Every breath carries a mix of chemicals shaped by the body’s metabolism. A new study suggests that some of those molecules may come from an unexpected source: the microbes living in the gut. By analyzing exhaled breath from children and mice, researchers found that chemical signals produced by gut bacteria show up in breath samples. Those signals reflected the composition of the gut microbiome and, in some cases, pointed to bacteria associated with asthma, which affects an estimated 5 million U.S. children.
The findings, published in Cell Metabolism, land amid growing evidence that disruptions in the gut microbiome are linked to a range of diseases, from metabolic disorders to immune conditions. Yet tracking those microbial changes typically requires stool samples and genetic sequencing, making routine or rapid monitoring difficult outside research settings. Breath-based detection, the authors suggest, could offer a faster, less invasive window into microbial activity.
“Rapid assessment of the gut microbiome’s health could significantly enhance clinical care, especially for young children,” said Andrew L. Kau, senior author on the study, in a press release.
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How the Gut Microbiome Leaves a Chemical Trail
Gut microbes survive by breaking down food components that the human body cannot digest on its own. In the process, they release small molecules known as volatile organic compounds, or VOCs. Some of these compounds enter the bloodstream and are eventually expelled through the lungs during normal breathing, where they can be captured and analyzed.
The research team set out to test whether those microbial byproducts could act as a chemical fingerprint of the gut microbiome.
They conducted a study involving 27 children between the ages of six and 12. Each participant provided both breath and stool samples. The researchers analyzed the stool to identify which microbes were present in the gut, then compared those results with the chemical compounds detected in exhaled breath.
They found that the compounds captured in breath closely matched those known to be produced by the microbes identified in stool. In other words, breath samples reflected the composition of the gut microbiome without requiring direct access to the intestines.
The team confirmed the finding in mice by transplanting specific bacteria into animals raised without gut microbes of their own. The introduced microbes could be identified through compounds detected in breath, strengthening the link between breath chemistry and gut microbial activity.
Predicting Asthma-Linked Bacteria From Breath
The researchers then asked whether breath analysis could distinguish between healthy microbial communities and those associated with disease.
They compared breath and stool samples from healthy children with samples from children diagnosed with asthma. Pediatric asthma has previously been linked to increased levels of a gut bacterium called Eubacterium siraeum.
Using breath samples alone, the researchers were able to predict the abundance of this bacterium in children with asthma. That level of sensitivity suggests breath analysis could help flag microbiome changes associated with disease, even when those changes are not outwardly visible.
Toward a Non-Invasive Microbiome Test
One of the biggest challenges in translating microbiome research into clinical care is speed. Sequencing and analyzing microbial DNA can take days or weeks, limiting its usefulness for routine monitoring or early intervention.
“One of the key barriers to integrating our knowledge of the microbiome into clinical care is the time it takes to analyze the data on the microbiome,” said first author Ariel J. Hernandez-Leyva in a press release. “Breath analysis offers a promising, non-invasive way to probe the gut microbiome and can transform how we diagnose disease in medicine.”
While more research is needed before microbiome breath tests become part of everyday medical practice, the findings suggest that a simple breath sample could someday provide a practical window into the microbial communities shaping human health.
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