Modulating the microbiota : engineering tools for the abundant gut commensal genus, bacteroides
Abstract/Contents
- Abstract
- The gut microbiota is a unique ecosystem, hallmarked by the extreme density of microbes coexisting and competing for nutrients. This microbial organ plays an important role in human health, influencing host functions as diverse as metabolism, the immune system, and the brain. Given its extensive interaction with the host and its natural position as a malleable portion of the host's genetic makeup, the gut microbiota is an ideal place for the deployment of engineered cell-based therapeutics. There are many hurdles associated with engineering gut bacteria for therapeutic purposes, and the work described herein centers on solutions to some of those problems. As a foundation, we focus on the Bacteroides genus for tool development given the abundance of these organisms in the average American gut, as well as their highly evolved, gut-specific sense and response systems. First, we describe the discovery of a strong, constitutive promoter that functions across the Bacteroides genus. We characterize this promoter at the nucleic acid level, and develop a set of reliable, predictable, and generalizable promoters for gene expression in the Bacteroides. We use this set of promoters to discover new biogeographical information about crypt occupancy in the distal gut, and posit usefulness of this promoter set in engineering therapeutic Bacteroides. Second, we discuss the development of a system that enables reliable integration and population control of an exogenous Bacteroides strain into a pre-existing microbiota. This tool relies on administration of a privileged nutrient source to the strain of interest, and demonstrates the dominant role of nutrient access to establish a population in the gut. The ability to integrate and control a strain of interest across diverse microbiotas will be critical to success of engineered therapeutic cells in people, and this system sets the stage for this strategy. Third, we describe the development of a system to secrete protein cargo of interest from members of the Bacteroides genus. We discover a novel secreted protein in Bacteroides thetaiotaomicron, and develop a method to secrete peptide cargo that is released from the carrier protein upon exposure to gut proteases. The ability to secrete proteins of interest will be an important tool for designing iv cell-based therapeutics that interact with host receptor proteins, or with other bacterial cells in the gut, and the work here presents one solution. In sum, this work puts forth a toolbox for designing and engineering Bacteroides cells. These tools can be utilized both to investigate and discover new biology in the gut microbiota, and can also be applied to making cell-based therapies, an important new direction in medicine.
Description
| Type of resource | text |
|---|---|
| Form | electronic; electronic resource; remote |
| Extent | 1 online resource. |
| Publication date | 2017 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Associated with | Stanley, Elizabeth Joy |
|---|---|
| Associated with | Stanford University, Department of Microbiology and Immunology. |
| Primary advisor | Sonnenburg, Justin, 1973- |
| Thesis advisor | Sonnenburg, Justin, 1973- |
| Thesis advisor | Endy, Andrew D |
| Thesis advisor | Huang, Kerwyn Casey, 1979- |
| Thesis advisor | Relman, David A |
| Advisor | Endy, Andrew D |
| Advisor | Huang, Kerwyn Casey, 1979- |
| Advisor | Relman, David A |
Subjects
| Genre | Theses |
|---|
Bibliographic information
| Statement of responsibility | Elizabeth Joy Stanley. |
|---|---|
| Note | Submitted to the Department of Microbiology and Immunology. |
| Thesis | Thesis (Ph.D.)--Stanford University, 2017. |
| Location | electronic resource |
Access conditions
- Copyright
- © 2017 by Elizabeth Joy Stanley
- License
- This work is licensed under a Creative Commons Attribution Non Commercial 3.0 Unported license (CC BY-NC).
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