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DNA Research Advance Access originally published online on October 17, 2008
DNA Research 2008 15(6):375-386; doi:10.1093/dnares/dsn026
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© The Author 2008. 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

Complete Genome Sequence and Comparative Analysis of the Wild-type Commensal Escherichia coli Strain SE11 Isolated from a Healthy Adult

Kenshiro Oshima1 {dagger}, Hidehiro Toh1,2 {dagger}, Yoshitoshi Ogura3,4, Hiroyuki Sasamoto1, Hidetoshi Morita5, Sang-Hee Park6, Tadasuke Ooka4, Sunao Iyoda7, Todd D. Taylor2, Tetsuya Hayashi3,4, Kikuji Itoh6 and Masahira Hattori1,8,*

1 Kitasato Institute for Life Sciences, Kitasato University, 1-15-1 Kitasato, Sagamihara, Kanagawa 228-8555, Japan
2 RIKEN Advanced Science Institute, 1-7-22 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan
3 Frontier Science Research Center, University of Miyazaki, 5200 Kiyotake, Miyazaki 899-1692, Japan
4 Department of Infectious Diseases, Faculty of Medicine, University of Miyazaki, 5200 Kiyotake, Miyazaki 899-1692, Japan
5 School of Veterinary Medicine, Azabu University, 1-17-71 Fuchinobe, Sagamihara, Kanagawa 229-8501, Japan
6 Graduate School of Agricultural and Life Sciences, University of Tokyo, 1-1-1 Yayoi, Bunkyo, Tokyo 113-8657, Japan
7 Department of Bacteriology, National Institute of Infectious Diseases, 1-23-1 Toyama, Shinjuku, Tokyo 162-8640, Japan
8 Graduate School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa, Chiba 277-8561, Japan

Received 6 August 2008 ; accepted 16 September 2008.

We sequenced and analyzed the genome of a commensal Escherichia coli (E. coli) strain SE11 (O152:H28) recently isolated from feces of a healthy adult and classified into E. coli phylogenetic group B1. SE11 harbored a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes. None of the SE11 genes had sequence similarity to known genes encoding phage- and plasmid-borne virulence factors found in pathogenic E. coli strains. The comparative genome analysis with the laboratory strain K-12 MG1655 identified 62 poorly conserved genes between these two non-pathogenic strains and 1186 genes absent in MG1655. These genes in SE11 were mostly encoded in large insertion regions on the chromosome or in the plasmids, and were notably abundant in genes of fimbriae and autotransporters, which are cell surface appendages that largely contribute to the adherence ability of bacteria to host cells and bacterial conjugation. These data suggest that SE11 may have evolved to acquire and accumulate the functions advantageous for stable colonization of intestinal cells, and that the adhesion-associated functions are important for the commensality of E. coli in human gut habitat.

Key words: Escherichia coli; commensal; human gut; genome sequencing

* To whom correspondence should be addressed. Tel. +81 4-7136-4070. Fax. +81 4-7136-4084. E-mail: hattori{at}k.u-tokyo.ac.jp

Edited by Katsumi Isono

{dagger} K.O. and H.T. contributed equally to this work.


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