Research Thrust 1

Research Thrust 1 (RT1): Measuring the Built Environment Microbiome

RT1 focuses on measuring what microbes are present in buildings, how they move, and what they do, creating the foundation for healthier indoor environments.

Researchers in RT1 develop advanced tools to detect, track, and interpret microbes in homes, hospitals, and other built environments. By combining cutting edge genomic methods with chemical and environmental sensors, this thrust makes it possible to move beyond simple notions of clean versus dirty and toward a more precise understanding of indoor microbial health.

A key challenge RT1 addresses is microbial “dark matter,” the large fraction of microbes that cannot be grown in the lab and are therefore poorly understood. Using genome enabled and multi omics approaches, RT1 researchers identify previously hidden microbes, characterize their functions, and determine how microbial communities change across spaces, surfaces, and over time.

RT1 integrates data from personal microbiomes, environmental samples, and building level measurements to identify microbial and chemical signatures linked to health risks such as pathogens and mold. These data feed directly into PreMiEr’s predictive models and intervention strategies, enabling earlier detection of problems and more targeted responses.

Together, RT1 delivers the core measurement and sensing capabilities needed to monitor indoor microbiomes in real time, laying the groundwork for smart buildings that support human health rather than undermine it.

Currently Funded Projects

  • Research Team: Rachel Noble (UNCCH, lead), Barbara Turpin (UNCCH), Glenn Morrison (UNCCH), Boyuan Chen (DUKE),  Liesl Jeffers-Francis (NCAT), Kristen Landreville (NCSU), Megan Lott (UNCCH), Benjamin Callahan (NCSU), Denene Blackwood (UNCCH), Sherlynette Pérez Castro (UNCCH), Jorden Rabasco (NCSU), Ugonna Morikwe (NCAT), Rachel Bangle (NCAT), Megan Hill (DUKE).

    Description: Precision microbiome engineering of built environments (BE) over the coming decade will require a dynamic and iterative understanding of disease agents (pathogens), native, and beneficial microbial communities. Building on standardized workflows for surface and aerosol sampling using both active and passive approaches, as well as innovative microbiome assessment and data mining tools, our proposed Year 4 project will accomplish a multi-pronged effort for developing, validating, integrating, and implementing engineering solutions that target both fungal and bacterial communities. In year 3, the PreMiEr NSF ERC RT1 team advanced this vision by a) building industry partnerships and identifying candidate technologies for BE testing, b) integrating measurement and sensor science with the SEI core to capture homeowner perceptions of bacterial and fungal mold and related mitigation, and c) refining molecular and culture-based tools to fit applications for residential and clinical BE. This foundation enables RT1 team to pivot from measurement development toward problem identification and testing of market-relevant mitigation strategies. Central to Year 4 will be the launch of a PreMiEr-wide database with standardized metadata capture to ensure consistent documentation of experimental design and data analysis across diverse BE. Nested into the PreMiEr Center-wide database will be a fungal mold reference database that will serve as a global resource for fungal mold related BE intervention testing, and biomarker/sensor validation and development. Additional aims include: 1) a cross RT1/RT2/RT3 mold remediation study testing aerosolized biotic inoculants in the Home@Duke testbed, 2) microbial profiling of urban, low resource households to evaluate the feasibility of microbiome engineering strategies, 3) expanded studies of residential mold perceptions and mitigation in rural communities, and 4) iterative engagement with industry partners to identify, validate, and commercialize microbiome engineering solutions. Together, these activities will deliver next-generation tools and engineering solutions to interrogate and reshape microbiome-BE interactions, advancing both discovery and practical interventions for healthier indoor BE spaces.

Previously Funded Projects

  • Status: Part of the PreMiEr core project “Healthcare Settings Measurements” effective September 1, 2024

    Faculty: Joe Brown (UNCCH, lead), Lawrence David (Duke), Anthony Fodor (CHAR), Claudia Gunsch (Duke),

    Description: 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.

  • Status: Sunset effective September 1, 2024.

