This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Download to citation manager
Right arrowReprints and Permissions
Right arrow Copyright Information
Right arrow Books from ASM Press
Right arrow MicrobeWorld
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Wilson, K. H.
Right arrow Articles by Andersen, G. L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Wilson, K. H.
Right arrow Articles by Andersen, G. L.
Agricola
Right arrow Articles by Wilson, K. H.
Right arrow Articles by Andersen, G. L.

 Previous Article  |  Next Article 

Applied and Environmental Microbiology, May 2002, p. 2535-2541, Vol. 68, No. 5
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.5.2535-2541.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.

High-Density Microarray of Small-Subunit Ribosomal DNA Probes

Kenneth H. Wilson,1 Wendy J. Wilson,2 Jennifer L. Radosevich,2 Todd Z. DeSantis,2 Vijay S. Viswanathan,2 Thomas A. Kuczmarski,2 and Gary L. Andersen2*

Veterans Affairs Medical Center and Duke University Medical Center, Durham, North Carolina 27710,1 Lawrence Livermore National Laboratory, Livermore, California 945502

Received 26 September 2001/ Accepted 2 January 2002

Ribosomal DNA sequence analysis, originally conceived as a way to provide a universal phylogeny for life forms, has proven useful in many areas of biological research. Some of the most promising applications of this approach are presently limited by the rate at which sequences can be analyzed. As a step toward overcoming this limitation, we have investigated the use of photolithography chip technology to perform sequence analyses on amplified small-subunit rRNA genes. The GeneChip (Affymetrix Corporation) contained 31,179 20-mer oligonucleotides that were complementary to a subalignment of sequences in the Ribosomal Database Project (RDP) (B. L. Maidak et al., Nucleic Acids Res. 29:173-174, 2001). The chip and standard Affymetrix software were able to correctly match small-subunit ribosomal DNA amplicons with the corresponding sequences in the RDP database for 15 of 17 bacterial species grown in pure culture. When bacteria collected from an air sample were tested, the method compared favorably with cloning and sequencing amplicons in determining the presence of phylogenetic groups. However, the method could not resolve the individual sequences comprising a complex mixed sample. Given these results and the potential for future enhancement of this technology, it may become widely useful.

* Corresponding author: Mailing address: Biology and Biotechnology Res. Program, Lawrence Livermore National Laboratory, 7000 East Ave., L-441, Livermore, CA 94550. Phone: (925) 423-2525. Fax: (925) 422-2282. E-mail: andersen2{at}llnl.gov.

Applied and Environmental Microbiology, May 2002, p. 2535-2541, Vol. 68, No. 5
0099-2240/02/$04.00+0     DOI: 10.1128/AEM.68.5.2535-2541.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.



This article has been cited by other articles:

