Genetic influence on the composition of the ocular microbiome in preweaned beef calves

Infectious bovine keratoconjunctivitis (IBK), commonly known as bovine pinkeye, is a disease that infects the ocular surface and surrounding tissue which is a concern to animal health and welfare as well as producer economics. Vaccinations have been shown to have variable efficacy, while limited genetics studies using either ulcer scores or binary health phenotypes have suggested that direct genetic selection for resistance would be slow. Therefore, an investigation into the host genetic component of the ocular microbiome was conducted. Animals were genotyped using either a 50K or 100K commercial genotyping array. After filtering for common markers, there were 35,374 markers available for analysis. Ocular microbiome samples were taken on approximately 600 preweaned beef calves at four time points. From these, amplicon sequence variants (ASV) were extracted and taxonomy assigned using the V4 region of the 16S rRNA gene. Four metrics of alpha diversity (observed richness, Chao1 index, Simpson index, and Shannon index) and the log-transformed relative abundance (RA) of each ASV at each sampling time point were used as phenotypes in a univariate animal model. The observed richness and Chao1 index had heritability estimates of approximately 0.15 at sample times 1 and 3 with estimates of 0 at sample times 2 and 4. Conversely, the Simpson and Shannon indices had heritability estimates ranging from approximately 0.12 to 0.03 at sample times 1 and 4, with estimates near zero for sample times 2 and 3. The RAs of 59% of ocular bacterial community were influenced by host genetics at various sampling times. Estimates of heritability ranged from 0 to 0.60, depending on time and level of taxonomic classification. A small collection of microbes previously associated with IBK (specifically Moraxella bovis, Moraxella bovoculi, and Mycoplasma bovoculi) had moderate to high heritability estimates at multiple sampling time points. This indicates selection for reduced pathogen load is possible.