Characterization and manipulation of bacterial microbiomes in domestic animals

动物在不同的身体部位藏匿着复杂的、多样化的、通常定义不清的微生物种群。虽然定义不明确，但很明显，这些种群(微生物区系)及其遗传要素和相互作用的总和(微生物组)在各种疾病的发展和预防中发挥着关键作用，包括传统上认为不具有传染性的疾病。新技术彻底改变了我们对人体微生物群的理解，从而为开发和测试动物的新型和非抗菌预防和治疗方法创造了独特的机会。安全有效的生物治疗(基于微生物的)方法预防或治疗疾病的潜力非常有吸引力，特别是考虑到抗菌素耐药性的流行限制了现有的治疗选择，并对动物使用抗菌剂进行了日益严格的审查。然而，只有正确地了解宿主的“正常”微生物种群，才能适当地开发和评估生物治疗方法。 该计划将描述选定家畜物种不同解剖部位的微生物群，这将提供重要信息，帮助了解这些种群是如何发展以及如何修改它们的。它将补充申请人正在进行的初步微生物组研究，以及他的实验室在传染病、胃肠学和益生菌治疗方面的专业知识。 该计划将使用下一代测序和生物信息学的最新进展来描述和比较选定的小猪、马驹和狗的微生物群，并探索使用生物治疗方法来治疗或预防疾病。该计划的具体目标是描述马驹和仔猪粪便微生物群的发育，评估粪便移植对马驹和仔猪肠道微生物群发育的影响，评估粪便移植的不同方法，描述健康狗和反复尿路感染(UTIs)犬的阴道微生物群，以开发潜在的生物治疗方法来预防复发UTIs。

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.