Assessment of the fecal microbiome of healthy rabbits (Oryctolagus cuniculus domesticus) compared with rabbits with gastrointestinal disease using next-generation DNA sequencing.

OBJECTIVE

To determine the normal fecal microbiome of healthy rabbits in comparison to rabbits with gastrointestinal (GI) disease. Next-generation DNA sequencing was used to identify the primary bacteria and fungi in the microbiome.

METHODS

Fecal pellets from 25 clinically healthy rabbits and 25 rabbits experiencing GI disease were collected. Next-generation DNA sequencing was performed targeting the ITS-2 region for mycobiome, and the V1-V3 region of the 16S rRNA for bacteriome analysis. ITS-2 stands for internal transcribed spacer 2, a region of DNA in fungi that is used to identify and classify species.

RESULTS

In healthy rabbit feces, Bacteroidales sp, Odoribacter sp, Paraprevotella xylaniphila, Lachnospiraceae sp, Papillibacter sp, Akkermansia sp, and Ruminococcus sp were noted to be more prevalent. Comparatively, Lachnoclostridium sp, Anaerotruncus sp, Subdoligranulum sp, and B uniformis were found in greater abundance in rabbits with GI disease. Only 1 fungal species, Malassezia restricta, was significantly enriched in the GI disease group.

CONCLUSIONS

Next-generation DNA sequencing technology can be used to evaluate the microbiome of the rabbit GI tract through fecal material and can provide a clinically accessible testing method for veterinarians.

CLINICAL RELEVANCE

Numerous bacteria and fungi in the fecal samples of healthy rabbits were identified that could be considered markers of gastrointestinal health; similarly, specific bacteria and fungi were noted in greater abundance in rabbits with GI disease, which should be further investigated for their importance in causing, contributing to, or as the result of clinical disease. These findings support the use of next-generation DNA sequencing in order to diversify our understanding of the microbiome of rabbit feces, aid in clinical diagnosis, and provide support for the need for more specific probiotic supplements for rabbits.