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The human gut community is composed of metabolically versatile anaerobic microorganisms from a large number of interrelated taxonomic orders that mostly belong to the Bacteria domain. Recent availability of complete genomes for thousands of microbial gut species and expansion of the human gut metagenomics and metatranscriptomic data sets open new opportunities to develop and apply the comparative genomics approaches for identification of essential enzymes, transporters and regulators involved in key metabolic pathways, and provide the basis for genomic assignment of metabolic phenotypes to gut bacterial species.