Research Thrust 1

Tracking tools and the exploration of microbial “dark matter”

Research Thrust 1 (RT1) combines multi-omic investigations to determine the mechanisms of microbial colonization and aims to develop sensor and tracking technologies for diagnosing built environment health at varying resolutions (i.e., personal, room, and building level).

RT1 researchers will develop tracking tools that combine phylogenetic and functional aspects through the integration of personal and environmental microbiome data with microbial dark matter characteristics. These tools will include genome-enabled approaches that can target uncultivated microbial taxa and increase our understanding of microbial diversity, phylogenetic relationships, metabolic capabilities, and interactions in the built environment as well as functional approaches via meta-omics. In combination, these approaches will deepen our databases enabling the identification of key molecules and the development of sensors for health assessment of the built environment.

Projects in RT1 will apply and expand fundamental knowledge in microbiome monitoring. We will begin by developing approaches for monitoring and connecting the personal and the environmental microbiome as well as determine functional signatures that can diagnose built environment health. RT1 data will provide the early building blocks for monitoring the built environment microbiome as well that of its occupants, identifying the biomarkers that signal a healthy built environment, and inform PreMiEr’s future sensor development work.

Currently funded projects

Assessing sensitivity and variability in molecular detection methods for surface and air microbiome samples from urban indoor spaces

A challenge for metagenomics projects is standardization and validation of both detection methods and computational analysis methods. This project will establish a common set of best practices for sampling, validation, analysis and modeling for PreMiEr. This project also aligns with the ERC’s Engineering Workforce Development foundation: surface sampling and microbiome analysis will be carried out in an undergraduate Genomic Biotechnology laboratory course at UNC Charlotte and microbiome data analysis using PreMiEr datasets will be introduced in a graduate Genomics course offered annually by PI Gibas.

Collaborations 

   

   

Cynthia Gibas

Cynthia Gibas

UNC Charlotte, Project Lead

Anthony Fodor

Anthony Fodor

UNC Charlotte

Rachel Noble

Rachel Noble

UNC Chapel Hill

Barbara Turpin

Barbara Turpin

UNC Chapel Hill

Claudia Gunsch

Claudia Gunsch

Duke

Joe Brown

Joe Brown

UNC Chapel Hill

Jill Stewart

Jill Stewart

UNC Chapel Hill

Glenn Morrison

Glenn Morrison

UNC Chapel Hill

Microbiome and pathogen exposure in Bolivian homes

The majority of the world’s population lives in environments with many of the same characteristics found in PreMiEr’s Bolivian homes test bed. Building on a foundation of international collaboration and experience, this project partners with Bolivian scientists to conduct a pilot cross-sectional study in the city of La Paz exploring household microbiomes in a setting where engineering controls are minimal. Longer-term goals of the work are to (i) characterize the built environment microbiome in Bolivian households, (ii) evaluate associations with environmental and building characteristics, e.g., construction materials, floor type, or presence of mold, pets and other animals, ventilation, sanitation, water infrastructure; and (iii) develop and implement low-cost engineering controls to reduce exposures in this setting.

Collaborations 

   

   

Joe Brown

Joe Brown

UNC Chapel Hill, Project Lead

Claudia Gunsch

Claudia Gunsch

Duke

Anthony Fodor

Anthony Fodor

UNC Charlotte

Lawrence David

Lawrence David

Duke

Developing tools to characterize fungal contamination in the built environment: special focus on the Southeastern USA and on rural underserved areas

One class of biological agents in the indoor environment, fungal molds, is particularly strongly related to exposure to dampness in the indoor environment, and proliferates in areas of inadequate ventilation.  Additionally, climate change is increasing the intensity and frequency of wet weather events, and flooding, both causative agents of fungal mold. This project seeks to increase understanding, measurement, and remediation of fungal mold exposures in built environments.

Collaborations 

   

     

Rachel Noble

Rachel Noble

UNC Chapel Hill, Project Lead

Joe Brown

Joe Brown

UNC Chapel Hill

Jill Stewart

Jill Stewart

UNC Chapel Hill

Cynthia Gibas

Cynthia Gibas

UNC Charlotte

Jennifer Kuzma

Jennifer Kuzma

NC State

Glenn Morrison

Glenn Morrison

UNC Chapel Hill

Barbara Turpin

Barbara Turpin

UNC Chapel Hill

Claudia Gunsch

Claudia Gunsch

Duke

Environmental antimicrobial resistance (AMR) in the built environment

Antimicrobial resistance (AMR) is an increasing threat to public health and modern medicine. No standard methods exist for measuring antimicrobial resistance in the built environment, and the environmental dimensions of AMR remain poorly understood. This project will develop tools and recommendations for measuring antimicrobial resistance in the built environment, provide insights on the sensitivity of sequencing methods in detecting priority antibiotic resistance genes, and give recommendations for appropriate indicators.

Collaborations 

   

Jill Stewart

Jill Stewart

UNC Chapel Hill, Project Lead

Liesl Jeffers-Francis

Liesl Jeffers-Francis

N.C. A&T

Rachel Noble

Rachel Noble

UNC Chapel Hill

Joe Brown

Joe Brown

UNC Chapel Hill

Cynthia Gibas

Cynthia Gibas

UNC Charlotte

Premise plumbing and pathogens: Links to waterborne urinary tract infections

Among potential health risks, water may be an underrecognized but important route of uropathogen transmission causing urinary tract infections (UTIs). This project will conduct a pilot study investigating uropathogenic E. coli in the San Cristobal water system of Galápagos, Ecuador following a documented decrease in UTIs after installation of a new water treatment plant in order to model transmission dynamics of waterborne UTIs.

External collaborators: Galapagos Science Center, Universidad San Francisco de Quito (USFQ)

Collaborations 

Jill Stewart

Jill Stewart

UNC Chapel Hill, Project Lead

Evaluation of lunar regolith on Streptococcus mutans biofilms grown in simulated microgravity

As we continue to push boundaries of exploration in extreme environments, we must consider the impact that it has on the evolutionary response of the microbes that we carry to the built environment, in this case, outer space or to the lunar surface. This project represents a singular opportunity to study the evolutionary pressures of a novel environment before an associated built environment actually exists. Unique environmental stresses on the adaption of an oral bacterium are studied.

Collaborations 

Misty Thomas

Misty Thomas

N.C. A&T, Project Lead

Joseph Graves, Jr.

Joseph Graves, Jr.

N.C. A&T