Comparison of the red fox gut microbiota among different habitat types in southern Anatolia

Environmental conditions, especially diet, affect the diversity of gut microbiota (GM). This diversity within and between populations may influence the host’s health and fitness and, therefore, play an important role in adaptation. Regarding this, we collected fecal samples from natural, rural, suburban, and urban habitats to reveal the interaction between diet and compositional diversity of GM of a generalist carnivore, the red fox. The prokaryotic diversity of fecal microbiota was investigated by sequencing the 16S rRNA gene V3-V4 regions. A total of 46 archaeal and bacterial phyla were identified, with Bacillota being the most common phylum in most samples. The dominant genera in the GM of the red fox were Collinsella, Fusobacterium, Faecalibacterium, Escherichia-Shigella, and Blautia. Fusobacterium showed higher relative abundance in suburban (16.0%), natural (11.0%), and rural habitats (10.8%) compared to urban habitats (2.0%), indicating dietary differences of the red foxes that feed close to human settlements. Despite the observed differences in specific taxa, the overall microbial diversity remained relatively stable across the habitats. Our study determined the compositional changes of the GM of a wild animal for the first time in the Anatolian peninsula and revealed the effects of dietary changes, especially urbanization, on the diversity of GM of red foxes.