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New Methods to Access Microbial Diversity for Small Molecule Discovery

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Natural Products

Abstract

Natural-product-derived drugs are a major portion of the total number of approved drugs in the antibacterial area. The majority of bacteria and fungi in the environment is only known by molecular fingerprints and has resisted cultivation. Therefore, new methods have been developed to access this tremendous microbial diversity for the discovery of novel small molecules. These culture-dependent and -independent methods include a novel high-throughput cultivation technology as well as a recombinant approach to discover and express novel natural products.

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References

  1. Fleming A. On the antibacterial action of cultures of a Penicillium, with a special reference to their use in the isolation of B. influenze. Brit J Exp Path 1929;10:226–236.

    CAS  Google Scholar 

  2. Vicente MF, Basilio A, Cabello A, Peláez F. Microbial natural products as a source of antifungals. Clin Microbiol Infect 2003;9:15–32.

    PubMed  CAS  Google Scholar 

  3. Strohl WR. Industrial antibiotics: today and the future. In: Strohl WR (ed), Biotechnology of Antibiotics. Marcel Dekker, New York: 1997; pp. 1–47.

    Google Scholar 

  4. Demain AL, Lancini G. Bacterial pharmaceutical products. In: Dworkin Mea (ed), The Prokaryotes: An Evolving Electronic Resource for the Microbiological Community. New-York: Springer-Verlag, 2001; http://link.springer-ny.com/link/service/books/10125/.

    Google Scholar 

  5. Lazzarini A, Cavaletti L, Toppo G, Marinelli F. Rare genera of actinomycetes as potential producers of new antibiotics. Antonie van Leeuwenhoek 2001;79:399–405.

    PubMed  CAS  Google Scholar 

  6. Bellais S, Poirel L, Leotard S, Naas T, Nordmann P. Genetic diversity of carbapenem-hydrolyzing metallo-beta-lactamases from Chryseobacterium (Flavobacterium) indologenes. Antimicrob Agents Chemother 2000;44:3028–3034.

    PubMed  CAS  Google Scholar 

  7. Golakoti T, Yoshida WY, Chaganty S, Moore RE. Isolation and structure determination of nostocyclopeptides A1 and A2 from the terrestrial cyanobacterium Nostoc sp. ATCC53789. J Nat Prod 2001;64:54–59.

    PubMed  CAS  Google Scholar 

  8. Kawulka K, Sprules T, McKay RT, et al. Structure of subtilosin A, an antimicrobial peptide from Bacillus subtilis with unusual posttranslational modifications linking cysteine sulfurs to alpha-carbons of phenylalanine and threonine. J Am Chem Soc 2003;125:4726–4727.

    PubMed  CAS  Google Scholar 

  9. Reichenbach H. Myxobacteria, producers of novel bioactive substances. J Ind Microbiol Biotechnol 2001;27:149–156.

    PubMed  CAS  Google Scholar 

  10. Silver L, Bostian K. Screening of natural products for antimicrobial agents. Eur J Clin Microbiol Infect Dis 1990;9:455–461.

    PubMed  CAS  Google Scholar 

  11. Strohl WR. The role of natural products in a modern drug discovery program. Drug Discov Today 2000;5:39–41.

    PubMed  Google Scholar 

  12. Silva CJ, Brian P, Peterson T. Screening of combinatorial biology libraries for natural products discovery. In: Seethala R, Fernandes PB (eds), Handbook of Drug Screening. New York: Marcel Dekker, 2001; pp. 357–382.

    Google Scholar 

  13. Zähner H, Fiedler H-P. The need for new antibiotics: possible ways forward. In: Russell NJ (ed), Fifty Years of Antimicrobials: Past Perspectives and Future Trends. Cambridge University Press, Cambridge, England: 1995; pp. 67–84.

    Google Scholar 

  14. Class S. Pharma Overview. Chem Eng News 2002;80:39–49.

    Google Scholar 

  15. Newman DJ, Cragg GM, Snader KM. Natural products as sources of new drugs over the period 1981-2002. J Nat Prod 2003;66:1022–1037.

    PubMed  CAS  Google Scholar 

  16. Walsh C. Where will new antibiotics come from? Nat Rev Microbiol 2003;1:65–70.

    PubMed  CAS  Google Scholar 

  17. Torsvik V, Salte K, Sørheim R, Goksøyr J. Comparison of phenotypic diversity and DNA heterogeneity in a population of soil bacteria. Appl Environ Microbiol 1990;56:776–781.

