Biotechnology and Applied Microbiology

  • Eugene Rosenberg
Reference work entry


This chapter places applied microbiology and biotechnology into a historical perspective and then presents an overview of some of the general principles related to the biotechnology of prokaryotes. Topics discussed include antibiotics, biochemical engineering, applications of genetic engineering, bioremediation, bacterial pharmaceutical products, diagnostic microbiology, food microbiology, and legal protection in biotechnology. Applied microbiology is constantly expanding and new areas are being created. In the near future, the fields of prebiotics and probiotics, enzyme engineering, applied microbial ecology, and biofuels look particularly promising.


Alcoholic Fermentation Strain Improvement Lactic Acid Fermentation Food Microbiology Diagnostic Microbiology 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Aharonowitz Y, Cohen G (1981) The microbiological production of pharmaceuticals. Sci Am 245:106–119CrossRefGoogle Scholar
  2. Baylinski DA, Wirsen CE, Jannasch HW (1989) Microbial utilization of naturally occurring hydrocarbons at the Guaymas Basin hydrothermal vent site. Appl Environ Microbiol 55:2832–2836Google Scholar
  3. Bengmark S (1998) Ecological control of the gastrointestinal tract. Gut 42:2–7PubMedCrossRefGoogle Scholar
  4. Biello D (2010) Meet the microbes eating the gulf oil spill. Sci Am 303:14–17Google Scholar
  5. Cani PD, Delzenne NM (2009) The role of the gut microbiota in energy metabolism and metabolic disease. Curr Pharm Des 15:1546–1558PubMedCrossRefGoogle Scholar
  6. Cases I, Lorenzo V (2005) Genetically modified organisms for the environment: stories of success and failure and what we have learned from them. Int Microbiol 8:213–222PubMedGoogle Scholar
  7. Cernilia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3:351–368CrossRefGoogle Scholar
  8. Chakrabarty AM, Gunsalus IC (1971) Degradative pathways specified by extrachromosomal gene clusters. Pseudomonas Genet 68:510Google Scholar
  9. Chapin-Robertson K (1993) Use of molecular diagnostics in sexually transmitted diseases: critical assessment. Diagn Microbiol Infect Dis 16:173–184PubMedCrossRefGoogle Scholar
  10. Chen W, Bruhlmann F, Richins RD, Mulchandani A (1999) Engineering of improved microbes and enzymes for bioremediation. Curr Opin Biotechnol 10:137–141PubMedCrossRefGoogle Scholar
  11. Davis BD (1948) Isolation of biochemically deficient mutants of bacteria by penicillin. J Am Chem Soc 70:4267PubMedCrossRefGoogle Scholar
  12. Demain AL, Adrio JL (2008) Strain improvement for production of pharmaceuticals and other microbial metabolites by fermentation. Prog Drug Res 6:253–289Google Scholar
  13. Dubos RJ (1950) Louis Pasteur: free lance of science. Little, Brown and Company, BostonGoogle Scholar
  14. Elander RP (1966) Two decades of strain development in antibiotic-producing microorganisms. Dev Ind Microbiol 7:61–73Google Scholar
  15. Eron JJ, Gorczyc P, Kaplan JC, D’Aquila RT (1992) Susceptibility testing by polymerase chain reaction DNA quantitation: a method to measure drug resistance of human immunodeficiency virus type 1 isolated. Proc Natl Acad Sci 89:3241–3245PubMedCrossRefGoogle Scholar
  16. Fenical W (1993) Chemical studies of marine bacteria: developing a new resource. Chem Rev 93:1673–1683CrossRefGoogle Scholar
  17. Fenical W (1997) New pharmaceuticals from marine organisms. Trends Biotechnol 15:339–341PubMedCrossRefGoogle Scholar
  18. Ferrer-Miralles N, Domingo-Espin J, Corcero JL, Vasquez E, Villaverde A (2009) Microbial factories for recombinant pharmaceuticals. Microb Cell Fact 8:17–25PubMedCrossRefGoogle Scholar
  19. Gaden EL (1981) Production methods in industrial microbiology. Sci Am 245:134–145CrossRefGoogle Scholar
  20. Gerhardt P (ed) (1981) Manual of methods for general bacteriology. ASM, Washington, DCGoogle Scholar
  21. Glazer AN, Nikaido H (1995) Microbial biotechnology: fundamentals of applied microbiology. W. H. Freeman, New YorkGoogle Scholar
  22. Godfrey T, West S (1996) Industrial enzymology. In: Godfrey T, West S (eds) The application of enzymes in industry, 2nd edn. Stockton, New YorkGoogle Scholar
  23. Guarino A (1997) Oral bacterial therapy reduces the duration of symptoms and of viral excretion in children with milk diarrhea. J Pediatr Gastroenterol Nutr 25:516–519PubMedCrossRefGoogle Scholar
  24. Guerreiro MA, Andrietta SR, Maugeri F (1997) Expert system for the design of an industrial fermentation plant for the production of alcohol. J Chem Technol Biot 68:163–170CrossRefGoogle Scholar
  25. Hagedom S, Kaphammer B (1994) Microbial biocatalysis in the generation of flavor and fragrance chemicals. Annu Rev Microbiol 48:773–800CrossRefGoogle Scholar
  26. Hale YM, Melton ME, Lewis JS, Willis DE (1993) Evaluation of PACE 2 Neiseria gonorrhoeae assay by three public health laboratories. J Clin Microbiol 31:451–453PubMedGoogle Scholar
  27. Hammes BD, Higgins SJ (1995) Gene probes: a practical approach. Oxford University Press, New York, pp 1–288Google Scholar
  28. Hapfelmeier S, Lawson MAE, Slack E et al (2010) Reversible microbial colonization of germ-free mice reveals the dynamics of IgA immune responses. Science 328:1705–1709PubMedCrossRefGoogle Scholar
  29. Hill RT, Fenical W (2010) Pharmaceuticals from marine natural products: surge or ebb? Curr Opin Biotechnol 6:777–779CrossRefGoogle Scholar
  30. Holzapfel HH (1998) Overview of gut flora and probiotics. Int Food Microbiol 41:85–101CrossRefGoogle Scholar
  31. Hutchinson CR (1998) Combinational biosynthesis for new drug discovery. Curr Opin Microbiol 1:319–329PubMedCrossRefGoogle Scholar
  32. Hutchinson CR, Fujii I (1995) Polyketide synthase gene manipulation: a structure-function approach in engineering novel antibiotics. Annu Rev Microbiol 49:201–238PubMedCrossRefGoogle Scholar
  33. Ivanov II, Littman DR (2011) Modulation of immune homeostasis by commensal bacteria. Curr Opin Microbiol 14:106–114PubMedCrossRefGoogle Scholar
  34. Jones D, