Characterization of nasal cavity microbiome from healthy rabbits (Oryctolagus cuniculus domesticus) using next-generation DNA sequencing and geographically specific bacterial and fungal differences

Abstract

Background

Upper respiratory infections in rabbits (Oryctolagus cuniculus domesticus) present common yet challenging cases for veterinary practitioners. While conventional cultures may only grow a small percentage of microbes, next-generation DNA sequencing (NGS) can be more effective at revealing fastidious or novel organisms. This study aimed to characterize the rabbit nasal cavity microbiome and determine potential geographical differences.

Animals

Clinically healthy pet rabbits from California (CA, n = 25) and Alabama (AL, n = 24), United States.

Methods

Samples were collected via standard protocol of swabbing both nasal cavities. The bacterial and fungal microbiomes were profiled using NGS, targeting the 16S rRNA V1 to V3 region for bacteria and ITS-2 for fungi.

Results

In total, 186 bacterial taxa were detected, 9 representing at least 1% of the microbiome. In each sample, a mean of 37.5 ± standard deviation (SD) of 18 bacterial taxa were detected (mean 36.79 ± SD 19.8 in the AL group, and a mean of 38.20 ± and SD of 17.1 in the CA group). The most abundant bacterial taxa were species within the Pseudomonadales order (mean 12.7% ± SD 17), Moraxella cuniculi (mean 11.9% ± SD 18), and Neisseriaceae sp. (mean 8.5% ± SD 9). Although rabbits were considered healthy, a species within the Mycoplasma genus was detected in 37 out of 49 samples (mean 4.7% ± SD 9). The Helicobacter genus (mean 3.7% ± SD 5.5) and the Campylobacteraceae order (mean 2.84% ± SD 6.1) were also present. The fungal mycobiome was more diverse than the bacteriome, with the most abundant fungal taxa being a species within the Cladosporium genus (mean 38.1% ± SD 25), followed by a species within the Alternaria genus (mean 5.5% ± SD 8), a species within the Pleosporales order (mean 3.8% ± SD 10), Alternaria infectoria-rosae (mean 3.72% ± SD 6.8), Vishniacozyma victoriae (mean 2.93% ± SD 4.4), and a species within the Microascus (Scopularipsis) genus (mean 1.02% ± SD 5.1). Twenty-three fungal taxa were more abundant in the CA group, and 3 species were more common in the AL group.

Clinical Relevance

Findings from this study establish the healthy rabbit nasal cavity microbiome and mycobiome using NGS for veterinary professionals to use a comparison for rabbits with upper respiratory signs.