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Open Access Highly Accessed Methodology article

Evaluation method for the potential functionome harbored in the genome and metagenome

Hideto Takami1*, Takeaki Taniguchi2, Yuki Moriya3, Tomomi Kuwahara4, Minoru Kanehisa3 and Susumu Goto3

Author affiliations

1 Microbial Genome Research Group, Japan Agency for Marine-Earth Science & Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, 237-0061, Japan

2 Advanced Science & Innovation Group, Mitsubishi Research Institute Inc. (MRI), 2-10-3, Nagata-cho, Chiyoda-ku, Tokyo, 100-8141, Japan

3 Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan

4 Department of Microbiology, Faculty of Medicine, Kagawa University, 1750-1 Miki, Kagawa, 761-0793, Japan

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Citation and License

BMC Genomics 2012, 13:699  doi:10.1186/1471-2164-13-699

Published: 12 December 2012

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.