Probing gut bacterial physiology and antibiotic action in complex environments
Abstract/Contents
- Abstract
- For decades, research on bacterial physiology has been conducted in standardized conditions in monocultures, ignoring the natural community context of most species. As a result, predicting the effect of perturbations such as antibiotics on gut microbial communities remains highly challenging despite its paramount importance. Mechanistic understanding of human gut microbiota ecology has also been hampered by limited throughput and the fact that key parameters often cannot be precisely tuned or measured in animal models. During this PhD, I developed tools and systems to interrogate bacterial physiology in complex communities and within animal hosts, and used these tools to make seminal discoveries regarding how life in a community alters the behaviors of individuals. The gut microbiota of the laboratory fruit fly is a low diversity consortium with 5 bacterial species from the Lactobacillus and Acetobacter genera, all of which can be cultured in vitro. I leveraged the simplicity and manipulability of this microbiota to study the role of metabolic cross feeding on growth and antibiotic action. Using in vitro synthetic communities composed of Lactobacillus and Acetobacter species, I discovered non-canonical tolerance to rifampin and erythromycin that is induced by interspecies interactions and mediated by changes in pH due to metabolic cross-feeding. Additionally, I developed imaging techniques to visualize individual bacterial cells within live fruit flies, opening the door to studying single-cell bacterial physiology within intact hosts. To enable quantitative, systematic experimentation on the human gut microbiota, I developed culturing techniques to directly compare responses in vitro and in humanized mice. I compared the sensitivity of gut commensals in vitro and in humanized mice to explore the role of heterogeneous environments and community composition in antibiotic action. I then cultured hundreds of communities that resemble the human gut microbiota using fecal samples as inocula for high-throughput liquid culturing. In vitro antibiotic treatment of these communities recapitulated changes observed in vivo in mice, and uncovered different modes of recovery, highlighting the capabilities of this methodology. .
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2021; ©2021 |
| Publication date | 2021; 2021 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Aranda-Díaz, Andrés Jesus |
|---|---|
| Degree supervisor | Huang, Kerwyn Casey, 1979- |
| Thesis advisor | Huang, Kerwyn Casey, 1979- |
| Thesis advisor | Fischbach, Michael |
| Thesis advisor | Monack, Denise M |
| Thesis advisor | Sonnenburg, Justin, 1973- |
| Degree committee member | Fischbach, Michael |
| Degree committee member | Monack, Denise M |
| Degree committee member | Sonnenburg, Justin, 1973- |
| Associated with | Stanford University, Department of Bioengineering |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Andrés Aranda-Díaz. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2021. |
| Location | https://purl.stanford.edu/tx547gq0625 |
Access conditions
- Copyright
- © 2021 by Andres Jesus Aranda Diaz
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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