Traditional microbiology requires days or weeks to determine the pathogen and its antibiotic susceptibilities. Thus, an opportunity exists to develop rapid diagnostic tests to facilitate informed decision making by veterinarians and cattle producers. A critical gap to make this possible is to be able to predict which antibiotic will be effective in a particular patient. This will require rapid determination of the pathogen and its associated susceptibility profile. Genetic determinants of antibiotic resistance in some species have not been effective in predicting antibiotic susceptibility. We are utilizing comparative genomics to determine the best determinants of antimicrobial resistance in animal pathogens.

Gut microbes are crucial to the regulation of animal health and performance. Healthy and balanced gut microbial community would improve the performance of production animals, such as greater feed efficiency, lower diarrhea rate, greater marketing weight, etc. Greater growth performance is critical in increasing profits and animal welfare while reducing the environmental impact in animal husbandry. To our knowledge, environment and host genotype shape the gut microbiome collectively while the influence of genotype declines as time passed. Thus, we hope to find a robust and stable gut microbiome which associated with greater animal performance under the artificial simulation of natural selection.

Bovine respiratory disease (BRD) is ongoing health and economic issue in the dairy and beef cattle industry. Multiple risk factors make an animal susceptible to BRD and its diagnosis and treatment are a challenge for producers. The species Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis have been associated with BRD mortalities. We aim to characterize the cattle nasal microbiome as a potential additional diagnostic method to identify BRD-affected animals and to develop strategies to prevent the development of BRD.

The microbiome may aid in keeping animals pathogen free. The microbiome may act directly on pathogens to inhibit their growth or to occupy its niche in the host. The microbiome also might trigger the host to inhibit the pathogen. Following the lead of research in humans, probiotics (Clostridium scindens) and fecal transplantation have proven efficient in eliminating Clostridium difficile. In similar fashion, it seems feasible to decrease colonization of animal pathogens by means of competitive exclusion. The success of microbiome approaches will depend on our ability to be able to efficiently colonize the animal intestinal tract and to direct the composition of this complex community.