  • Hamady, M., Knight, R. (2009). Microbial community profiling for human microbiome projects: Tools, techniques, and challenges. Genome Res 19: 1141-1152 [Abstract] [Full Text]  
  • van Doorn, R., Slawiak, M., Szemes, M., Dullemans, A. M., Bonants, P., Kowalchuk, G. A., Schoen, C. D. (2009). Robust Detection and Identification of Multiple Oomycetes and Fungi in Environmental Samples by Using a Novel Cleavable Padlock Probe-Based Ligation Detection Assay. Appl. Environ. Microbiol. 75: 4185-4193 [Abstract] [Full Text]  
  • Paliy, O., Kenche, H., Abernathy, F., Michail, S. (2009). High-Throughput Quantitative Analysis of the Human Intestinal Microbiota with a Phylogenetic Microarray. Appl. Environ. Microbiol. 75: 3572-3579 [Abstract] [Full Text]  
  • Miller, S. M., Tourlousse, D. M., Stedtfeld, R. D., Baushke, S. W., Herzog, A. B., Wick, L. M., Rouillard, J. M., Gulari, E., Tiedje, J. M., Hashsham, S. A. (2008). In Situ-Synthesized Virulence and Marker Gene Biochip for Detection of Bacterial Pathogens in Water. Appl. Environ. Microbiol. 74: 2200-2209 [Abstract] [Full Text]  
  • Huyghe, A., Francois, P., Charbonnier, Y., Tangomo-Bento, M., Bonetti, E.-J., Paster, B. J., Bolivar, I., Baratti-Mayer, D., Pittet, D., Schrenzel, J., and the Geneva Study Group on Noma (GESNOMA), (2008). Novel Microarray Design Strategy To Study Complex Bacterial Communities. Appl. Environ. Microbiol. 74: 1876-1885 [Abstract] [Full Text]  
  • Fierer, N., Liu, Z., Rodriguez-Hernandez, M., Knight, R., Henn, M., Hernandez, M. T. (2008). Short-Term Temporal Variability in Airborne Bacterial and Fungal Populations. Appl. Environ. Microbiol. 74: 200-207 [Abstract] [Full Text]  
  • Griffin, D. W. (2007). Atmospheric Movement of Microorganisms in Clouds of Desert Dust and Implications for Human Health. Clin. Microbiol. Rev. 20: 459-477 [Abstract] [Full Text]  
  • Lin, B., Blaney, K. M., Malanoski, A. P., Ligler, A. G., Schnur, J. M., Metzgar, D., Russell, K. L., Stenger, D. A. (2007). Using a Resequencing Microarray as a Multiple Respiratory Pathogen Detection Assay. J. Clin. Microbiol. 45: 443-452 [Abstract] [Full Text]  
  • Liu, W.-T., Guo, H., Wu, J.-H. (2007). Effects of Target Length on the Hybridization Efficiency and Specificity of rRNA-Based Oligonucleotide Microarrays. Appl. Environ. Microbiol. 73: 73-82 [Abstract] [Full Text]  
  • Malanoski, A. P., Lin, B., Wang, Z., Schnur, J. M., Stenger, D. A. (2006). Automated identification of multiple micro-organisms from resequencing DNA microarrays. Nucleic Acids Res 34: 5300-5311 [Abstract] [Full Text]  
  • Chandler, D. P., Jarrell, A. E., Roden, E. R., Golova, J., Chernov, B., Schipma, M. J., Peacock, A. D., Long, P. E. (2006). Suspension Array Analysis of 16S rRNA from Fe- and SO42-Reducing Bacteria in Uranium-Contaminated Sediments Undergoing Bioremediation.. Appl. Environ. Microbiol. 72: 4672-4687 [Abstract] [Full Text]  
  • Peplies, J., Lachmund, C., Glockner, F. O., Manz, W. (2006). A DNA Microarray Platform Based on Direct Detection of rRNA for Characterization of Freshwater Sediment-Related Prokaryotic Communities.. Appl. Environ. Microbiol. 72: 4829-4838 [Abstract] [Full Text]  
  • DeSantis, T. Z., Hugenholtz, P., Larsen, N., Rojas, M., Brodie, E. L., Keller, K., Huber, T., Dalevi, D., Hu, P., Andersen, G. L. (2006). Greengenes, a Chimera-Checked 16S rRNA Gene Database and Workbench Compatible with ARB.. Appl. Environ. Microbiol. 72: 5069-5072 [Abstract] [Full Text]  
  • Sanguin, H., Remenant, B., Dechesne, A., Thioulouse, J., Vogel, T. M., Nesme, X., Moenne-Loccoz, Y., Grundmann, G. L. (2006). Potential of a 16S rRNA-Based Taxonomic Microarray for Analyzing the Rhizosphere Effects of Maize on Agrobacterium spp. and Bacterial Communities.. Appl. Environ. Microbiol. 72: 4302-4312 [Abstract] [Full Text]  
  • Lin, B., Wang, Z., Vora, G. J., Thornton, J. A., Schnur, J. M., Thach, D. C., Blaney, K. M., Ligler, A. G., Malanoski, A. P., Santiago, J., Walter, E. A., Agan, B. K., Metzgar, D., Seto, D., Daum, L. T., Kruzelock, R., Rowley, R. K., Hanson, E. H., Tibbetts, C., Stenger, D. A. (2006). Broad-spectrum respiratory tract pathogen identification using resequencing DNA microarrays. Genome Res 16: 527-535 [Abstract] [Full Text]  
  • Wick, L. M., Rouillard, J. M., Whittam, T. S., Gulari, E., Tiedje, J. M., Hashsham, S. A. (2006). On-chip non-equilibrium dissociation curves and dissociation rate constants as methods to assess specificity of oligonucleotide probes. Nucleic Acids Res 34: e26-e26 [Abstract] [Full Text]  
  • Palmer, C., Bik, E. M., Eisen, M. B., Eckburg, P. B., Sana, T. R., Wolber, P. K., Relman, D. A., Brown, P. O. (2006). Rapid quantitative profiling of complex microbial populations. Nucleic Acids Res 34: e5-e5 [Abstract] [Full Text]  
  • Bontemps, C., Golfier, G., Gris-Liebe, C., Carrere, S., Talini, L., Boivin-Masson, C. (2005). Microarray-Based Detection and Typing of the Rhizobium Nodulation Gene nodC: Potential of DNA Arrays To Diagnose Biological Functions of Interest. Appl. Environ. Microbiol. 71: 8042-8048 [Abstract] [Full Text]  
  • Pozhitkov, A., Chernov, B., Yershov, G., Noble, P. A. (2005). Evaluation of Gel-Pad Oligonucleotide Microarray Technology by Using Artificial Neural Networks. Appl. Environ. Microbiol. 71: 8663-8676 [Abstract] [Full Text]  
  • Davignon, L., Walter, E. A., Mueller, K. M., Barrozo, C. P., Stenger, D. A., Lin, B., on behalf of the Epidemic Outbreak Surveillance Co, (2005). Use of Resequencing Oligonucleotide Microarrays for Identification of Streptococcus pyogenes and Associated Antibiotic Resistance Determinants. J. Clin. Microbiol. 43: 5690-5695 [Abstract] [Full Text]  
  • Smoot, L.M., Smoot, J.C., Smidt, H., Noble, P.A., Konneke, M., McMurry, Z.A., Stahl, D.A. (2005). DNA Microarrays as Salivary Diagnostic Tools for Characterizing the Oral Cavity's Microbial Community. ADR 18: 6-11 [Full Text]  
  • Park, H., Jang, H., Song, E., Chang, C. L., Lee, M., Jeong, S., Park, J., Kang, B., Kim, C. (2005). Detection and Genotyping of Mycobacterium Species from Clinical Isolates and Specimens by Oligonucleotide Array. J. Clin. Microbiol. 43: 1782-1788 [Abstract] [Full Text]  
  • Loy, A., Schulz, C., Lucker, S., Schopfer-Wendels, A., Stoecker, K., Baranyi, C., Lehner, A., Wagner, M. (2005). 16S rRNA Gene-Based Oligonucleotide Microarray for Environmental Monitoring of the Betaproteobacterial Order "Rhodocyclales". Appl. Environ. Microbiol. 71: 1373-1386 [Abstract] [Full Text]  
  • Castiglioni, B., Rizzi, E., Frosini, A., Sivonen, K., Rajaniemi, P., Rantala, A., Mugnai, M. A., Ventura, S., Wilmotte, A., Boutte, C., Grubisic, S., Balthasart, P., Consolandi, C., Bordoni, R., Mezzelani, A., Battaglia, C., De Bellis, G. (2004). Development of a Universal Microarray Based on the Ligation Detection Reaction and 16S rRNA Gene Polymorphism To Target Diversity of Cyanobacteria. Appl. Environ. Microbiol. 70: 7161-7172 [Abstract] [Full Text]  
  • Thompson, F. L., Iida, T., Swings, J. (2004). Biodiversity of Vibrios. Microbiol. Mol. Biol. Rev. 68: 403-431 [Abstract] [Full Text]  
  • Krause, D. O., Smith, W. J. M., McSweeney, C. S. (2004). Use of community genome arrays (CGAs) to assess the effects of Acacia angustissima on rumen ecology. Microbiology 150: 2899-2909 [Abstract] [Full Text]  
  • Chandler, D. P., Jarrell, A. E. (2004). Automated Purification and Suspension Array Detection of 16S rRNA from Soil and Sediment Extracts by Using Tunable Surface Microparticles. Appl. Environ. Microbiol. 70: 2621-2631 [Abstract] [Full Text]  
  • Steward, G. F., Jenkins, B. D., Ward, B. B., Zehr, J. P. (2004). Development and Testing of a DNA Macroarray To Assess Nitrogenase (nifH) Gene Diversity. Appl. Environ. Microbiol. 70: 1455-1465 [Abstract] [Full Text]  
  • Jenkins, B. D., Steward, G. F., Short, S. M., Ward, B. B., Zehr, J. P. (2004). Fingerprinting Diazotroph Communities in the Chesapeake Bay by Using a DNA Macroarray. Appl. Environ. Microbiol. 70: 1767-1776 [Abstract] [Full Text]  
  • Zoetendal, E. G., Collier, C. T., Koike, S., Mackie, R. I., Gaskins, H. R. (2004). Molecular Ecological Analysis of the Gastrointestinal Microbiota: A Review. J. Nutr. 134: 465-472 [Abstract] [Full Text]  
  • Adamczyk, J., Hesselsoe, M., Iversen, N., Horn, M., Lehner, A., Nielsen, P. H., Schloter, M., Roslev, P., Wagner, M. (2003). The Isotope Array, a New Tool That Employs Substrate-Mediated Labeling of rRNA for Determination of Microbial Community Structure and Function. Appl. Environ. Microbiol. 69: 6875-6887 [Abstract] [Full Text]  
  • Sebat, J. L., Colwell, F. S., Crawford, R. L. (2003). Metagenomic Profiling: Microarray Analysis of an Environmental Genomic Library. Appl. Environ. Microbiol. 69: 4927-4934 [Abstract] [Full Text]  
  • Urakawa, H., El Fantroussi, S., Smidt, H., Smoot, J. C., Tribou, E. H., Kelly, J. J., Noble, P. A., Stahl, D. A. (2003). Optimization of Single-Base-Pair Mismatch Discrimination in Oligonucleotide Microarrays. Appl. Environ. Microbiol. 69: 2848-2856 [Abstract] [Full Text]  
  • Chandler, D. P., Newton, G. J., Small, J. A., Daly, D. S. (2003). Sequence versus Structure for the Direct Detection of 16S rRNA on Planar Oligonucleotide Microarrays. Appl. Environ. Microbiol. 69: 2950-2958 [Abstract] [Full Text]  
  • Reyes-Lopez, M. A., Mendez-Tenorio, A., Maldonado-Rodriguez, R., Doktycz, M. J., Fleming, J. T., Beattie, K. L. (2003). Fingerprinting of prokaryotic 16S rRNA genes using oligodeoxyribonucleotide microarrays and virtual hybridization. Nucleic Acids Res 31: 779-789 [Abstract] [Full Text]  
  • Loy, A., Horn, M., Wagner, M. (2003). probeBase: an online resource for rRNA-targeted oligonucleotide probes. Nucleic Acids Res 31: 514-516 [Abstract] [Full Text]  


Copyright © 2009 by the American Society for Microbiology.   For an alternate route to Journals.ASM.org, visit: http://intl-journals.asm.org | More Info»