Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples

被引:85
作者
Abe, Takashi [1 ]
Sugawara, Hideaki
Kinouchi, Makoto
Kanaya, Shigehiko
Ikemura, Toshimichi
机构
[1] Grad Univ Adv Studies Sokendai, Natl Inst Genet, Ctr Informat Biol, Shizuoka 4118540, Japan
[2] Yamagata Univ, Fac Engn, Dept Biosyst Engn, Yamagata 9928510, Japan
[3] Nara Inst Sci & Technol, Grad Sch Informat Sci, Dept Bioinformat & Genomes, Nara 6300101, Japan
[4] Grad Univ Adv Studies Sokendai, Ctr Adv Res, Kanagawa 2400193, Japan
关键词
self-organizing map; environmental samples; metagenome; phylogenetic classification; SOM;
D O I
10.1093/dnares/dsi015
中图分类号
Q3 [遗传学];
学科分类号
071007 ; 090102 ;
摘要
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.
引用
收藏
页码:281 / 290
页数:10
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