Graduate Thesis Or Dissertation


Structure and Dynamics of the Canine (Canis familiaris) Nasal Microbiome Public Deposited

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  • The diverse community of bacteria living within and on host organisms, known as the microbiome, has an important role in maintaining host health. Dysbiosis, known as a change in the healthy community of the microbiome, has been associated with a number of diseases across host organisms and body sites including asthma, pneumonia, gastrointestinal disorders, obesity, and depression. Because of the close connection with host health, understanding what processes are driving the structure of the healthy microbiome and how the microbial community changes with disease and environmental perturbations are crucial in agricultural, medical, and potentially conservation applications. From the perspective of the microbiome these applications represent potential ecosystem services and understanding what drives them encapsulates enduring questions in ecology, concerning ecosystem stability and species coexistence — the processes that underpin biodiversity over space and time and in response to perturbations and (anthropogenic) change. In my research I explore a novel field system for addressing these questions consisting of the nasal microbiomes of canines (Canis familiaris) living within the Oregon Humane Society. The overall goal is to elucidate the processes driving the structure of the nasal microbiome during health and disease, and to understand how host demography and pathogen dynamics may influence diversity and stability of microbiomes. In this dissertation I explore several mechanisms that may influence the canine nasal microbiome diversity within and among hosts, including: infection with respiratory pathogens; host demographic variables such as age; host contact patterns such as whether dogs were housed in the same kennel or area of the shelter; and microbe-microbe interactions, including co-occurrence that may represent commensalism or mutualism, and negatively associated taxa possibly representing competition or competitive exclusion. First, I characterize the differences between the healthy microbiome and the microbiome of dogs experiencing respiratory disease as well as the pathogen community in both healthy and sick dogs. Then I explore differences between hosts that explain community variation based on host demographics combined with community assembly theory (defined as the process by which species colonize and interact to form local communities) to understand how the healthy microbiome changes throughout an organism’s life both long-term (comparing young and adult canines) and short term (via contact with other hosts). Finally, I use network analysis methods to understand how microbial interactions could structure the microbiome and identify co-occurrence patterns and influential taxa whose removal or change in abundance may have consequences on the rest of the microbiome. This research helps provide a better understanding of how the microbiome is formed throughout the lives of the host and how it changes as a result of the environment, invading pathogens, and the host itself. Understanding how the healthy microbiome is structured and maintained during health and disease is crucial as we continue to seek treatments that may involve manipulating the microbiome for complex diseases, such as those affecting the respiratory tract of animals.
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