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Pathogens 2013, 2(4), 591-605; doi:10.3390/pathogens2040591
Article

Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification

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Received: 2 August 2013; in revised form: 16 October 2013 / Accepted: 24 October 2013 / Published: 30 October 2013
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
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Abstract: The microflora in environmental water consists of a high density and diversity of bacterial species that form the foundation of the water ecosystem. Because the majority of these species cannot be cultured in vitro, a different approach is needed to identify prokaryotes in environmental water. A novel DNA microarray was developed as a simplified detection protocol. Multiple DNA probes were designed against each of the 97,927 sequences in the DNA Data Bank of Japan and mounted on a glass chip in duplicate. Evaluation of the microarray was performed using the DNA extracted from one liter of environmental water samples collected from seven sites in Japan. The extracted DNA was uniformly amplified using whole genome amplification (WGA), labeled with Cy3-conjugated 16S rRNA specific primers and hybridized to the microarray. The microarray successfully identified soil bacteria and environment-specific bacteria clusters. The DNA microarray described herein can be a useful tool in evaluating the diversity of prokaryotes and assessing environmental changes such as global warming.
Keywords: metagenome; microarray; 16S rRNA; WGA; pathogenic bacteria metagenome; microarray; 16S rRNA; WGA; pathogenic bacteria
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MDPI and ACS Style

Akama, T.; Kawashima, A.; Tanigawa, K.; Hayashi, M.; Ishido, Y.; Luo, Y.; Hata, A.; Fujitani, N.; Ishii, N.; Suzuki, K. Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification. Pathogens 2013, 2, 591-605.

AMA Style

Akama T, Kawashima A, Tanigawa K, Hayashi M, Ishido Y, Luo Y, Hata A, Fujitani N, Ishii N, Suzuki K. Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification. Pathogens. 2013; 2(4):591-605.

Chicago/Turabian Style

Akama, Takeshi; Kawashima, Akira; Tanigawa, Kazunari; Hayashi, Moyuru; Ishido, Yuko; Luo, Yuqian; Hata, Akihisa; Fujitani, Noboru; Ishii, Norihisa; Suzuki, Koichi. 2013. "Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification." Pathogens 2, no. 4: 591-605.


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