Development of a Meta-Information System for Microbial Resources

  • Yu Jae-Woo (proBionic Corp., Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Chung Won-Hyong (proBionic Corp.) ;
  • Sohn Tae-Kwon (proBionic Corp.) ;
  • Park Yong-Ha (proBionic Corp., Biological Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB)) ;
  • Kim Hong-Ik (proBionic Corp.)
  • Published : 2006.02.01

Abstract

Microbes are one of the most important bioresources in bioindustry and provide high economic values. Although there are currently about 6,000 bacterial species with validly published names, microbiologists generally assume that the number may account for less than 1% of the bacterial species present on Earth. To discover the remaining species, studies of metagenomes, metabolomes, and proteomes related to microbes have recently been carried out in various fields. We have constructed an information system that integrates various data on microbial resources and manages bioinformation to support efficient research of microorganisms. We have designated this system 'Bio-Meta Information System (Bio-MIS).' Bio-MIS consists of an integrated microbial resource database, a microbial resource input system, an integrated microbial resource search engine, a microbial resource online distribution system, a portal service, and management via the Internet. In the future, this system is expected to be connected with various public databases. We plan to implement useful bioinformatics software for analyzing microbial genome resources. The Web site is accessible at http://biomis.probionic.com.

Keywords

References

  1. Ahn, G.-T., J.-H. Kim, K.-M. Kang, M.-J. Lee, and I.-S. Han. 2004. BioPlace: A web-based collaborative environment for effective genome research. J. Microbiol. Biotechnol. 14: 1081-1085
  2. Bruskiewich, R. M., A. B. Cosico, W. Eusebio, A. M. Portugal, L. M. Ramos, M. T. Reyes, M. A. B. Sallan, V. J. M. Ulat, X. Wang, K. L. McNally, R. S. Hamilton, and C. G.. McLaren. 2003. Linking genotype to phenotype: The international rice information system (IRIS). Bioinformatics 19: i63-i65 https://doi.org/10.1093/bioinformatics/btg1006
  3. Bull, A. T., A. C. Ward, and M. Goodfellow. 2000. Search and discovery strategies for biotechnology: The paradigm shift. Microbiol. Molec. Biol. Rev. 64: 573-606 https://doi.org/10.1128/MMBR.64.3.573-606.2000
  4. Cole, J. R., B. Chai, T. L. Marsh, R. J. Farris, Q. Wang, S. A. Kulam, S. Chandra, D. M. McGarrell, T. M. Schmidt, G. M. Garrity, and J. M. Tiedje. 2001. The ribosomal database project (RDP-II): Previewing a new autoaligner that allows regular updates and the new prokaryotic taxonomy. Nucleic Acids Res. 29: 123-125 https://doi.org/10.1093/nar/29.1.123
  5. Demain, A. L. 2001. Genetics and microbiology of industrial microorganisms. J. Ind. Microbiol. Biotechnol. 27: 352- 356 https://doi.org/10.1038/sj.jim.7000187
  6. Desvaux, M. 2004. Mapping of carbon flow distribution in the central metabolic pathways of Clostridium cellulolyticum: Direct comparison of bacterial metabolism with a soluble versus an insoluble carbon source. J. Microbiol. Biotechnol. 14: 1200-1210
  7. Do, J. H., M. J. Anderson, D. W. Denning, and E. Bornberg- Bauer. 2004. Inference of Aspergillus fumigatus pathways by computational genome analysis: Tricarboxylic acid cycle (TCA) and glyoxylate shunt. J. Microbiol. Biotechnol. 14: 74-80
  8. Gelbart, W. M. 1998. Databases in genomic research. Science 282: 659-661 https://doi.org/10.1126/science.282.5389.659
  9. Hong, S. H., S. Y. Moon, and S. Y. Lee. 2003. Prediction of maximum yields of metabolites and optimal pathways for their production by metabolic flux analysis. J. Microbiol. Biotechnol. 13: 571-577
  10. Janssen, P., A. J. Enright, B. Audit, I. Cases, L. Goldovsky, N. Harte, V. Kunin, and C. A. Ouzounis. 2003. COmplete GENome tracking (COGENT): A flexible data environment for computational genomics. Bioinformatics 19: 1451-1452 https://doi.org/10.1093/bioinformatics/btg161
  11. Kim, T.-W., S.-H. Jung, J.-Y. Lee, S.-K. Choi, S.-H. Park, J.- S. Jo, and H.-Y. Kim. 2003. Identification of lactic acid bacteria in kimchi using SDS-PAGE profiles of whole cell proteins. J. Microbiol. Biotechnol. 13: 119-124
  12. Korth, H. F. and A. Silberschatz. 1991. Database System Concepts, pp. 53-91. 2nd Ed. McGraw-Hill Inc., 2 Penn Plaza, New York, U.S.A
  13. Larsen, N., R. Overbeek, S. Pramanik, T. M. Schmidt, E. E. Selkov, O. Strunk, J. M. Tiedje, and J. W. Urbance. 1997. Towards microbial data integration. J. Ind. Microbiol. Biotechnol. 18: 68-72 https://doi.org/10.1038/sj.jim.2900366
  14. Nelson, K. E. 2003. The future of microbial genomics. Environ. Microbiol. 5: 1223-1225 https://doi.org/10.1111/j.1462-2920.2003.00505.x
  15. Lee, J.-Y. and N. G. Lee. 2004. Transcriptional responses of human respiratory epithelial cells to nontypeable Haemophilus influenzae infection analyzed by high density cDNA microarrays. J. Microbiol. Biotechnol. 14: 836-843
  16. Paerl, H. W. and T. F. Steppe. 2003. Scaling up: The next challenge in environmental microbiology. Environ. Microbiol. 5: 1025-1038 https://doi.org/10.1046/j.1462-2920.2003.00504.x
  17. Peterson, J. D., L. A. Umayam, T. Dickinson, E. K. Hickey, and O. White. 2003. The comprehensive microbial resource. Nucleic Acids Res. 31: 442-443 https://doi.org/10.1093/nar/gkg039
  18. Stein, L. D. 2003. Integrating biological databases. Nature Rev. Genet. 4: 337-345 https://doi.org/10.1038/nrg1065
  19. Tiedje, J. M. 1995. Approaches to the comprehensive evaluation of prokaryotic diversity of a habitat, pp. 73-87. In D. Allsopp, R. R. Colwell, and D. L. Hawksworth (eds.), Microbial Diversity and Ecosystem Function. CAB International, Wallingford, U.K
  20. Torsvik, V. and L. Ovreas. 2002. Microbial diversity and function in soil: From genes to ecosystems. Curr. Opin. Microbiol. 5: 240-245 https://doi.org/10.1016/S1369-5274(02)00324-7
  21. Yagisawa, M. 2000. Trends in exploratory research of microbial metabolite part 1; 50 years from the discovery of penicillin. Bioscience and Industry 58: 12-17
  22. http://www.tigr.org/tigr-scripts/CMR2/CMR_Content.spl (The Comprehensive Microbial Resource)
  23. http://rdp.cme.msu.edu/html/ (The Ribosomal Database Project)