Comprehensive Analysis of Prokaryotes in Environmental Water Using DNA Microarray Analysis and Whole Genome Amplification
by
Takeshi Akama 1, Akira Kawashima 1, Kazunari Tanigawa 1, Moyuru Hayashi 1, Yuko Ishido 1, Yuqian Luo 1, Akihisa Hata 2, Noboru Fujitani 2, Norihisa Ishii 3 and Koichi Suzuki 1,*
Takeshi Akama 1, Akira Kawashima 1, Kazunari Tanigawa 1, Moyuru Hayashi 1, Yuko Ishido 1, Yuqian Luo 1, Akihisa Hata 2, Noboru Fujitani 2, Norihisa Ishii 3 and Koichi Suzuki 1,*
1
Laboratory of Molecular Diagnostics, Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 189-0002, Japan
2
Department of Medical Risk Management, Faculty of Risk Management, Chiba Institute of Science, Faculty of Risk and Crisis Management, Choshi, Chiba 288-0025, Japan
3
Leprosy Research Center, National Institute of Infectious Diseases, Tokyo 189-0002, Japan
*
Author to whom correspondence should be addressed.
Pathogens 2013, 2(4), 591-605; https://doi.org/10.3390/pathogens2040591
Received: 2 August 2013 / Revised: 16 October 2013 / Accepted: 24 October 2013 / Published: 30 October 2013
(This article belongs to the Special Issue Bacterial Pathogenomics: From Technology to Application)
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.
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Keywords:
metagenome; microarray; 16S rRNA; WGA; pathogenic bacteria
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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.
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