    PubMed  CAS  Google Scholar 

  18. Torsvik V, Øvreås L, Thingstad TF. Prokaryotic diversity-magnitude, dynamics, and controlling factors. Science 2002;296:1064–1066.

    PubMed  CAS  Google Scholar 

  19. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ. Counting the uncountable: statistical approaches to estimating microbial diversity. Appl Environ Microbiol 2001;67:4399–4406.

    PubMed  CAS  Google Scholar 

  20. Dykhuizen DE. Santa Rosalia revisited: why are there so many species of bacteria? Antonie van Leeuwenhoek 1998;73:25–33.

    PubMed  CAS  Google Scholar 

  21. Amann RI, Ludwig W, Schleifer K-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 1995;59:143–169.

    PubMed  CAS  Google Scholar 

  22. Whitman WB, Coleman DC, Wiebe WJ. Prokaryotes: the unseen majority. Proc Natl Acad Sci USA 1998;95:6578–6583.

    PubMed  CAS  Google Scholar 

  23. Gray KA, Richardson TH, Kretz K, et al. Rapid evolution of reversible denaturation and elevated melting temperature in a microbial haloalkane dehalogenase. Adv Synth Catal 2001;343:607–617.

    CAS  Google Scholar 

  24. DeSantis G, Zhu Z, Greenberg WA, et al. An enzyme library approach to biocatalysis: development of nitrilases for enantioselective production of carboxylic acid derivatives. J Am Chem Soc 2002;124:9024–9025.

    PubMed  CAS  Google Scholar 

  25. Dunbar J, Barns SM, Ticknor LO, Kuske CR. Empirical and theoretical bacterial diversity in four Arizona soils. Appl Environ Microbiol 2002;68:3035–3045.

    PubMed  CAS  Google Scholar 

  26. Richardson TH, Tan X, Frey G, et al. A novel, high performance enzyme for starch liquefaction. Discovery and optimization of a low pH, thermostable alpha-amylase. J Biol Chem 2002;277: 26,501–26,507.

    PubMed  CAS  Google Scholar 

  27. Keller M, Zengler K. Tapping into microbial diversity. Nat Rev Microbiol 2004;2:141–150.

    PubMed  CAS  Google Scholar 

  28. Hugenholtz P, Pitulle C, Hershberger KL, Pace NR. Novel division level bacterial diversity in a Yellowstone hot spring. J Bacteriol 1998;180:366–376.

    PubMed  CAS  Google Scholar 

  29. Curtis TP, Sloan WT, Scannell JW. Estimating prokaryotic diversity and its limits. Proc Natl Acad Sci USA 2002;99:10,494–10,499.

    PubMed  CAS  Google Scholar 

  30. Venter JC, Remington K, Heidelberg JF, et al. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004;304:66–74.

    PubMed  CAS  Google Scholar 

  31. Woese CR, Stackebrandt E, Macke TJ, Fox GE. A phylogenetic definition of the major eubacterial taxa. Syst Appl Microbiol 1985;6:143–151.

    PubMed  CAS  Google Scholar 

  32. Rappé MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol 2003;57: 369–394.

    PubMed  Google Scholar 

  33. Dojka MA, Harris JK, Pace NR. Expanding the known diversity and environmental distribution of an uncultured phylogenetic division of bacteria. Appl Environ Microbiol 2000;66:1617–1621.

    PubMed  CAS  Google Scholar 

  34. Rosselló-Mora R, Amann R. The species concept for prokaryotes. FEMS Microbiol Rev 2001;25:39–67.

    Article  PubMed  Google Scholar 

  35. DSMZ. http://www.dsmz.de/bactnom/bactname.htm. Bacterial nomenclature up-to-date, 2003.

  36. Dictionary of Natural Products New York: Chapman & Hall/CRC, 2003.

    Google Scholar 

  37. Keller NP, Hohn TM. Metabolic pathway gene clusters in filamentous fungi. Fungal Genet Biol 1997;21:17–29.

    PubMed  CAS  Google Scholar 

  38. Yu TW, Bai L, Clade D, et al. The biosynthetic gene cluster of the maytansinoid antitumor agent ansamitocin from Actinosynnema pretiosum. Proc Natl Acad Sci USA 2002;99:7968–7973.

