Garza, D.R. et al. Nat. Microbiol. 3, 456–460 (2018).

Metabolic profiling of microbial environments such as the human gut has lagged behind surveys of genetic material, which are generally cheaper and less challenging to carry out. Shotgun metagenomic sequencing provides quantitative information about what genes are present in a community, but it is not straightforward to predict metabolic status from these data. To bridge the gap, Garza et al. introduce MAMBO (metabolomic analysis of metagenomes using flux balance analysis and optimization), which assesses and optimizes correlations between genome-scale, constraint-based metabolic models and microbial abundance profiles obtained from shotgun sequence data. MAMBO inference of the metabolomics environment for several human body sites is consistent with measured metabolomes, which provides support for the approach as a step toward mechanistic modeling of microbial ecology.