- This event has passed.
ChE PhD Dissertation Defense: Justin Hayes
March 11, 2026 @ 11:00 am - 1:30 pm
Name:
Justin Hayes
Title:
Leveraging Synthetic Biology and Gut-on-chip Systems to Interrogate and Modulate Intestinal H₂S
Date:
03/11/2026
Time:
11:00:00 AM
Committee Members:
Prof. Benjamin Woolston (Advisor)
Prof. Ryan Koppes (Advisor)
Prof. Abigail Koppes
Philip Strandwitz
Location:
Cabral Center
Abstract:
Hydrogen sulfide (H2S) is a gaseous and reactive molecule fundamental to human biology. The gut microbiota is a major producer of sulfide, yet our understanding of how it impacts intestinal diseases is poorly understood. Many studies are contradicting, some suggesting it drives diseases like inflammatory bowel disease (IBD) and colorectal cancer, while others suggest it has anti-inflammatory properties and can promote wound healing. Emerging research suggests its role in health is concentration dependent. Contributing to this confusion is the difficulty in controlling sulfide concentration in vitro and in vivo due to its gaseous and reactive nature. Thus, studying the molecule has been a bottleneck in understanding its fundamental role in human health and translating these findings as treatments. The goal of this thesis is to use engineered bacteria as systems for controlling sulfide concentration in intestinal environments. Metabolic engineering of bacteria offers a method for continuous and tunable production and degradation of sulfide in intestinal environments. These engineered bacteria hold promise as tools for investigating its dose-dependent roles in human health and for therapeutic uses.
Within the thesis, a panel of engineered bacteria was developed to titrate the level of H2S across the putative gut physiological concentration range. To do so, sulfur metabolism of Escherichia coli (E. coli) was engineered via gene knockouts, overexpression of putative L-cysteine desulfidases and transporters, and use of different strength promoters to drive gene expression. In an in vitro setting, these strains titrated H2S across a 53-fold range, spanning the putative gut concentration range. The work also contributed to the general knowledge of E. coli sulfide biology and the role of these desulfidases and transporters in its production.
These strains were used in human gut-on-chip systems to explore the concentration dependent impacts of H2S on human gut epithelial cell biology. The engineered bacteria titrated sulfide across a 16-fold range on chip, and the effects on gut permeability, metabolism, and gene expression were investigated. The data show the engineered bacteria are superior to sodium sulfide at maintaining specific H2S levels on chip, critical for studying the impacts on epithelial biology. Increasing sulfide levels significantly elevated gene expression associated with DNA damage and an increase in thiosulfate levels, and a non-significant trend towards higher gut permeability. Broadly, the platform represents a new method to investigate the fundamental role of volatile and reactive molecules on the gut environment.
Beyond in vitro studies, the thesis aimed to develop strains for functionality in vivo, which would enable exploring the impacts of sulfide in animals. The intestinal tract is a complex organ, with strong longitudinal differences in pH, metabolic environment, oxygen tension, microbiota abundance, secreted host factors, and more. Considering these variables in engineered strain design is critical. For design inspiration, human fecal microbiota communities were used to probe how the human gut microbiota degrade and produce sulfide. E. coli was engineered to produce and consume H2S under several complex in vitro environments, including in the presence of human fecal microbiota, under different oxygen tensions, and diverse nutrient environments.
The strains that successfully modified H2S in these in vitro screens were tested in vivo to demonstrate proof-of-concept data. The H2S-producing engineered bacteria successfully delivered and elevated H2S in the mouse upper gut. The engineered strain was superior to the gold-standard sulfide delivery molecule, GYY4137, at elevating intestinal levels. This highlights the value of this microbe as a tool for probing H2S hypotheses and as a translational tool for precise H2S delivery. The H2S-consuming strains were also tested in vivo but failed to demonstrate significant reductions in sulfide levels. Testing in ex vivo small intestinal extracts demonstrated significant sulfide reduction by the microbe, underscoring the challenges of creating in vivo models for H2S elevation and degradation.
Overall, the thesis represents several contributions to scientific knowledge and the development of new research tools. These include a deeper understanding of E. coli sulfur metabolism and the development of microbial tools as novel H2S delivery vehicles. Further, this thesis developed a gut-chip workflow for probing how gaseous molecules impact the gut, generated insights into human gut microbiota sulfide metabolism, and a general framework for designing and evaluating engineered bacteria destined for in vivo use.
After receiving a BS in chemical engineering and BA in Spanish from the University of Rhode Island, Justin Hayes, PhD’26, chemical engineering, began his PhD program at Northeastern in 2020 and is supported by a National Science Foundation Graduate Research Fellowship. He is advised by Ryan Koppes, associate professor of chemical engineering, and Benjamin Woolston, assistant professor of chemical engineering. Hayes’ research focuses on understanding how gut microbial metabolism impacts human health. Insights from his research are being leveraged to develop probiotic therapeutics and medical foods for individuals suffering from gastrointestinal disease.