Evaluation of the bacterial ocular surface microbiome in clinically normal horses before and after treatment with topical neomycin-polymyxin-bacitracin

Next generation sequencing (NGS) studies have demonstrated a rich and diverse ocular surface-associated microbiota in people that was previously undetected by traditional culture-based methods. The ocular surface microbiome of horses has yet to be investigated using NGS techniques. This study aimed to determine the bacterial composition of the ocular surface microbiome in healthy horses, and to identify whether there are microbial community changes over time and following topical antibiotic use. One eye of 12 horses was treated 3 times daily for 1 week with neomycin-polymyxin-bacitracin ophthalmic ointment. Contralateral eyes served as untreated controls. The inferior conjunctival fornix of both eyes was sampled at baseline prior to initiating treatment (day 0), after 1 week of treatment (day 7), and 4 weeks after concluding treatment (day 35). Genomic DNA was extracted from ocular surface swabs and sequenced using primers that target the V4 region of bacterial 16S rRNA. At baseline, the most abundant phyla identified were Proteobacteria (46.1%), Firmicutes (24.6%), Actinobacteria (12.6%), and Bacteroidetes (11.2%). The most abundant families included Pasteurellaceae (13.7%), Sphingomonadaceae (7.9%), an unclassified Order of Cardiobacteriales (7.7%), and Moraxellaceae (4.8%). Alpha and beta diversity measurements were unchanged in both treatment and control eyes over time. Overall, the major bacterial taxa on the equine ocular surface remained stable over time and following topical antibiotic therapy.