Microbiomes in Canidae

• Published in: Ecology and evolution Vol. 11; no. 24; pp. 18531 - 18539
• Main Authors: Biles, Tyler L., Beck, Harald, Masters, Brian S.
• Format: Journal Article
• Language: English
• Published: England John Wiley & Sons, Inc 01-12-2021; John Wiley and Sons Inc; Wiley
• Subjects: Anthropogenic factors; anthropogenic stress; Bacteria; Battlefields; Canidae; canids; Canis latrans; coyote; Coyotes; Cytochromes; Digestive system; Disturbances; DNA sequencing; Dysbacteriosis; dysbiosis; Enzymes; Foxes; Gastrointestinal tract; gut microbiome; Human impact; Human influences; Intestinal microflora; Land use; Microbiomes; Mitochondria; National parks; Parks & recreation areas; Physiology; Polymerase chain reaction; Range extension; red fox; rRNA 16S; Stress (physiology); Sympatric populations; Sympatry; Taxonomy; Vulpes vulpes; United States > US; California; red fox; canids; gut microbiome; anthropogenic stress; coyote; dysbiosis
• ISSN: 2045-7758; 2045-7758
• DOI: 10.1002/ece3.8449

Because of their range expansion across North America, coyotes (Canis latrans) now occur sympatrically with numerous other predator species, including red foxes (Vulpes vulpes). This raises several interesting ecological questions, including if and how sympatry affects the diet and gut microbiomes of coyotes and red foxes. We examined the gut microbiomes of sympatric populations of coyotes and red foxes within two different National Parks in Virginia, USA, that differ in land use, vegetation, and anthropogenic disturbance: Prince William Forest Park (PRWI) and Manassas National Battlefield Park (MANA). From 2012 to 2017, scat samples from PRWI and MANA were collected and analyzed. Polymerase chain reaction (PCR) amplification of a region of the mitochondrial cytochrome‐b gene followed by restriction enzyme digestion of the PCR product was used to determine the origin of each scat sample. Next‐Generation DNA sequencing of a hypervariable 16S rRNA gene region was used to determine gut microbiome information about the scat samples. There was no evidence for a difference between the gut microbiomes of red foxes in either location, or for a difference between the gut microbiomes of red foxes at either location and coyotes at the location with lower human disturbance, PRWI. However, the gut microbiomes of coyotes at the location with higher anthropogenic disturbances, MANA, revealed a marked change from those found in red foxes at either location and from those in coyotes at the location with lower disturbances. The gut microbiomes of coyotes subjected to greater human impact may provide evidence of dysbiosis, indicative of increased physiological stress and reduced health. We discuss our observations in the context of understanding anthropogenic impacts on coyote and red fox interactions. Our results suggest that physiological stress in the form of human disturbance may play an important role in the composition of the gut microbiome of coyotes, which can affect their overall health.
In this study, we examined the gut microbiomes of sympatric populations of coyotes (Canis latrans) and red foxes (Vulpes vulpes) from two US National Parks, each with a different level of human disturbance. We used Next‐Generation DNA sequencing of a hypervariable 16S rRNA gene region to determine the composition of the gut microbiome of coyotes and red foxes. Some of our findings indicated that while the gut microbiomes of red foxes did not differ between the two National Parks, it was distinct for coyotes between the two parks. Thus, we provide evidence that human disturbance could lead to dysbiosis, physiological stress, and reduced health in coyotes.