Abstract

Background

   One of the main goals of genomic analysis is to elucidate the
   comprehensive functions (functionome) in individual organisms or a
   whole community in various environments. However, a standard evaluation
   method for discerning the functional potentials harbored within the
   genome or metagenome has not yet been established. We have developed a
   new evaluation method for the potential functionome, based on the
   completion ratio of Kyoto Encyclopedia of Genes and Genomes (KEGG)
   functional modules.

Results

   Distribution of the completion ratio of the KEGG functional modules in
   768 prokaryotic species varied greatly with the kind of module, and all
   modules primarily fell into 4 patterns (universal, restricted,
   diversified and non-prokaryotic modules), indicating the universal and
   unique nature of each module, and also the versatility of the KEGG
   Orthology (KO) identifiers mapped to each one. The module completion
   ratio in 8 phenotypically different bacilli revealed that some modules
   were shared only in phenotypically similar species. Metagenomes of
   human gut microbiomes from 13 healthy individuals previously determined
   by the Sanger method were analyzed based on the module completion
   ratio. Results led to new discoveries in the nutritional preferences of