The human gut is home to trillions of beneficial microbes that play important roles in health. While disruptions to this delicate gut microbiome community of bacteria and viruses have been linked to obesity, asthma, cancer, and other illnesses, quick diagnostic tools to identify changes to the microbiome that might be addressed to treat such conditions are lacking.
Researchers at Washington University School of Medicine in St. Louis (WashU Medicine) and the Children’s Hospital of Philadelphia have now shown that disease-associated bacteria in the gut can be detected through exhaled breath. They found that chemicals released by gut microbes and captured as volatile organic compounds (VOCs) from the breath of children and mice can reveal the composition of the bacteria living in the intestines. The team’s study also showed that breath samples from children with asthma could predict the presence of a bacterium linked to the condition.
The findings, they suggest, could pave the way for a rapid, noninvasive test to monitor and diagnose gut health issues simply by breathing into a device. “Rapid assessment of the gut microbiome’s health could significantly enhance clinical care, especially for young children,” said Andrew L. Kau, MD, PhD, an associate professor in the John T. Milliken Department of Medicine at WashU Medicine. “Early detection could lead to prompt interventions for conditions like allergies and serious bacterial infections in preterm infants. This study lays the groundwork for developing such crucial diagnostic tools.”
In their paper in Cell Metabolism, titled “The gut microbiota shapes the human and murine breath volatilome,” senior author Kau and colleagues concluded, “Altogether, our studies identify microbe-derived VOCs in breath, show that gut bacterial metabolism directly contributes to mammalian breath VOC profiles, and inform the development of noninvasive microbiome diagnostics.” The paper’s first author is Ariel J. Hernandez-Leyva, a WashU Medicine MD/PhD student, and the co-corresponding author is Audrey R. Odom John, MD, PhD, the Stanley Plotkin Endowed Chair in Pediatric Infectious Diseases at Children’s Hospital of Philadelphia.
“Medical decision-making often relies on the measurement of biomarkers that are associated with a disease state and provide prognostic or diagnostic information,” the authors wrote. While many clinical biomarkers require invasive samples, exhaled breath represents one potential noninvasive approach to biomarker identification, the investigators continued. “One promising avenue for biomarker identification is in exhaled breath, which is readily obtained and comprised of diverse compounds whose abundances are linked to human health.”
While the body produces its own VOCs, microbes digesting food that the body cannot, also release VOCs that are excreted from the body through exhaled breath. “In addition to compounds produced endogenously by the body, many VOCs emitted by humans are derived from the metabolism of host-colonizing microbes,” the authors noted. Kau and colleagues wondered if the types of compounds in breath can help identify the bacterial composition of the gut microbiome.
To investigate this further, Hernandez-Leyva and colleagues conducted a clinical study at WashU Medicine with children aged six to 12 years. The researchers analyzed the breath and stool samples of 27 healthy children for microbe-derived compounds and gut microbes, respectively, to figure out which microbes were linked with which breath compounds.
The team found that the compounds in the children’s breath matched the compounds known to be produced by the microbes present in their stool samples, confirming that breath is a good proxy for the microbial community in the gut. “In healthy children, we found that breath VOC composition (or volatilome), assessed by gas chromatography-mass spectrometry, correlates with gut microbiome composition and function,” they wrote. The team obtained similar results in mice by transplanting bacteria from human samples into animals without gut microbes of their own (gnotobiotic mice), and found again that gut bacteria can be identified from breath compounds. “By capturing exhaled breath from human-stool-colonized and monocolonized gnotobiotic mice, we profiled breath VOCs and discovered that murine breath is also significantly influenced by the gut microbiome,” they stated.
The researchers also compared breath and stool samples from healthy children to samples from children with asthma. Pediatric asthma—which affects nearly five million kids in the United States—is associated with an increased intestinal abundance of the bacterium Eubacterium siraeum. Through breath analysis, they were able to predict the abundance of E. siraeum in kids with asthma. “Even with the limited sample size and the presence of potential confounders, we were able to affirm previously described relationships between E. siraeum and individuals with asthma and describe breath VOC changes that may predict its abundance in the gut,” they noted.
Such information on E. siraeum abundance could be valuable for spotting early signs of microbiome changes that might exacerbate asthma symptoms, the authors suggested. Similarly, routine screening of microbiome health through breath tests in infants born prematurely, for instance, might spot disruptions to the developing microbiome that portend infection.
The results of the new study may help inform the development of a noninvasive microbiome breath test. Breath tests for detecting microbes have previously been developed by WashU Medicine researchers, including one that can detect the COVID-19 virus in less than a minute.
“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 Hernandez-Leyva. “Breath analysis offers a promising, noninvasive way to probe the gut microbiome and can transform how we diagnose disease in medicine.” In their paper the team concluded, “Together, these experiments show that the gut microbiota helps shape the host breath VOC profile and establishes models to further interrogate the relationship of the gut microbiota with breath biomarkers … As we gain additional insights into the relationship between specific gut taxa and breath VOCs, we expect that breathomics will ultimately represent a powerful diagnostic tool to facilitate rapid, non-invasive interrogation of gut microbiota health and disease.”