    Faculty: Cynthia Gibas (CHAR, lead), Joe Brown (UNCCH), Anthony Fodor (CHAR), Joshua Granek (Duke), Claudia Gunsch (Duke), Glenn Morrison (UNCCH), Rachel Noble (UNCCH), Jessica Schlueter (CHAR), Jill Stewart (UNCCH), Barbara Turpin (UNCCH)

    Description: 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.

  • Status: Sunset effective September 1, 2024.

    Faculty: Misty Thomas (NCAT, lead), Joseph Graves Jr. (NCAT), Jenora Waterman (NCAT)

    Description: 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.

  • Status: Sunset effective September 1, 2024.

    Faculty: Jill Stewart (UNCCH, lead), Joe Brown (UNCCH), Cynthia Gibas (CHAR), Liesl Jeffers-Francis (NCAT), Rachel Noble (UNCCH)

    Description: 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.

  • Status: Sunset effective September 1, 2024.

    Faculty: Jill Stewart (UNCCH, lead)

    Description: 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)

  • Status: Wastewater effort sunset effective September 1, 2024; Healthcare-associated component part of PreMiEr core project “Healthcare Settings Measurements” effective September 1, 2024

    Faculty: Lawrence David (Duke, lead), Joe Brown (UNCCH), Benjamin Callahan (NCSU), Anthony Fodor (CHAR), Claudia Gunsch (Duke), Liesl Jeffers-Francis (NCAT), Rachel Noble (UNCCH), Yi-Hui Zhou (NCSU)

    Description: Diet is a key factor shaping the gut microbiome and is also a source of bacteria and pathogens for the household environmental microbiome. However, sampling food intake and microbial communities at the individual household level may be both time-consuming and expensive; such surveys will be costly to scale to community or population levels. This project hypothesizes that households in the same community share similar dietary and microbial patterns, and that variations in food consumption and microbiome are much larger across communities than within them. Thus, as a “community summary,” wastewater treatment plants (WWTPs) become a candidate for estimating and predicting household food consumption and microbiome structure.

  • Status: Part of PreMiEr core project “Measurement of Residential Built Environments” effective September 1, 2024

    Faculty: Liesl Jeffers-Francis (NCAT, lead), Christopher Cummings (NCAT), Dongyang Deng (NCAT), Joseph Graves Jr. (NCAT), Jennifer Kuzma (NCSU)

    Description: Redlining, implemented during the mid-20th century, systematically denied resources and opportunities to communities based on their racial or ethnic composition. Although redlining has officially ended, its lasting consequences continue to shape health outcomes.  The aim of this research project is to investigate the identity of microbes (bacteria, fungi, and viruses) present in redlining districts compared to non-redlining districts in North Carolina and to explore their correlation with diseases commonly found in minoritized populations/groups. By analyzing the microbial composition in these distinct socio-economic areas, we aim to address the knowledge gap regarding the potential impact of historical discriminatory practices on microbial diversity and associated health outcomes.

  • Status: Sunset effective September 1, 2025.

    Faculty: Joe Brown (UNCCH, lead), Deverick Anderson (DUKE), Benjamin Callahan (NCSU), Lawrence David (DUKE), Cynthia Gibas (CHAR), Joshua Granek (DUKE), Claudia Gunsch (DUKE), Megan Lott (UNCCH), Rachel Noble (UNCCH), Jessica Schlueter (CHAR).

    Description: The microbiomes of healthcare environments, such as hospitals and nursing homes, can significantly impact the health of the humans that occupy those spaces. This project has primary goal of understanding these microbiomes with special attention to harmful organisms such as ESKAPEE pathogens, and especially in plumbing systems that can lead to localized outbreaks. By a) understanding the community structures of the microorganisms that inhabit these environments, b) developing technologies to sample and monitor the environment, c) isolating and sequencing relevant built environment isolates, and d) improving bioinformatic tools for studying and understanding built environment microbiomes, ultimately this project aims to provide the necessary context and systems understanding required for engineering healthcare spaces for beneficial outcomes. Additional aspects of this project include comparing home and hospital microbiomes and evaluating their effects on patient recoveries. Test beds for this project include hospitals in both North and South America, operated under different conditions.