Our body hosts diverse species of microbes like bacteria, fungi, and archaea, which form the human microbiome. Changes in the microbiome composition have been linked to a range of diseases, including non-alcoholic fatty liver disease (NAFLD), inflammatory bowel disease (IBD), and cancer. Currently, analyzing blood, mucus, urine, and fecal matter helps measure biomarkers, which are quantifiable compounds that serve as indicators of different aspects of health and disease. Breath is another waste product that could be used in research and, eventually, clinical practice.
Breath is a rich, compound matrix that originates from both internal and external sources, containing many volatile metabolites, commonly called volatile organic compounds (VOCs). Exhaled VOCs derive from the bloodstream and enter the breath through blood–air alveolar exchange, meaning breath is enriched with VOCs originating from metabolic processes throughout the body.
Each microbe species has its unique form of metabolism that yields specific volatile by-products such as short-chain fatty acids (SCFAs). Consequently, the composition of breath is contingent on the types of microbes present. Alterations in breath VOCs serve as biomarkers, reflecting the changes in microbial activity, which could be driving factors for disease.
Why use breath?
Currently, fecal analysis is used to study microbiomes. This method, while informative, possesses certain limitations that can result in nonrepresentative studies, such as potential distortion of microbial composition due to fecal matter storage in the rectum. When working with fecal samples, there is a risk of introducing variability during handling, primarily due to the loss of highly volatile compounds before they reach the detection equipment. Analyzing breath is a promising alternative as it can identify many of the same VOCs originating from microbes as those found in fecal samples and also has numerous advantages over other sampling mediums.
There are many benefits of using breath testing: Breath sample collection is noninvasive, enabling patient comfort and eliminating the risk of surrounding tissue damage or infection, generally involved with more invasive procedures such as tissue biopsies. A large volume of breath can be obtained at regular, short intervals, facilitating continuous tracking of various metabolic pathways over time. In addition, there is no need for patients to make clinic visits for breath tests when portable sampling collection kits and devices are available.
Studying the breath microbiome
There are many promising breath biomarker studies: For example, gut bacteria such as Lactobacillus can overproduce ethanol from pyruvate, resulting in these patients having higher levels of circulating ethanol in the blood, which can contribute to liver disease. Ethanol is readily detectable in breath and quantifying it could indicate whether the gut microbiome is overproducing ethanol, enabling better clinical management of liver disease.
IBD has also been associated with changes in the gut microbiota. Phenol is produced from phyla such as Proteobacteria, Actinobacteria, and Fusobacteriota, and is altered in the breath of Crohn’s disease patients, linking underlying shifts in microbiota composition to IBD development.
Small intestinal bacterial overgrowth (SIBO) and carbohydrate malabsorption (CM) can be diagnosed using a breath test, whereby a test substrate is administered when the patient is fasting, and variations in hydrogen and methane levels are monitored in exhaled breath. Gut bacteria that ferment carbohydrates in the large intestine produce these gases. An early peak in hydrogen and methane levels indicates that fermentation has begun early in the small intestine, a characteristic of SIBO. Breath analysis also shows potential in the early diagnosis of respiratory diseases such as asthma and cystic fibrosis, metabolic diseases such as diabetes, and neurodegenerative diseases such as Parkinson’s.
Studying the microbiome has unveiled a profound connection between the body’s internal microbial community and various disease states. Traditional methods of analyzing body fluids and waste products have provided crucial insights into these mechanisms, but breath analysis emerges as a promising complementary technique for further understanding the microbiome’s impact on health.
A plethora of biologically relevant VOCs are found in breath, which can provide a window into the intricate relationship between the microbiome and disease. As our understanding of this relationship continues to evolve, breath analysis stands as a valuable tool in unraveling the complexities of the microbiome's role in human health.