Abstract With increased intensification of livestock production, the rate of disease susceptibility and emergence of pathogens has increased. Currently in the beef cattle industry, infectious bovine keratoconjunctivitis (IBK), is a problematic disease that is not well understood where vaccines have shown to have low efficacy. This is partly due to the lack of understanding of the ocular microbiome, where IBK disease progression may be a result of a polymicrobial disease due to certain bacterial and/or viral taxa predisposing the animal to infection. To understand the microbial ecology of IBK we used metagenomic shotgun sequencing to characterize the bovine ocular microbiome and virome. Infected and healthy beef calves were sampled before, during, and after IBK infection and shotgun metagenomic sequencing was performed to identify microbial changes during IBK infection. Preliminary data showed that we were able to identify 230 contigs consisting of bacteriophages such as Escherichia virus, Bacillus virus, Corynebacterium virus, and Mycoplasma virus. Out of the 230 bacteriophages, 213 of them are lytic phages. Additionally, preliminary data showed bacteria contigs such as Moraxella bovoculi, and Mycoplasma bovoculi Like IBK, the rate of disease emergence has increased in the last decade. As such, rapid in-field surveillance tools are greatly needed to monitor the emergence of known and unknown pathogens for early intervention. Current tools such as RT-PCR and enzyme linked immunosorbent assay (ELISA) require previous genomic knowledge to detect pathogens and are limited to the pathogen of interest. We have developed a long-read sequencing-based surveillance tool that eliminates the need of prior knowledge to detect both bacterial and viral pathogens simultaneously. The approach we developed can rapidly and accurately identify pathogens within clinical samples in as short as 12 h from sample collection to results. Here we present sequence-based microbiome studies and tools to help understand disease etiology and develop novel surveillance tools to improve food security within the livestock industry.