    PubMed  CAS  Google Scholar 

  39. Pasteur L. Animalcules infusoires vivant sans gaz oxygène libre et déterminant des fermentations. CR Acad Sci 1861;52:344–347.

    Google Scholar 

  40. Koch R. Untersuchungen über Bakterien VI. Verfahren zur Untersuchung, zum Conservieren und Photographieren. Beitr Biol Pflanz 1877;2:399–434.

    Google Scholar 

  41. Beijerinck WM. Ueber Spirillum desulfuricans als Ursache von Sulfatreduktion. Zentralblatt Bakteriol 1895;1:1–9, 49-59, 104-114.

    Google Scholar 

  42. Winogradsky S. Ueber Schwefelbacterien. Botanische Zeitung 1887;45:489–507, 513-523, 529-539, 545-559, 569-576, 585-594 and 606-610.

    Google Scholar 

  43. Ferguson RL, Buckley EN, Palumbo AV. Response of marine bacterioplankton to differential filtration and confinement. Appl Environ Microbiol 1984;47:49–55.

    PubMed  CAS  Google Scholar 

  44. Eilers H, Pernthaler J, Glöckner FO, Amann R. Culturability and in situ abundance of pelagic bacteria from the North Sea. Appl Environ Microbiol 2000;66:3044–3051.

    PubMed  CAS  Google Scholar 

  45. Staley JT, Konopka A. Measurement of in situ activities of nonphotosynthetic microorganisms in aquatic and terrestrial habitats. Annu Rev Microbiol 1985;39:321–346.

    PubMed  CAS  Google Scholar 

  46. Xu HS, Roberts N, Singleton FL, Attwell RW, Grimes DJ, Colwell RR. Survival and viability of nonculturable Escherichia coli and Vibrio cholerae in the estuarine and marine environment. Microb Ecol 1982;8:313–323.

    Google Scholar 

  47. Janssen PH, Yates PS, Grinton BE, Taylor PM, Sait M. Improved culturability of soil bacteria and isolation in pure culture of novel members of the divisions Acidobacteria, Actinobacteria, Proteobacteria, and Verrucomicrobia. Appl Environ Microbiol 2002;68:2391–2396.

    PubMed  CAS  Google Scholar 

  48. Chin KJ, Hahn D, Hengstmann U, Liesack W, Janssen PH. Characterization and identification of numerically abundant culturable bacteria from the anoxic bulk soil of rice paddy microcosms. Appl Environ Microbiol 1999;65:5042–5049.

    PubMed  CAS  Google Scholar 

  49. Sait M, Hugenholtz P, Janssen PH. Cultivation of globally distributed soil bacteria from phylogenetic lineages previously only detected in cultivation-independent surveys. Environ Microbiol 2002;4:654–666.

    PubMed  CAS  Google Scholar 

  50. Joseph SJ, Hugenholtz P, Sangwan P, Osborne CA, Janssen PH. Laboratory cultivation of widespread and previously uncultured soil bacteria. Appl Environ Microbiol 2003;69:7210–7215.

    PubMed  CAS  Google Scholar 

  51. Guan LL, Onuki H, Kamino K. Bacterial growth stimulation with exogenous siderophore and synthetic N-acyl homoserine lactone autoinducers under iron-limited and low-nutrient conditions. Appl Environ Microbiol 2000;66:2797–2803.

    PubMed  CAS  Google Scholar 

  52. Guan LL, Kamino K. Bacterial response to siderophore and quorum-sensing chemical signals in the seawater microbial community. BMC Microbiol 2001;1:27.

    PubMed  CAS  Google Scholar 

  53. Bussmann I, Philipp B, Schink B. Factors influencing the cultivability of lake water bacteria. J Microbiol Methods 2001;47:41–50.

    PubMed  CAS  Google Scholar 

  54. Bruns A, Cypionka H, Overmann J. Cyclic AMP and acyl homoserine lactones increase the cultivation efficiency of heterotrophic bacteria from the Central Baltic Sea. Appl Environ Microbiol 2002;68:3978–3987.

    PubMed  CAS  Google Scholar 

  55. Bruns A, Nübel U, Cypionka H, Overmann J. Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton. Appl Environ Microbiol 2003;69: 1980–1989.

    PubMed  CAS  Google Scholar 

  56. Button DK, Schut F, Quang P, Martin R, Roberston BR. Viability and isolation of marine bacteria by dilution culture: theory, procedures, and initial results. Appl Environ Microbiol 1993;59:881–891.

