assessments sites (e.g., prominence old growth forest versus human-built impervious surfaces, presence of refuse bins, human foot-traffic); however, post hoc quantification of normalized difference vegetation index (NDVI) and normalized difference built-up index (NDBI) estimates (surrounding locations of sample collection) demonstrate clear differences in both the amount of vegetated area (NDVIexurban = 0.426 ± 0.074; NDVIurban = 0.267 ± 0.081) and the footprint of human-built construc..., , # Seasonal dynamics in the mammalian microbiome between disparate environments This README was generated on 2023-11-03 by Mason Stothart GENERAL INFORMATION 1. Title of Dataset: Grey squirrel feces 16S rRNA gene amplicon Meta-Data and R script 2. Author Information A. Principal Investigator Contact Information Name: Amy E.M. Newman Institution: University of Guelph Address: 474-570 Gordon St, Guelph, ON N1G 1Y2 Email: [[e-mail]](mailto:[e-mail]) B. Associate or Co-investigator Contact Information Name: Mason Stothart Institution: University of Calgary Address: 3280 Hospital Drive NW Calgary Email: [[e-mail]](mailto:[e-mail]) 3. Date of data collection (single date, range, approximate date): 2016-05-01 - 2018-03-01 4. Geographic location of data collection : Guelph Ontario, Canada & rare Charitable Research Reserve Cambridge, Canada 5. Information about funding sources that s...