The feline cutaneous and oral microbiota are influenced by breed and environment

Abstract

Previous research revealed the feline skin bacterial microbiota to be site-specific and the fungal microbiota to be individual-specific. The effect of other factors, such as genotype and environment, have not yet been studied in cats, but have been shown to be potentially important in shaping the cutaneous microbiota of other animals. Therefore, the objectives of this study were to evaluate the effect of these factors on the bacterial and fungal microbiota of feline skin and oral cavity. The influence of genotype was assessed through the analysis of different cat breeds, and the influence of environment through comparison of indoor and outdoor cats. DNA was extracted from skin and oral swabs, and bacterial and fungal next-generation sequencing were performed. Analysis of the skin microbiota of different cat breeds revealed significant differences in alpha diversity, with Sphynx and Bengal cats having the most diverse communities. Many taxa were found to be differentially abundant between cat breeds, including Veillonellaceae and Malassezia spp. Outdoor environment exposure had considerable influence on beta diversity, especially in the oral cavity, and resulted in numerous differentially abundant taxa. Our findings indicate that the oral bacterial microbiota and both fungal and bacterial microbiota of feline skin are influenced by breed, and to a lesser degree, environment.

Fig 1. Comparing alpha diversity as measured by the Shannon diversity index between cat breeds and indoor and outdoor cats.

Comparing alpha diversity of (a) bacterial communities between cat breeds (p<0.0001), (b) bacterial communities between indoor and outdoor cats (p = 0.2509), (c) fungal communities between cat breeds (p<0.0001), and (d) fungal communities between indoor and outdoor cats (p = 0.8340) using the Shannon diversity metric. Lines show significant pairwise tests where p<0.01. Sample sizes (bacterial sequencing, fungal sequencing): Bengal (54, 54), Cornish Rex (45, 45), Devon Rex(19, 19), Domestic/Indoor (55, 59), Siberian (29, 30), Sphynx (70, 69), and Outdoor (60, 58).

Fig 2. Principle coordinate analysis (PCoA) plots of beta diversity distance matrices comparing different cat breeds and indoor and outdoor cats.

Comparing beta diversity of (a) bacterial communities on the dorsum between cat breeds with the weighted UniFrac metric, (b) fungal communities on the dorsum between cat breeds with the Bray-Curtis metric, (c) bacterial communities in the oral cavity between indoor and outdoor cats with the Bray-Curtis metric, and (d) bacterial communities in the oral cavity between indoor and outdoor cats with the weighted UniFrac metric. R and p-values are from analysis of similarities (ANOSIM) test of beta diversity distance matrices.

Fig 3. Average relative abundance of bacterial taxa.

The average relative abundance of bacterial taxa across the different cat breeds and outdoor cats including all body sites and separated by body site.

Fig 4. Bacteria found to be differentially abundant between indoor and outdoor cats as determined by LEfSe.

When comparing all body sites, many taxa were identified as differentially abundant between indoor and outdoor cats.

Fig 5. Average relative abundance of fungal taxa.

The average relative abundance of fungal taxa across the different cat breeds and outdoor cats including all body sites and separated by body site.