Date of Award

Spring 5-15-2023

Author's School

McKelvey School of Engineering

Author's Department

Energy, Environmental & Chemical Engineering

Degree Name

Doctor of Philosophy (PhD)

Degree Type



The gut microbiome is increasingly understood to play a key role in human health. Commensal gut microbes influence immunity, pathogen colonization, digestion, and brain chemistry, to name a few impacts on host physiology. As such, efforts to diagnose and treat diseases through manipulation of the microbiome are becoming more commonplace. To date, these efforts revolve around introducing defined native consortia or a single engineered strain. Engineered strains, compared to consortia, offer the advantages of known mechanisms of action, more predictable pharmacokinetics and pharmacodynamics, and easier manufacturing, among others. Safe and effective engineered strains should sense and respond to the gut environment and/or disease state, robustly maintain their engineered function while transiting the gut, and not horizontally transfer any engineered genes. While current efforts have begun to address these issues, more biosensors responsive to the gut environment are needed, as are simpler methods to stably maintain newly endowed genetic functions. To address these challenges, this dissertation describes the development of 1) a computational method to understand and engineer a protein transcription factor to specifically respond to different neuroactive aromatic molecules found in the gut, 2) the experimental and mathematical characterization of a transcription factor sensitive to extracellular propionate, a common short-chain fatty acid found in the large intestine, and 3) an antibiotic resistance gene-free plasmid selection and maintenance system that enables long-term plasmid maintenance in uncontrolled environments and cannot be a vector for the spread of antibiotic resistance. Together, these tools will enable bioengineers to develop smarter and more robust engineered bacteria for the treatment and diagnosis of diseases.


English (en)


Yinjie Tang

Committee Members

Gautam Dantas, Rafaelo Galvao, Joshua Yuan, Fuzhong Zhang,

Available for download on Thursday, June 06, 2024