Subsystem-based annotation and prediction of functional capabilities (inferred metabolic phenotypes) of MAGs and cultured 
MAG and isolate genes were assigned functions, and metabolic pathways were reconstructed using a combination of (1) public-domain tools for sequence alignment and clustering; (2) custom scripts to process the results of sequence alignments (for example, for domain annotation in multifunctional proteins); and (3) a reference collection of 2,856 human gut bacterial genomes for which we have reconstructed and manually curated metabolic pathways related to 98 distinct metabolites and 106 metabolic phenotypesOur annotation workflow is shown in Supplementary Fig. 