Research Thrust 2
Targeted delivery methods
Projects in Research Thrust 2 (RT2), the “Modification” thrust, build and adapt the tools needed for engineering the microbiomes in the built environment as well as enabling functional modulation in a established microbial communities. Projects follow a tiered approach of physical and chemical modifications of the built environment at the first tier, followed by introduction of beneficial microbes, and finally developing synthetic biology methods for the targeted removal of unwanted organisms or traits.
Currently funded projects
Microbiome engineering: Physico-chemical treatments
The first tier of microbiome engineering projects examines physical and chemical properties of built environment systems and their impacts on the composition and traits of the resulting microbial communities. Lines of research within this project include the examination of common materials used in systems such as building plumbing, chemical cleaning regimes, and their impacts on the colonization and proliferation of microbes such as pathogenic ESKAPEE bacteria. Another aspect of this project looks at how the differences in the structures of engineered nanomaterials may be effective in preventing microbial colonization, while also examining the impacts of exposure of those materials on evolving microbial resistance over relevant time frames.
Misty Thomas
N.C. A&T
Project Lead
Joseph Graves, Jr.
N.C. A&T
Project Co-Lead
A-Andrew Jones
Duke
Jenora Waterman
N.C. A&T
Mark Wiesner
Duke
Microbiome engineering: Probiotic inoculants
Projects in this second tier of built environment intervention develop approaches for delivering stable commensal microbial cocktails to exclude unwanted organisms in built environment systems such as ESKAPEE pathogens. Although these approaches are more sophisticated in terms of microbiome engineering compared to those utilized in the “Physico-chemical treatments” project described above, the solutions developed in this project still maintain a relatively low barrier for implementation in healthcare settings because they rely on non-engineered microbes. Furthermore, many of these approaches in this project adapt existing therapeutic technologies to novel applications in other domains. Researchers in this project strongly integrate with PreMiEr’s Societal and Ethical Implications (SEI) Core and Innovation Ecosystem (IE) to consider the regulatory framework that may hinder translation.
Ophelia Venturelli
Duke
Project Lead
Claudia Gunsch
Duke
Lingchong You
Duke
Microbiome engineering: Synthetic biology
Research approaches in this third tier of engineering solutions to the healthcare built environment use case develop whole microbiome solutions for the targeted delivery of genetic material and the interruption of naturally occurring horizontal gene transfer of antibiotic resistance plasmids. Although these projects are the most avant-garde, they face the highest implementation barriers. Specific approaches include: a) engineering synthetic phage for selectively eliminating bacteria from the built environment microbiome and/or modulating their function, b) developing chemical and genetic tools to enable targeted suppression or elimination of plasmids harboring resistance genes, and c) engineering solutions for biocontainment and promotion of safe deployment of genetically engineered microbes through sensors that enable engineered microbes to perform self-killing or destruction of engineered DNA upon exit from their intended environment.
Nathan Crook
NC State
Project Lead
Robert Newman
N.C. A&T
John Rawls
Duke
Yi-Hui Zhou
NC State
Microbiome engineering: Residential built environments
Bacteriophage and mycoviruses selectively target bacteria and fungi, respectively. Though these microbial viruses have long been proposed for controlling pathogens relevant to human health, they have not been extensively applied to modulate microbiomes in the built environment. This project will target residential built environments to isolate relevant fungi and their associated mycoviruses and apply genetic engineering approaches to generate virus-infected isogenic strains to target fungal populations. Tools developed in this project may also be applied to healthcare settings, including bacteriophage that respond to quorum sensing (QS) signals used by ESKAPEE pathogens.
Jeseth Delgado Vela
Duke
Project Lead
Nicole Rockey
Duke
Project Co-Lead
Kevin Garcia
NC State
Robert Newman
N.C. A&T
Previously Funded Projects
Developing engineering tools for plumbing-associated microbes
Status: Currently part of PreMiEr core project “Microbiome Engineering: Synthetic Biology” effective September 1, 2024
Faculty: Nathan Crook (NCSU, lead), Kevin Garcia (NCSU), Claudia Gunsch (Duke), Jennifer Kuzma (NCSU), Robert Newman (NCAT), Lingchong You (Duke), Yi-Hui Zhou (NCSU)
Description: This project develops plasmid and phage systems for the genetic manipulation of microbes in the built environment. These tools will allow 1) upregulation/downregulation/knockout of individual genes within built environment microbes, and 2) delivery of genetic material to specific microbes in situ, paving the way for functional studies. As a representative and important “built environment” habitat, this project is focusing on premise plumbing, including sinks, drains, and toilets.
Evaluation of biopolymeric microcapsules for the delivery of targeted microbes in premise plumbing systems
Status: Currently part of PreMiEr core project “Microbiome Engineering: Probiotic Inoculants” effective September 1, 2024
Faculty: Claudia Gunsch (Duke), Deverick Anderson (Duke), Sandra Clinton (CHAR), Lawrence David (Duke), Liesl Jeffers-Francis (NCAT), Joshua Granek (Duke), A-Andrew Jones (Duke), Lingchong You (Duke)
Description: Traditionally, waterborne disease outbreaks have been prevented through centralized water treatment in utility water treatment plants. However, several CDC studies have shown that a significant number of waterborne disease outbreaks result from opportunistic pathogens that reside in premise plumbing environments as opposed to those associated with either water treatment plants or water supplies. This project will identify and characterize opportunistic pathogens in hospital and home premise plumbing systems. The project also considers how the environment as well as an individual’s oral and skin microbiome may contribute to the development of premise plumbing biofilms and investigates potential exposure pathways.
Linking physical and chemical properties of premise plumbing and microbial biofilms
Status: Some aspects currently part of PreMiEr core project “Microbiome Engineering: Physico-Chemical Treatments” effective September 1, 2024
Faculty: Sandra Clinton (CHAR), Claudia Gunsch (Duke), Jacelyn Rice-Boayue (NCSU), Mark Wiesner (Duke)
Description: Premise plumbing comprises the complete hot and cold water systems in a building and includes everything from the hot water heater and HVAC to the showers, faucets, sinks, and toilets. These systems are composed of a variety of materials (e.g. copper, PVC, PEX) that result in an environment that varies both temporally and spatially in its physical and chemical properties. This project collects fine scale data on the materials commonly used in premise plumbing and uses it to create a set of known substrates of varying properties that can be used to grow and characterize biofilms under varying environmental conditions.
Identifying determinants of microbial fitness in the built environment
Status: Currently part of PreMiEr core project “Microbiome Engineering: Synthetic Biology” effective September 1, 2024
Faculty: John Rawls (Duke), Joe Brown (UNCCH), Nathan Crook (NCSU), Glenn Morrison (UNCCH), Barbara Turpin (UNCCH), Lingchong You (Duke)
Description: A fundamental challenge in microbiome science is to understand the mechanisms that determine fitness of individual community members in a given habitat. The objective of this project is to establish multiple complementary approaches to defining genes and traits that confer fitness to members of built environment microbiomes. Planned methods include transposon insertion, heterologous expression, and high-throughput sequencing.