An altered microbiome in urban coyotes mediates relationships between anthropogenic diet and poor health

Abstract

Generalist species able to exploit anthropogenic food sources are becoming increasingly common in urban environments. Coyotes (Canis latrans) are one such urban generalist that now resides in cities across North America, where diseased or unhealthy coyotes are frequently reported in cases of human-wildlife conflict. Coyote health and fitness may be related to habitat use and diet via the gut microbiome, which has far-reaching effects on animal nutrition and physiology. In this study, we used stomach contents, stable isotope analysis, 16S rRNA gene amplicon sequencing, and measures of body condition to identify relationships among habitat use, diet, fecal microbiome composition, and health in urban and rural coyotes. Three distinct relationships emerged: (1) Urban coyotes consumed more anthropogenic food, which was associated with increased microbiome diversity, higher abundances of Streptococcus and Enterococcus, and poorer average body condition. (2) Conversely, rural coyotes harbored microbiomes rich in Fusobacteria, Sutterella, and Anaerobiospirillum, which were associated with protein-rich diets and improved body condition. (3) Diets rich in anthropogenic food were associated with increased abundances of Erysipelotrichiaceae, Lachnospiraceae, and Coriobacteriaceae, which correlated with larger spleens in urban coyotes. Urban coyotes also had an increased prevalence of the zoonotic parasite Echinococcus multilocularis, but there were no detectable connections between parasite infection and microbiome composition. Our results demonstrate how the consumption of carbohydrate-rich anthropogenic food by urban coyotes alters the microbiome to negatively affect body condition, with potential relationships to parasite susceptibility and conflict-prone behavior.

Host and geographic differences in prevalence and diversity of gastrointestinal helminths of foxes (Vulpes vulpes), coyotes (Canis latrans) and wolves (Canis lupus) in Québec, Canada

“…As a result, this could alter the risk of transmission of these wildlife reservoired parasites, all of which can transmit to dogs, and many to people ( Echinococcus , diphyllobothriid cestodes, Toxocara , Metorchis , and Alaria spp.) ( Manlick and Pauli, 2020 ; Sugden et al, 2020 ). Continued studies of host-parasite interaction and parasite distributions are needed to detect changes in parasite communities as a result of climate and landscape alterations.…”

“…Parasite communities in these hosts can serve as indicators of intact trophic relationships for indirectly transmitted parasites, one example being the important zoonotic cestodes of the genus Echinococcus . Urbanization impacts ecosystems, affecting the gut microbiota of generalist canid species following consumption of anthropogenic food, resulting in higher parasite susceptibility ( Sugden et al, 2020 ). Still, studies describing parasite diversity and prevalence in wild canids from the province of Québec are lacking ( Table 1 ).…”

Dietary niche breadth influences the effects of urbanization on the gut microbiota of sympatric rodents

“…No previous study has contrasted the response of the gut microbiota of multiple animal species within the same urban areas. (Fuirst et al, 2018;Littleford-Colquhoun et al, 2019;Murray et al, 2020;Phillips et al, 2018;Sugden et al, 2020;Teyssier et al, 2018Teyssier et al, , 2020. Not only does each animal species harbor their own unique gut microbiota (Kohl et al, 2018), interspecific differences in ecological traits effects their interaction with novel anthropogenic environments and their associated stressors, in turn affecting the gut microbiota.…”

“…One area of recent but rapidly growing interest is how urbanization affects the gut microbiota of wildlife (Fuirst et al, 2018;Littleford-Colquhoun et al, 2019;Murray et al, 2020;Phillips et al, 2018;Sugden et al, 2020;Teyssier et al, 2018Teyssier et al, , 2020. The gut microbial communities of animals play a pivotal role in development (Fraune & Bosch, 2010), nutritional uptake (Hooper et al, 2002), and general immune system function (Schluter et al, 2020).…”

“…A handful of recent studies have shown changes in the gut microbial communities of urban animals as compared to conspecifics in less urbanized environments, but the degree and directions were equivocal among host taxonomic groups and study area (Fuirst et al, 2018;Littleford-Colquhoun et al, 2019;Murray et al, 2020;Phillips et al, 2018;Sugden et al, 2020;Teyssier et al, 2018Teyssier et al, , 2020. Importantly, no study has compared the gut microbial communities between sympatric species with different dietary niches within the same urban environments.…”