The mass spectrometry of microbiome-mediated metabolism of food: challenges and opportunities.

With the exception of molecules acquired through the lungs, skin absorption, or part of a medication regime, nearly all molecules in our bodies originate from the food and drinks we consume. A single meal typically contains at least thousands of unique molecules, which are then metabolized by both the microbiome and the host. While core metabolism - traditionally represented in biochemical maps - is well studied, most microbial metabolites derived from food metabolism remain to be discovered. Although data resources on food metabolites exist, there are limited resources that link food to microbiome-mediated metabolism and the net effects of such metabolism in the context of human health. Therefore, we provide insights into how emerging mass spectrometry-based strategies can be used to enhance our understanding of the diet-microbiome-host relationship. Given that microbiome and diet are a malleable component of metabolism within a human ecosystem, understanding the diet-microbiome-host axis presents a significant opportunity for improving health.