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DNA Research Advance Access originally published online on January 10, 2006
DNA Research 2005 12(5):281-290; doi:10.1093/dnares/dsi015
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© The Author 2006. Kazusa DNA Research Institute
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions@oxfordjournals.org

Novel Phylogenetic Studies of Genomic Sequence Fragments Derived from Uncultured Microbe Mixtures in Environmental and Clinical Samples

Takashi Abe1,*, Hideaki Sugawara1, Makoto Kinouchi2, Shigehiko Kanaya3 and Toshimichi Ikemura4

1Center for Information Biology, National Institute of Genetics, The Graduate University for Advanced Studies (Sokendai) Mishima, Shizuoka 411-8540, Japan
2Department of Bio-System Engineering, Faculty of Engineering, Yamagata University Yonezawa, Yamagata 992-8510, Japan
3Department of Bioinformatics and Genomes, Graduate School of Information Science, Nara Institute of Science and Technology Takayama, Ikoma, Nara 630-0101, Japan
4The Graduate University for Advanced Studies (Sokendai), Hayama Center for Advanced Research Hayama-cho, Kanagawa 240-0193, Japan

A self-organizing map (SOM) was developed as a novel bioinformatics strategy for phylogenetic classification of sequence fragments obtained from pooled genome samples of uncultured microbes in environmental and clinical samples. This phylogenetic classification was possible without either orthologous sequence sets or sequence alignments. We first constructed SOMs for tetranucleotide frequencies in 210 000 5 kb sequence fragments obtained from 1502 prokaryotes for which at least 10 kb of genomic sequence has been deposited in public DNA databases. The sequences could be classified primarily according to phylogenetic groups without information regarding the species. We used the SOM method to classify sequence fragments derived from environmental samples of the Sargasso Sea and of an acidophilic biofilm growing in acid mine drainage. Phylogenetic diversity of the environmental sequences was effectively visualized on a single map. Sequences that were derived from a single genome but cloned independently could be reassociated in silico. G + C% has been used for a long period as a fundamental parameter for phylogenetic classification of microbes, but the G + C% is apparently too simple a parameter to differentiate a wide variety of known species. Oligonucleotide frequency can be used to distinguish the species because oligonucleotide frequencies vary significantly among their genomes.

Key words: self-organizing map; environmental samples; metagenome; phylogenetic classification; SOM

*To whom correspondence should be addressed. Tel. +81-55-981-6835, Fax. +81-55-981-6896, Email: takaabe{at}genes.nig.ac.jp

Communicated by Katsumi Isono


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