Quantitative characterization of microbial communities micro-biogeography during infectious disease.

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Barraza Enciso, Juan
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Spatial structure, the arrangement of organisms in space, is an essential feature of life. It provides a mechanism for speciation, promotes niche development and shapes community function. Many methods exist to characterize the spatial structure of communities of animals and plants, but few exist for microbial communities, which impact many aspects of life, including human health. Interactions between microbes within a community during infection often result in increased tolerance to antibiotics and worse clinical outcomes. My thesis draws upon techniques from molecular biology, fluorescence microscopy, community ecology and computer science to build a framework to quantitatively characterize the spatial structure of microbial communities at the micron scale and aims to characterize bacterial interactions during infection and their impact on human health. Interactions can be broadly classified as competitive or cooperative, and I use two different infection models to explore each one. To observe the impact competitive interactions, I use a model community of P. aeruginosa and S. aureus in a mouse chronic wound infection model. These two microbes co-exist in many infections, but most of their characterized interactions involve growth inhibition and killing. To observe the impact of cooperative interactions, I use Streptococcus gordonii and Aggregatibacter actinomycetemcomitans in a mouse abscess model. These two microbes co-exist in the oral cavity and exchange nutrients, including lactate, to grow more effectively. By capturing images of these bacterial communities during infection and analyzing them, we identify how interactions within microbial communities impact the aggregation, abundance, and distribution in space of its members. Specifically, P. aeruginosa-secreted antimicrobial HQNO increases the number of planktonic cells in S. aureus and increases the micron-scale enrichment distance between these two microbes. We also show that lactate released by S. gordonii reduces the micron-scale enrichment distance between S. gordonii and A. actinomycetemcomitans. Overall, this works focused on developing tools for the exploration of micron-scale spatial structure and its impact on bacterial physiology during infection.
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