Isolation of Uncultivable Anaerobic Thermophiles of the Family Clostridiaceae Requiring Growth-Supporting Factors

  • Kim, Joong-Jae (Department of Biological Sciences, Graduate School of Science, Osaka University) ;
  • Kim, Hee-Na (Department of Biological Sciences, Graduate School of Science, Osaka University) ;
  • Masui, Ryoji (Department of Biological Sciences, Graduate School of Science, Osaka University) ;
  • Kuramitsu, Seiki (Department of Biological Sciences, Graduate School of Science, Osaka University) ;
  • Seo, Jin-Ho (Department of Agricultural Biotechnology, Seoul National University) ;
  • Kim, Kwang (Department of Biological Sciences, Graduate School of Science, Osaka University) ;
  • Sung, Moon-Hee (Department of Bio & Nanochemistry, Kookmin University, BioLeaders Corporation)
  • Published : 2008.04.30

Abstract

Novel groups of uncultivable anaerobic thermophiles were isolated from compost by enrichment cultivation in medium with a cell-free extract of Geobacillus toebii. The cell-free extract of G. toebii provided the medium with growth-supporting factors (GSF) needed to cultivate the previously uncultured microorganisms. Twenty-nine GSF-requiring candidates were successfully cultivated, and 16 isolated novel bacterial strains were classified into three different groups of uncultivable bacteria. The similarity among these 16 isolates and a phylogenetic analysis using 16S rRNA gene sequences revealed that these GSF-requiring strains represented novel groups within the family Clostridiaceae.