    PubMed  Google Scholar 

  57. Kaeberlein T, Lewis K, Epstein SS. Isolating “uncultivable” microorganisms in pure culture in a simulated natural environment. Science 2002;296:1127–1129.

    PubMed  CAS  Google Scholar 

  58. Zengler K, Toledo G, Rappe M, et al. Cultivating the uncultured. Proc Natl Acad Sci USA 2002;99:15,681–15,686.

    PubMed  CAS  Google Scholar 

  59. Connon SA, Giovannoni SJ. High-throughput methods for culturing microorganisms in verylow-nutrient media yield diverse new marine isolates. Appl Environ Microbiol 2002;68:3878–3885.

    PubMed  CAS  Google Scholar 

  60. Morris RM, Rappe MS, Connon SA, et al. SAR11 clade dominates ocean surface bacterioplankton communities. Nature 2002;420:806–810.

    PubMed  CAS  Google Scholar 

  61. Orsini F, Ami D, Villa AM, Sala G, Bellotti MG, Doglia SM. FT-IR microspectroscopy for microbiological studies. J Microbiol Methods 2000;42:17–27.

    PubMed  CAS  Google Scholar 

  62. Wenning M, Seiler H, Scherer S. Fourier-transform infrared microspectroscopy, a novel and rapid tool for identification of yeasts. Appl Environ Microbiol 2002;68:4717–4721.

    PubMed  CAS  Google Scholar 

  63. Short JM. Recombinant approaches for accessing biodiversity. Nat Biotechnol 1997;15:1322–1323.

    PubMed  CAS  Google Scholar 

  64. Short JM et al. Patents US 5,763,239; US 5,958,672; US 6,001,574; US 6,004,788; US 6,030,779; US 6,054,267; US 6,057,103; US 6,168,919; US 6,174,673; US 6,368,798; US 6,444,426; US 6,455,254; AU718,573; AU 720,334; AU 756,201 (1201-1AU).

    Google Scholar 

  65. Greenberg WA, Varvak A, Hanson SR, et al. Development of an efficient, scalable, aldolasecatalyzed process for enantioselective synthesis of statin intermediates. Proc Natl Acad Sci USA 2004;101:5788–5793.

    PubMed  CAS  Google Scholar 

  66. Robertson DE, Steer BA. Recent progress in biocatalyst discovery and optimization. Curr Opin Chem Biol 2004;8:141–149.

    PubMed  CAS  Google Scholar 

  67. Schloss PD, Handelsman J. Biotechnological prospects from metagenomics. Curr Opin Biotechnol 2003;14:303–310.

    PubMed  CAS  Google Scholar 

  68. Rondon MR, Raffel SJ, Goodman RM, Handelsman J. Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus. Proc Natl Acad Sci USA 1999;96:6451–6455.

    PubMed  CAS  Google Scholar 

  69. Rondon MR, August PR, Bettermann AD, et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl Environ Microbiol 2000;66:2541–2547.

    PubMed  CAS  Google Scholar 

  70. Wang GY, Graziani E, Waters B, et al. Novel natural products from soil DNA libraries in a streptomycete host. Org Lett 2000;2:2401–2404.

    PubMed  CAS  Google Scholar 

  71. MacNeil IA, Tiong CL, Minor C, et al. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J Mol Microbiol Biotechnol 2001;3:301–308.

    PubMed  CAS  Google Scholar 

  72. Piel J. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc Natl Acad Sci USA 2002;99:14,002–14,007.

    PubMed  CAS  Google Scholar 

  73. Hopwood DA. Streptomyces genes: from Waksman to Sanger. J Ind Microbiol Biotechnol 2003;30:468–471.

    PubMed  CAS  Google Scholar 

  74. Martin JF, Liras P. Organization and expression of genes involved in the biosynthesis of antibiotics and other secondary metaboites. Annu Rev Microbiol 1989;43:173–206.

    PubMed  CAS  Google Scholar 

  75. Hidaka T, Goda M, Kuzuyama T, Takei N, Hidaka M, Seto H. Cloning and nucleotide sequence of fosfomycin biosynthetic genes of Streptomyces wedmorensis. Mol Gen Genet 1995;249:274–280.

