title: Evaluation method for the potential functionome harbored in the genome and metagenome.
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 gut microbes, believed to be one of the mutualistic representations of gut microbiomes to avoid nutritional competition with the host.
  
  
  CONCLUSIONS
  The method developed in this study could characterize the functionome harbored in genomes and metagenomes. As this method also provided taxonomical information from KEGG modules as well as the gene hosts constructing the modules, interpretation of completion profiles was simplified and we could identify the complementarity between biochemical functions in human hosts and the nutritional preferences in human gut microbiomes. Thus, our method has the potential to be a powerful tool for comparative functional analysis in genomics and metagenomics, able to target unknown environments containing various uncultivable microbes within unidentified phyla.
authors.affiliation: Microbial Genome Research Group, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, 237-0061, Japan. takamih@jamstec.go.jp
authors.forename: Hideto
authors.initials: H
authors.lastname: Takami
authors.forename: Takeaki
authors.initials: T
authors.lastname: Taniguchi
authors.forename: Yuki
authors.initials: Y
authors.lastname: Moriya
authors.forename: Tomomi
authors.initials: T
authors.lastname: Kuwahara
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
mesh_terms: D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D041981:Gastrointestinal Tract / Q000382:microbiology*; D023281:Genomics / Q000379:methods*; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D011506:Proteins / Q000235:genetics / Q000502:physiology*; D013045:Species Specificity
chemical_list: D011506:Proteins