Exploring Exhaled Breath as a New Platform for Gut Microbiome-Based Diagnostics

Despite being one of the most accessible biological samples clinicians can obtain, exhaled breath contains a complex molecular signature that reflects processes occurring throughout the body. Growing interest in breath-based diagnostics has raised new questions about what these chemical signals truly represent and where they originate.

Emerging research links exhaled breath to the gut microbiome, offering insight into how microbial metabolism in the intestine may shape the volatile compounds detected in different parts of the body and how this connection could ultimately support new, noninvasive ways to assess health and disease.

“I think one of the questions that we've been aware of for a while is that we know that these metabolites that are produced by gut microbes circulate throughout the body,” senior study author Andrew Kau, MD, PhD, an associate professor in the John T. Milliken Department of Medicine at WashU Medicine, told HCPLive. “We came into this study asking if those metabolites actually show up in the breath, and is that something that we could use to look and see what the activity of gut microbes are in that moment.”

A single breath sample can contain hundreds of volatile organic compounds (VOCs), many of which have already been linked to infectious, metabolic, and inflammatory diseases. What has remained unclear is the origin of many of these compounds and to what extent gut microbes contribute to what clinicians measure in exhaled breath.

While Kau noted that prior work had already established communication between the gut and lung, as well as the ability of microbial metabolites to circulate systemically, he said what had not been rigorously tested was whether those gut-derived metabolites could be reliably detected in breath, and whether breath could serve as a real-time readout of microbial activity. To address this, investigators evaluated the question across multiple experimental systems, including mice, humans, and in vitro models.

“We went in testing this idea that gut microbes could directly contribute compounds that would show up in breath. While we showed that that is the case, we also showed that there's probably lots of other ways in which gut microbes influence the volatiles we see in the breath,” Kau said. “To me, that was a little bit surprising, and it's something that we're very interested in potentially following up on.”

In the study, they analyzed the breath and stool of 27 healthy children for microbe-derived compounds and gut microbes, respectively, and found that the compounds in the children’s breath matched the compounds known to be produced by the very microbes present in their stool. Of note, investigators obtained similar results in mice by transplanting bacteria into animals without gut microbes of their own and finding that gut bacteria can be identified from breath compounds.

Researchers additionally compared breath and stool samples from healthy children to samples from children with asthma and found that breath samples from children with asthma could predict the presence of E. siraeum, the bacterium linked to the condition.

Both experts underscored the potential clinical implications of this work. John described particular interest in neonatal care, where early microbial changes in the gut often precede bloodstream infections in premature infants. A breath-based approach could, in principle, allow clinicians to detect risk earlier and intervene before disease onset. Kau echoed this vision, pointing to broader applications in conditions linked to gut dysbiosis, such as malnutrition and allergic disease.

At the same time, the researchers acknowledged key challenges ahead.

“I think one of the ones that we're going to have to struggle with, and probably have to study specifically, is the impact of diet,” study author Audrey John, MD, PhD, Chief of the Division of Pediatric Infectious Diseases at Children's Hospital of Philadelphia, said. “We know that some of what you're seeing in the breath is coming from what people eat, and that obviously diet also influences the microbes themselves, so understanding to what degree the breath is influenced by the diet and in what ways the breath is influenced by the diet is going to be an important barrier.”

Diet and environmental exposures, they agreed, will need to be carefully studied, as both can influence breath composition and microbial behavior. Even so, both see breath analysis as a promising bridge between microbiome science and practical, point-of-care diagnostics that could make complex microbial insights far more accessible in clinical settings.

Editors’ Note: Kau reports relevant disclosures with Ancilia Biosciences, Inimune, NIH, and Doris Duke Charitable Foundation. John reports relevant disclosures with Pluton Biosciences, NIH, Department of Defense, USDA, Doris Duke Charitable Foundation, and the Bill and Melinda Gates Foundation.

References

1. WashU Medicine. Breath carries clues to gut microbiome health. EurekAlert! https://www.eurekalert.org/news-releases/1112879

2. Hernandez-Leyva AJ, Berna AZ, Bui MH, et al. The gut microbiota shapes the human and murine breath volatilome. Cell Metab. doi:10.1016/j.cmet.2025.12.013