    PubMed  CAS  Google Scholar 

  76. Hammer PE, Hill DS, Lam ST, Van Pée KH, Ligon JM. Four genes from Pseudomonas fluorescens that encode the biosynthesis of pyrrolnitrin. Appl Environ Microbiol 1997;63:2147–2154.

    PubMed  CAS  Google Scholar 

  77. Aparicio JF, Caffrey P, Gil JA, Zotchev SB. Polyene antibiotic biosynthesis gene clusters. Appl Microbiol Biotechnol 2003;61:179–188.

    PubMed  CAS  Google Scholar 

  78. August PR, Tang L, Yoon YJ, et al. Biosynthesis of the ansamycin antibiotic rifamycin: deductions from the molecular analysis of the rif biosynthetic gene cluster of Amycolatopsis mediterranei S699. Chem Biol 1998;5:69–79.

    PubMed  CAS  Google Scholar 

  79. Paradkar A, Trefzer A, Chakraburtty R, Stassi D. Streptomyces genetics: a genomic perspective. Crit Rev Biotechnol 2003;23:1–27.

    PubMed  CAS  Google Scholar 

  80. Malpartida F, Hopwood DA. Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host. Nature 1984;309:462–464.

    PubMed  CAS  Google Scholar 

  81. Omura S, Ikeda H, Ishikawa J, et al. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Natl Acad Sci USA 2001;98:12,215–12,220.

    PubMed  CAS  Google Scholar 

  82. Bentley SD, Chater KF, Cerdeño-Tárraga AM, et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 2002;417:141–147.

    PubMed  Google Scholar 

  83. Motamedi H, Hutchinson CR. Cloning and heterologous expression of a gene cluster for the biosynthesis of tetracenomycin C, the anthracycline antitumor antibiotic of Streptomyces glaucescens. Proc Natl Acad Sci USA 1987;84:4445–4449.

    PubMed  CAS  Google Scholar 

  84. Gould SJ, Hong ST, Carney JR. Cloning and heterologous expression of genes from the kinamycin biosynthetic pathway of Streptomyces murayamaensis. J Antibiot 1998;51:50–57.

    PubMed  CAS  Google Scholar 

  85. Bormann C, Mohrle V, Bruntner C. Cloning and heterologous expression of the entire set of structural genes for nikkomycin synthesis from Streptomyces tendae Tu901 in Streptomyces lividans. J Bacteriol 1996;178:1216–1218.

    PubMed  CAS  Google Scholar 

  86. Lacalle RA, Tercero JA, Jiménez A. Cloning of the complete biosynthetic gene cluster for an aminonucleoside antibiotic, puromycin, and its regulated expression in heterologous hosts. EMBO J 1992;11:785–792.

    PubMed  CAS  Google Scholar 

  87. Sanchéz C, Butovich IA, Braña AF, Rohr J, Méndez C, Salas JA. The biosynthetic gene cluster for the antitumor rebeccamycin: characterization and generation of indolocarbazole derivatives. Chem Biol 2002;9:519–531.

    PubMed  Google Scholar 

  88. Tang L, Shah S, Chung L, et al. Cloning and heterologous expression of the epothilone gene cluster. Science 2000;287:640–642.

    PubMed  CAS  Google Scholar 

  89. Julien B, Shah S. Heterologous expression of epothilone biosynthetic genes in Myxococcus xanthus. Antimicrob Agents Chemother 2002;46:2772–2778.

    PubMed  CAS  Google Scholar 

  90. Eppelmann K, Doekel S, Marahiel MA. Engineered biosynthesis of the peptide antibiotic bacitracin in the surrogate host Bacillus subtilis. J Biol Chem 2001;276:34,824–34,831.

    PubMed  CAS  Google Scholar 

  91. Kimura H, Miyashita H, Sumino Y. Organization and expression in Pseudomonas putida of the gene cluster involved in cephalosporin biosynthesis from Lysobacter lactamgenus YK90. Appl Microbiol Biotechnol 1996;45:490–501.

    PubMed  CAS  Google Scholar 

  92. Mercado-Blanco J, van der Drift KM, Olsson PE, Thomas-Oates JE, van Loon LC, Bakker PA. Analysis of the pmsCEAB gene cluster involved in biosynthesis of salicylic acid and the siderophore pseudomonine in the biocontrol strain Pseudomonas fluorescens WCS374. J Bacteriol 2001;183:1909–1920

    PubMed  CAS  Google Scholar 

  93. Thomson NR, Crow MA, McGowan SJ, Cox A, Salmond GP. Biosynthesis of carbapenem antibiotic and prodigiosin pigment in Serratia is under quorum sensing control. Mol Microbiol 2000;36:539–556.

