PhD Defense by Juan P Barraza

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In partial fulfillment of the requirements for the degree of


Doctor of Philosophy in Biology

In the

School of Biological Sciences


Juan P Barraza


Will defend his dissertation


Quantitative characterization of microbial communities

micro-biogeography during infectious disease.


Wednesday September 22nd, 2021

1 PM




 Thesis Advisor:

Marvin Whiteley, Ph.D.

School of Biological Sciences

Georgia Institute of Technology


Committee Members:

Sam Brown, Ph.D.

School of Biological Sciences

Georgia Institute of Technology


Brian Hammer, Ph.D.

School of Biological Sciences

Georgia Institute of Technology


William Ratcliff, Ph.D.

School of Biological Sciences

Georgia Institute of Technology


Peter Yunker, Ph.D.

School of Physics

Georgia Institute of Technology



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. The spatial structure of communities of animals and plants has been thoroughly characterized, but that of microbial communities, which impact many aspects of life including human health, is  poorly understood. 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 S. gordonii and A. actinomycetemcomitans in a mouse abscess model. These two microbes co-exist in the oral cavity and abscesses, and exchange nutrients, including lactate, to grow more effectively. We collected images of these bacterial communities during infection and identified how interactions within microbial communities can 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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