Skin and Gut Microbiome Features Associated with Resistance to Corynebacterium bovis-Associated Disease in Nude Mice (Mus musculus)

Corynebacterium bovis is an important opportunistic pathogen of immunodeficient mice and the etiologic agent of Corynebacterium-associated hyperkeratosis (CAH). Although disease severity varies, specific vendor-derived microbiomes have been shown to protect against CAH. Preinoculation with nonpathogenic Corynebacterium amycolatum prior to C. bovis infection has been demonstrated to limit disease severity. To define community features associated with protection, axenic outbred athymic nude mice stocks (A, B, and C) were reassociated with donor microbiomes from four vendor sources (A1, A2, B, and C) and topically challenged with C. bovis. C. amycolatum was added to the A1 microbiome in a separate group. Skin (Stock A) and fecal (Stocks A, B, and C) microbiomes were evaluated at 21 days post-inoculation via shotgun metagenomic sequencing. The A2 microbiome, previously associated with resistance to clinical disease and minimal skin pathology, exhibited greater cutaneous microbial evenness after challenge and significantly lower relative abundance of C. bovis than all other microbiome groups. Addition of C. amycolatum to the A1 microbiome did not fully confer disease protection and relative abundance was low, suggesting that sustained colonization by this organism was insufficient to explain the protective phenotype seen with the A2 microbiome. C. kroppenstedtii was detected in all A2 skin samples and was absent from all other groups. Several anaerobic taxa, including Duncaniella dubosii, D. muris, Bacteroides caecimuris, and Muribaculum gordoncarteri, were uniquely detected or enriched in the A2-associated microbiome, whereas Mammaliicoccus lentus and Staphylococcus nepalensis were absent from A2 but present in all nonprotective groups. Gut alpha diversity did not differ significantly among microbiomes, although several taxa, including segmented filamentous bacteria, were enriched in A2 feces. These findings associate resistance to CAH with preservation of cutaneous community structure, suppression of C. bovis prominence, and distinct microbial taxa. The identified organisms represent candidates for future mechanistic studies of microbiome-mediated colonization resistance.