 With the knowledge of the structures and functions of already characterized members of the enzyme family and the amino acid residues responsible, a sequence similarity network (SSN) is constructed to group together sequences of enzymes in clusters that share biological function.The SSN is used to interpret data generated by Short-BRED, a quantitative metagenomic analysis tool which uses the amino acid sequences of the enzyme family as input.Short-BRED identifies the unique sequence markers of each group of similar members and sequentially determines their abundance in the human microbiome.