    PubMed  CAS  Google Scholar 

  94. Brady SF, Chao CJ, Handelsman J, Clardy J. Cloning and heterologous expression of a natural product biosynthetic gene cluster from eDNA. Org Lett 2001;3:1981–1984.

    PubMed  CAS  Google Scholar 

  95. Brady SF, Clardy J. Long-chain N-acyl amino acid antibiotics isolated from heterologously expressed environmental DNA. J Am Chem Soc 2000;122:12,903–12,904.

    CAS  Google Scholar 

  96. Brady SF, Chao CJ, Clardy J. New natural product families from an environmental DNA (eDNA) gene cluster. J Am Chem Soc 2002;124:9968–9969.

    PubMed  CAS  Google Scholar 

  97. Gillespie DE, Brady SF, Bettermann AD, et al. Isolation of antibiotics turbomycin a and B from a metagenomic library of soil microbial DNA. Appl Environ Microbiol 2002;68:4301–4306.

    PubMed  CAS  Google Scholar 

  98. Zazopoulos E, Huang K, Staffa A, et al. A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nature Biotechnol 2003;21:187–190.

    CAS  Google Scholar 

  99. Ioannou PA, Amemiya CT, Garnes J, et al. A new bacteriophage P1-derived vector for the propagation of large human DNA fragments. Nature Genet 1994;6:84–89.

    PubMed  CAS  Google Scholar 

  100. Sosio M, Giusino F, Cappellano C, Bossi E, Puglia AM, Donadio S. Artificial chromosomes for antibiotic-producing actinomycetes. Nature Biotechnol 2000;18:343–345.

    CAS  Google Scholar 

  101. Shizuya H, Birren B, Kim UJ, et al. Cloning and stable maintenance of 300-kilobase-pair fragments of human DNA in Escherichia coli using an F-factor-based vector. Proc Natl Acad Sci USA 1992;89:8794–8797.

    PubMed  CAS  Google Scholar 

  102. Deckert G, Warren PV, Gaasterland T, et al. The complete genome of the hyperthermophilic bacterium Aquifex aeolicus. Nature 1998;392:353–358.

    PubMed  CAS  Google Scholar 

  103. Brosch R, Gordon SV, Billault A, et al. Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing, and comparative genomics. Infect Immun 1998;66:2221–2229.

    PubMed  CAS  Google Scholar 

  104. Xu Y, Jiang L, Murray BE, Weinstock GM. Enterococcus faecalis antigens in human infections. Infect Immun 1997;65:4207–4215.

    PubMed  CAS  Google Scholar 

  105. Tauch A, Homann I, Mormann S, et al. Strategy to sequence the genome of Corynebacterium glutamicum ATCC 13032: use of a cosmid and a bacterial artificial chromosome library. J Biotechnol 2002;95:25–38.

    PubMed  CAS  Google Scholar 

  106. Alduina R, De Grazia S, Dolce L, et al. Artificial chromosome libraries of Streptomyces coelicolor A3(2) and Planobispora rosea. FEMS Microbiol Lett 2003;218:181–186.

    PubMed  CAS  Google Scholar 

  107. Zhou J, Bruns MA, Tiedje JM. DNA recovery from soils of diverse composition. Appl Environ Microbiol 1996;62:316–322.

    PubMed  CAS  Google Scholar 

  108. Stein JL, Marsh TL, Wu KY, Shizuya H, DeLong EF. Characterization of uncultivated prokaryotes: isolation and analysis of a 40-kilobase-pair genome fragment from a planktonic marine archaeon. J Bacteriol 1996;178:591–599.

    PubMed  CAS  Google Scholar 

  109. Han J, Craighead HG. Separation of long DNA molecules in a microfabricated entropic trap array. Science 2000;288:1026–1029.

    PubMed  CAS  Google Scholar 

  110. Martin-Laurent F, Philippot L, Hallet S, et al. DNA extraction from soils: old bias for new microbial diversity analysis methods. Appl Environ Microbiol 2001;67:2354–2359.

