Coupling Targeted and Untargeted Mass Spectrometry for Metabolome-Microbiome-Wide Association Studies of Human Fecal Samples

Increasing appreciation of the gut microbiome’s role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays, and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies. Procrustes analysis revealed that untargeted approach provides a better correlation to microbiome data, associating specific metabolites with microbes that produce or process them. With the subset of over one hundred human fecal samples from the American Gut project, the implementation of the described coupled workflow revealed that targeted analysis using combination of single transition per compound with retent...