Protocol for isolation and analysis of small volatile microbiome metabolites from human or mouse samples

Metabolites are crucial for bidirectional communication between host and microbiome. We describe a protocol for the isolation of organic and aqueous metabolites from mucosal scrapes and feces from mouse and human samples. Although some of the most reactive organic compounds may be lost, this approach generates a functionally reproducible metabolic extract containing both host and microbial compounds appropriate for quantitative mass spectrometry and functional characterization. Our mass spectrometry approach identifies low-abundant and difficult to identify microbially derived metabolites. For complete details on the use and execution of this protocol, please refer to Bell et al. (2021) and Das et al. (2020).