Keywords

References

  1. Bae, J. W., J. J. Kim, C. O. Jeon, K. Kim, J. J. Song, S. G. Lee, H. Poo, C. M. Jung, Y. H. Park, and M. H. Sung. 2003. Application of denaturing gradient gel electrophoresis to estimate the diversity of commensal thermophiles. J. Microbiol. Biotechnol. 13: 1008-1012
  2. Bae, J. W., J. R. Park, Y. H. Chang, S. K. Rhee, B. C. Kim, and Y. H. Park. 2004. Clostridium hastiforme is a later synonym of Tissierella praeacuta. Int. J. Syst. Evol. Microbiol. 54: 947-949 https://doi.org/10.1099/ijs.0.63068-0
  3. Bae, J. W., S. K. Rhee, J. R. Park, B. C. Kim, and Y. H. Park. 2005. Isolation of uncultivated anaerobic thermophiles from compost by supplementing cell extract of Geobacillus toebii in enrichment culture medium. Extremophiles 9: 477-485 https://doi.org/10.1007/s00792-005-0467-y
  4. Christian, S. R., R. M. Goodman, and J. Handelsman. 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6: 981-989 https://doi.org/10.1111/j.1462-2920.2004.00664.x
  5. Clardy, J., M. A. Fischbach, and C. T. Walsh. 2006. New antibiotics from bacterial natural products. Nat. Biotechnol. 24: 1541-1550 https://doi.org/10.1038/nbt1266
  6. Farrow, J. A., P. A. Lawson, H. Hippe, U. Gauglitz, and M. D. Collins. 1995. Phylogenetic evidence that the Gram-negative nonsporulating bacterium Tissierella (Bacteroides) praeacuta is a member of the Clostridium subphylum of the Gram-positive bacteria and description of Tissierella creatinini sp. nov. Int. J. Syst. Bacteriol. 45: 436-440 https://doi.org/10.1099/00207713-45-3-436
  7. Felsenstein, J. 1989. PHYLIP - phylogeny inference package (Version 3.2). Cladistics 5: 164-166
  8. Hugenholtz, P. 2002. Exploring prokaryotic diversity in the genomic era. Genome Biol. 3: 1-8
  9. Ji, S. C., D. Kim, J. H. Yoon, T. K. Oh, and C. H. Lee. 2006. Sequence-based screening for putative polyketide synthase gene-harboring clones from a soil metagenome library. J. Microbiol. Biotechnol. 16: 153-157
  10. Kaeberlein, T., K. Lewis, and S. S. Epstein. 2002. Isolating "uncultivable" microorganisms in pure culture in a simulated natural environment. Science 296: 1127-1129 https://doi.org/10.1126/science.1070633
  11. Kim, D. Y., E. Rha, S. L. Choi, J. J. Song, S. P. Hong, M. H. Sung, and S. G. Lee. 2007. Development of bioreactor system for L-tyrosine synthesis using thermostable tyrosine phenollyase. J. Microbiol. Biotechnol. 17: 116-122
  12. Lee, S. G., S. P. Hong, Y. H. Choi, Y. J. Chung, and M. H. Sung. 1997. Thermostable tyrosine phenol-lyase of Symbiobacterium sp. SC-1: Gene cloning, sequence determination, and overproduction in Escherichia coli. Protein Expr. Purif. 11: 263-270 https://doi.org/10.1006/prep.1997.0792
  13. Nicholas, K. B., H. B. Jr. Nicholas, and D. W. Deerfield II. 1997. GeneDoc: Analysis and visualization of genetic variation. EMBNEW. News 4: 14
  14. Ohno, M., H. Shiratori, M. J. Park, Y. Saitoh, Y. Kumon, N. Yamashita, A. Hirata, H. Hishida, K. Ueda, and T. Beppu. 2000. Symbiobacterium thermophilum gen. nov., sp. nov., a symbiotic thermophile that depends on co-culture with a Bacillus strain for growth. Int. J. Syst. Evol. Microbiol. 50: 1829-1832 https://doi.org/10.1099/00207713-50-5-1829
  15. Park, S. J., C. H. Kang, and S. K. Rhee. 2006. Characterization of the microbial diversity in a Korean solar saltern by 16S rRNA gene analysis. J. Microbiol. Biotechnol. 16: 1640-1645
  16. Rhee, S. K., C. O. Jeon, J. W. Bae, K. Kim, J. J. Song, J. J. Kim, S. G. Lee, H. I. Kim, S. P. Hong, Y. H. Choi, S. M. Kim, and M. H. Sung. 2002. Characterization of Symbiobacterium toebii, an obligate commensal thermophile isolated from compost. Extremophiles 6: 57-64 https://doi.org/10.1007/s007920100233
  17. Rhee, S. K., S. G. Lee, S. P. Hong, Y. H. Choi, J. H. Park, C. J. Kim, and M. H. Sung. 2000. A novel microbial interaction: Obligate commensalism between a new Gram-negative thermophile and a thermophilic Bacillus strain. Extremophiles 4: 131-136 https://doi.org/10.1007/s007920070027
  18. Rhee, S. K., S. P. Hong, J. W. Bae, C. O. Jeon, S. G. Lee, J. J. Song, H. Poo, and M. H. Sung. 2001. Estimation of distribution of a commensal thermophile in soil by competitive quantitative PCR and terminal restriction fragment length polymorphism analysis. J. Microbiol. Biotechnol. 11: 940-945
  19. Slobodkin, A. I., T. P. Tourova, N. A. Kostrikina, A. M. Lysenko, K. E. German, E. A. Bonch-Osmolovskaya, and N. K. Birkeland. 2006. Tepidimicrobium ferriphilum gen. nov., sp. nov., a novel moderately thermophilic, Fe(III)-reducing bacterium of the order Clostridiales. Int. J. Syst. Evol. Microbiol. 56: 369-372 https://doi.org/10.1099/ijs.0.63694-0
  20. Stackebrandt, E. and B. M. Goebel. 1994. Taxonomic note: A place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int. J. Syst. Bacteriol. 44: 846-849 https://doi.org/10.1099/00207713-44-4-846
  21. Sung, M. H., J. W. Bae, J. J. Kim, K. Kim, J. J. Song, S. K. Rhee, C. O. Jeon, Y. H. Choi, S. P. Hong, S. G. Lee, J. S. Ha, and G. T. Kang. 2003. Symbiobacterium toebii sp. nov., commensal thermophile isolated from Korean compost. J. Microbiol. Biotechnol. 13: 1013-1017
  22. Tanaka, Y., S. Hanada, A. Manome, T. Tsuchida, R. Kurane, K. Nakamura, and Y. Kamagata. 2004. Catellibacterium nectariphilum gen. nov., sp. nov., which requires a diffusible compound from a strain related to the genus Sphingomonas for vigorous growth. Int. J. Syst. Evol. Microbiol. 54: 955-959 https://doi.org/10.1099/ijs.0.02750-0
  23. Tanaka, Y., S. Hanada, H. Tamaki, K. Nakamura, and Y. Kamagata. 2005. Isolation and identification of bacterial strains producing diffusible growth factor(s) for Catellibacterium nectariphilum strain AST4T. Microbes Environ. 20: 110-116 https://doi.org/10.1264/jsme2.20.110
  24. Thompson, J. D., T. J. Gibson, F. Plewniak, F. Jeanmougin, and D. G. Higgins. 1997. The ClustalX windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24: 4876- 4882
  25. Wang, Q., G. M. Garrity, J. M. Tiedje, and J. R. Cole. 2007. Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy. Appl. Environ. Microbiol. 73: 5261-5267 https://doi.org/10.1128/AEM.00062-07
  26. Yu, J., W. Chung, T. K. Sohn, Y. H. Park, and H. Kim. 2006. Development of a meta-information system for microbial resources. J. Microbiol. Biotechnol. 16: 178-183