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Nucleic Acids Research, 2003, Vol. 31, No. 2 e5
© 2003 Oxford University Press

NotI passporting to identify species composition of complex microbial systems

Veronika Zabarovska1, Alexey S. Kutsenko1,2, Lev Petrenko1, Gelena Kilosanidze1,3, Olle Ljungqvist4, Elisabeth Norin1, Tore Midtvedt1, Gösta Winberg1, Roland Möllby1, Vladimir I. Kashuba1, Ingemar Ernberg1 and Eugene R. Zabarovsky*,1,3

1 Microbiology and Tumor Biology Center, Center for Genomics and Bioinformatics, and Department of Cell and Molecular Biology, Karolinska Institute, 171 77 Stockholm, Sweden, 2 Center for Theoretical Problems of Physicochemical Pharmacology, Russian Academy of Sciences, 177 977 Moscow, Russia, 3 Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119 991 Moscow, Russia and 4 Center of Gastrointestinal Disease, Ersta Hospital, 116 91 Stockholm, Sweden

*To whom correspondence should be addressed at Microbiology and Tumor Biology Center, Karolinska Institute, Box 280, 171 77, Stockholm, Sweden. Tel: +46 8 728 6750; Fax: +46 8 319 470; Email: eugzab{at}ki.se
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors

We describe here a new method for large-scale scanning of microbial genomes on a quantitative and qualitative basis. To achieve this aim we propose to create NotI passports: databases containing NotI tags. We demonstrated that these tags comprising 19 bp of sequence information could be successfully generated using DNA isolated from intestinal or fecal samples. Such NotI passports allow the discrimination between closely related bacterial species and even strains. This procedure for generating restriction site tagged sequences (RSTS) is called passporting and can be adapted to any other rare cutting restriction enzyme. A comparison of 1312 tags from available sequenced Escherichia coli genomes, generated with the NotI, PmeI and SbfI restriction enzymes, revealed only 219 tags that were not unique. None of these tags matched human or rodent sequences. Therefore the approach allows analysis of complex microbial mixtures such as in human gut and identification with high accuracy of a particular bacterial strain on a quantitative and qualitative basis.


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E. R. Zabarovsky, L. Petrenko, A. Protopopov, O. Vorontsova, A. S. Kutsenko, Y. Zhao, G. Kilosanidze, V. Zabarovska, E. Rakhmanaliev, B. Pettersson, et al.
Restriction site tagged (RST) microarrays: a novel technique to study the species composition of complex microbial systems
Nucleic Acids Res., August 15, 2003; 31(16): e95 - e95.
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