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Applied and Environmental Microbiology, August 2001, p. 3677-3682, Vol. 67, No. 8
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.8.3677-3682.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.

Bacterial Species Determination from DNA-DNA Hybridization by Using Genome Fragments and DNA Microarrays

Jae-Chang Cho1 and James M. Tiedje1,2,*

Center for Microbial Ecology1 and Department of Microbiology and Molecular Genetics,2 Michigan State University, East Lansing, Michigan 48824

Received 28 November 2000/Accepted 18 May 2001

Whole genomic DNA-DNA hybridization has been a cornerstone of bacterial species determination but is not widely used because it is not easily implemented. We have developed a method based on random genome fragments and DNA microarray technology that overcomes the disadvantages of whole-genome DNA-DNA hybridization. Reference genomes of four fluorescent Pseudomonas species were fragmented, and 60 to 96 genome fragments of approximately 1 kb from each strain were spotted on microarrays. Genomes from 12 well-characterized fluorescent Pseudomonas strains were labeled with Cy dyes and hybridized to the arrays. Cluster analysis of the hybridization profiles revealed taxonomic relationships between bacterial strains tested at species to strain level resolution, suggesting that this approach is useful for the identification of bacteria as well as determining the genetic distance among bacteria. Since arrays can contain thousands of DNA spots, a single array has the potential for broad identification capacity. In addition, the method does not require laborious cross-hybridizations and can provide an open database of hybridization profiles, avoiding the limitations of traditional DNA-DNA hybridization.

* Corresponding author. Mailing address: Center for Microbial Ecology, Plant and Soil Sciences Bldg., Michigan State University, East Lansing, MI 48824. Phone: (517) 353-9021. Fax: (517) 353-2917. E-mail: tiedjej{at}msu.edu.

Applied and Environmental Microbiology, August 2001, p. 3677-3682, Vol. 67, No. 8
0099-2240/01/$04.00+0   DOI: 10.1128/AEM.67.8.3677-3682.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.


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