THE APPLICATION OF NEXT GENERATION SEQUENCING TO FURTHER UNDERSTAND THE MICROBIAL DYNAMICS OF BOVINE CLINICAL MASTITIS Erika Korzune Ganda, D.V.M., Ph. D. Cornell University 2017

Bovine mastitis is one of the greatest challenges faced by dairy farmers worldwide. In the United States, one in four cows experience at least one case of clinical mastitis throughout the lactation. This disease creates an enormous economic burden due to decreased milk production, treatment costs, and premature culling. Mastitis is also an important animal welfare issue. The main objective of the research carried out during this doctorate was to generate knowledge to better understand and offer directions for the proper treatment of bovine mastitis. This dissertation comprises four research articles that are organized into two components: The applied portion of this research aimed to evaluate a novel method for diagnosis of mastitis pathogens and its’s suitability for use in the field (chapter two). Next, we assessed the potential of trace mineral supplementation in helping animals with subclinical mastitis resolve the disease (chapter three). The basic component of these doctoral studies employed molecular techniques to further understand the dynamics of mastitis and antimicrobial treatment in naturally infected animals (chapter four) and experimentally infected animals (chapter five). A novel chromogenic method for identification of mastitis-associated pathogens is suitable for use under field conditions. The color-based and straightforward interpretation allows individuals with limited microbiology training to accurately diagnose the causative pathogen and provide basis for efficient selective antimicrobial therapy. Supplementation with trace minerals did not improve the overall cure of subclinical mastitis, nor decreased the overall incidence of clinical mastitis. However, we identified a tendency for improved subclinical mastitis cure in cows of third or greater lactation, and a decrease in the odds of having chronic clinical mastitis for primiparous cows. Longitudinal profiling of the milk microbiome revealed astonishing differences between healthy and mastitic milk. A significant reduction in microbial diversity was associated with disease in both naturally infected and experimentally challenged animals. Extended intramammary treatment with ceftiofur significantly decreased bacterial load, however such effect could only be observed during treatment administration. No differences on the microbial profile of mastitic or healthy milk due to antimicrobial treatment were observed. The capability of the milk microbiome to return to a healthy status in a relatively short period independent of intramammary antimicrobial therapy was observed consistently in both studies. The results observed here indicate that the milk harbors a resilient microbiome capable of restoring itself after mild and moderate cases of mastitis, independent of antimicrobial therapy.