Microbes: The invisible inhabitants
An ambitious study led by Yale Engineering explores how the microbes in our homes shape our health
This story originally appeared in Yale Engineering magazine.
Irvan Luhung, an environmental engineering research scientist, reaches up to swab the upper frame of the closet in the home office of a house in Branford, CT. He then plunges the swab and all its collected dust into a marked container of solution for later analysis. Then, it’s on to the next room to take some more samples.
It’s one small part of an ambitious, federally funded project that brings together an interdisciplinary team of researchers designed to provide some insight about when and how microbes in the home help and hurt us. With funding of up to $5 million from the Advanced Research Projects Agency for Health (ARPA-H), researchers from Yale Engineering, the Yale School of Medicine, and the Yale School of Public Health will visit 400 homes in the Southern Connecticut region, take samples of water, dust, and air, and conduct respiratory tests on the residents. One goal of the project is to create what the researchers call a Healthy Building Microbiome Index (HBMI), a quantitative metric that indicates the human health risks or benefits of a home’s microbiome. The HBMI could then be used to promote the best approaches for designing buildings for optimal well-being.
“We know all about allergens. We know about pathogens like tuberculosis, and we know about influenza. We don’t know about the [microbes] that help to make us healthy.
Jordan Peccia
Chemical & Environmental Engineering Professor
“The idea is to identify microbes that are closely associated with healthy and unhealthy buildings,” said Jordan Peccia, who’s leading the study. “We know all about allergens. We know about pathogens like tuberculosis, and we know about influenza. We don’t know about the ones that help to make us healthy.”
Studies have shown that the microbes a child is exposed to in the first six months to a year help determine the strength of their immune system. Researchers have also found that living in a home with greater microbial diversity lowers a child’s risk of developing asthma.
“We know that there are healthy exposures to microbes,” said Peccia, the Thomas E. Golden, Jr. Professor of Chemical & Environmental Engineering. “This is an attempt to find some associations between buildings where people are healthy and what that microbial ecology or those microbial communities look like in those buildings.”
Making the invisible visible, with sensors and swabs
Data collected from the Branford house, built in the 1880s, won’t be part of the study’s final results. The research team is using it as a test run — a way to iron out unanticipated wrinkles. For instance, when the researchers sample water from the upstairs shower, it leads to a short debate about whether it would be better to use a funnel or a larger container to collect the water. Considering how many variables there are in a large study like this, it’s no wonder that practice runs are pretty common.
A building’s design can have a significant impact on its microbial population. For example, better outdoor air ventilation can increase its microbial diversity. Older houses, like the one the researchers are using for their test run, tend to be better ventilated since they were built before construction technology allowed buildings to be so thoroughly sealed. In recent years, the design of housing in the U.S. has focused more on comfort and energy efficiency.
The 400 homes are divided into two groups; about half the buildings are occupied by people with various health issues, and residents of the other half are all considered healthy. The researchers plan to go into homes and sample the buildings’ microbiomes. In part, that involves sampling settled dust and different sources of water and then sequencing the DNA in those samples to determine what type of microbes are present. Settled dust is a particularly rich source of information since they can tell a lot about a home’s microbial activity over several months. Results from air samples tend to be more immediate.
Drew Gentner and his team will deploy numerous sensors in the homes and analyze a broad suite of chemical signatures that are in the homes.
“I’m really excited about this project,” said Gentner, professor of chemical & environmental engineering. “It’s a great opportunity to bring together a wide range of expertise that we have across Yale and to think holistically about human health in the indoor environment.”
The Yale faculty are working with Neighborhood Housing Services of New Haven, a nonprofit organization that works with housing in southern Connecticut.
“By working with this group, we’re able to reach the broader community better and look at a wide range of housing stock to consider how environmental disparities can play into this as well,” Gentner said.
The data generated by all this testing and sampling will be massive. That’s where another component of this collaboration comes in. Mark Gerstein, at the Yale School of Medicine, focuses on biomedical data science, and will be making sense of the data.
Getting the pulse
Researchers at the School of Public Health, led by Daniel Carrion, will help recruit the participants and arrange the home visits. Under the guidance of Sandra Zaeh from the Yale School of Medicine, they will also perform lung function testing on the participants, part of which involves having them blow into a tube so that the condensation from their breath can be then analyzed for various measures of health outcomes.
“One of the things we’re exploring is the status of the home and the quality of the home,” said Carrion, assistant professor of epidemiology. “I will be interested to see what those relationships are between the home microbiome that Jordan is interested in, the indoor air quality, and the quality of the home, and how those relate to respiratory health.”
As part of their practice run at the Branford house, Zaeh runs respiratory tests on one of the home’s residents, Allison Beaulieu, a program manager at the Yale School of Public Health and a member of the project’s research team. Zaeh uses a portable spirometer, a device to measure how much and how fast someone can breathe. It’s typically used to test and monitor for asthma, COPD and similar conditions. Zaeh also surveys Beaulieu with questions about their home and lifestyle.
“There’s a couple of different health outcomes that we’re looking at,” said Zaeh, a medical doctor who specializes in pulmonary and critical care. “One is a survey, and it’s talking about general health and lung health and asking a lot of questions, specifically related to pulmonary things. The second is measuring lung function.”
Zaeh said she’s glad that the Neighborhood Housing Services of New Haven is on board for the project. She’s worked with community organizations on previous studies, and said it contributes to a valuable perspective.
“I just think it adds such a different flavor because you actually have a sense of the pulse and of what’s going on,” she said. “I think we need those partners to do really good, meaningful work on the ground.”
This research was, in part, funded by the Advanced Research Projects Agency for Health (ARPA-H). The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the United States Government.
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Published Date
Apr 9, 2026
