The breath volatilome is shaped by the gut microbiota

The gut microbiota is widely implicated in host health and disease, inspiring a number of translational efforts to implement our growing body of knowledge in clinical settings. However, the need to characterize gut microbiota by its genomic content limits the feasibility of rapid, point-of-care diagnostics. However, the microbiota produce a diverse array of xenobiotic metabolites produced by the microbiota that disseminate into tissues, including volatile organic compounds (VOCs) that are excreted in breath. We anticipate that breath contains gut microbe-derived VOCs that inform the composition and metabolic state of the microbiota. To explore this idea, we compared the breath volatilome and fecal gut microbiomes of 37 healthy children and found that breath VOC composition is correlated with gut microbiomes. To experimentally interrogate this finding, we devised a method for capturing exhaled breath from gnotobiotic mice using the Flexivent FX1 system. Breath volatiles are then profiled with two-dimensional gas-chromatography mass-spectrometry (GCxGC-MS). We compared breath from donor mice sourced from different vendors, gnotobiotic mice colonized with cecal content harvested from donors, and germ-free controls and found that the murine breath profile is markedly shaped by the composition of the gut microbiota. We also find that VOCs produced by gut microbes in pure culture can be identified in vivo in the breath of mice monocolonized with the same bacteria. Altogether, our studies identify microbe-derived VOCs excreted in breath and support a mechanism by which gut bacterial metabolism directly contributes to the mammalian breath VOC profiles.