    PubMed  CAS  Google Scholar 

  111. Short JM et al. U.S. Patents: US 5,763239; US 5,763,239; US 6,001,574; US 6,057,103; US 6,174,673; US 6,368,798.

    Google Scholar 

  112. Palackal N, Brennan Y, Callen WN, et al. An evolutionary route to xylanase process fitness. Protein Sci 2004;13:494–503.

    PubMed  CAS  Google Scholar 

  113. Robertson DE, Chaplin JA, DeSantis G, et al. Exploring nitrilase sequence space for enantioselective catalysis. Appl Environ Microbiol 2004;70:2429–2436.

    PubMed  CAS  Google Scholar 

  114. Béjà O, Suzuki MT, Koonin EV, et al. Construction and analysis of bacterial artificial chromosome libraries from a marine microbial assemblage. Environ Microbiol 2000;2:516–529.

    PubMed  Google Scholar 

  115. Berry AE, Chiocchini C, Selby T, Sosio M, Wellington EMH. Isolation of high molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol Lett 2003;223:15–20.

    PubMed  CAS  Google Scholar 

  116. Courtois S, Cappellano CM, Ball M, et al. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Appl Environ Microbiol 2003;69:49–55.

    PubMed  CAS  Google Scholar 

  117. Gray KA, Richardson TH, Robertson DE, Swanson PE, Subramanian MV. Soil-based gene discovery: a new technology to accelerate and broaden biocatalytic applications. Adv Appl Microbiol 2003;52:1–27.

    PubMed  CAS  Google Scholar 

  118. Short JM. US 6,455,254.

    Google Scholar 

  119. Leadlay PF. Combinatorial approaches to polyketide biosynthesis. Curr Opin Chem Biol 1997;1:162–168.

    PubMed  CAS  Google Scholar 

  120. Hutchinson CR. Antibiotics from genetically engineered microorganisms. In: Strohl WR (ed), Biotechnology of Antibiotics. Vol. 82. Marcel Dekker, New York: 1997; pp. 683–702.

    Google Scholar 

  121. Zuber P, Marahiel MA. Structure, function, and regulation of genes encoding multidomain peptide synthetases. In: Strohl WR (ed), Biotechnology of Antibiotics. Vol. 82. Marcel Dekker, New York: 1997; pp. 187–216.

    Google Scholar 

  122. Strohl WR, Dickens ML, Rajgarhia VB, Woo AJ, Priestley ND. Anthracyclines. In: Strohl WR (ed), Biotechnology of Antibiotics. Vol. 82. Marcel Dekker, New York: 1997; pp. 577–657.

    Google Scholar 

  123. Ichinose K, Ozawa M, Itou K, Kunieda K, Ebizuka Y. Cloning, sequencing and heterologous expression of the medermycin biosynthetic gene cluster of Streptomyces sp. AM-7161: towards comparative analysis of the benzoisochromanequinone gene clusters. Microbiology 2003;149: 1633–1645.

    PubMed  CAS  Google Scholar 

  124. Izumikawa M, Murata M, Tachibana K, Ebizuka Y, Fujii I. Cloning of modular type I polyketide synthase genes from salinomycin producing strain of Streptomyces albus. Bioorg Med Chem 2003;11:3401–3405.

    PubMed  CAS  Google Scholar 

  125. Seow KT, Meurer G, Gerlitz M, Wendt-Pienkowski E, Hutchinson CR, Davies J. A study of iterative type II polyketide synthases, using bacterial genes cloned from soil DNA: a means to access and use genes from uncultured microorganisms. J Bacteriol 1997;179:7360–7368.

    PubMed  CAS  Google Scholar 

  126. Short JM et al. U.S. Patents: US 6,030,779; US 6,344,288 B1; US 6,368,798 B1; US 6,455,254 B1.

    Google Scholar 

  127. Short JM. WO0196551.

    Google Scholar 

  128. Donadio S, Monciardini P, Alduina R, et al. Microbial technologies for the discovery of novel bioactive metabolites. J Biotechnol 2002;99:187–198.

    PubMed  CAS  Google Scholar 

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© 2005 Humana Press Inc., Totowa, NJ

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Zengler, K., Paradkar, A., Keller, M. (2005). New Methods to Access Microbial Diversity for Small Molecule Discovery. In: Zhang, L., Demain, A.L. (eds) Natural Products. Humana Press. https://doi.org/10.1007/978-1-59259-976-9_12

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  • DOI: https://doi.org/10.1007/978-1-59259-976-9_12

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