Interrogating gut bacterial genomes for discovery of novel carbohydrate degrading enzymes

Individual human gut bacteria often encode hundreds of enzymes for degrading different polysaccharides. Identification of co-localized and co-regulated genes in these bacteria has been a successful approach to identify enzymes that participate in full or partial saccharification of complex carbohydrates, often unmasking novel catalytic activities. Here, we review recent studies that have led to the discovery of new activities from gut bacteria and summarize a general scheme for identifying gut bacteria with novel catalytic abilities, locating the enzymes involved and investigating their activities in detail. The strength of this approach is amplified by the availability of abundant genomic and metagenomic data for the human gut microbiome, which facilitates comparative approaches to mine existing data for new or orthologous enzymes.