Characterization and manipulation of bacterial microbiomes in domestic animals

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Animals harbour complex, diverse and typically poorly defined microbial populations at various body sites. While poorly defined, it is clear that these populations (the microbiota) and the sum of their genetic elements and interactions (the microbiome) play critical roles in both development and prevention of various diseases, including disease not classically considered to be infectious. New technologies have revolutionized our understanding of the body's microbiomes, thereby creating unique opportunities for development and testing of novel and non-antimicrobial preventive and therapeutic methods for animals. The potential for safe and effective biotherapeutic (microbial-based) approaches for prevention or treatment of disease is highly appealing, particularly given the epidemic of antimicrobial resistance that is both limiting available treatment options and increasing scrutiny of antimicrobial use in animals. Yet, only with proper understanding of the host's 'normal' microbial population can biotherapeutic approaches be properly developed and evaluated. This program will characterize the microbiomes of different anatomical sites of selected domestic animal species, something that will provide important information to help understand how these populations develop and how they can be modified. It will complement preliminary microbiome studies being performed by the Applicant, and his laboratory's expertise in infectious diseases, gastroenterology and probiotic therapy. This program will use recent advances in next generation sequencing and bioinformatics to describe and compare selected microbiomes in piglets, foals and dogs, and to explore the use of biotherapeutic approaches to treatment or prevention of disease. Specific objectives of this program are to characterize development of the fecal microbiome of foals and piglets, to evaluate the effect of fecal transplantation on the development foal and piglet intestinal microbiomes, to evaluate different approaches to fecal transplantation, to characterize the vaginal microbiome of healthy dogs and dogs with recurrent urinary tract infections (UTIs) to enable development of a potential biotherapeutic approach for prevention of recurrent UTIs.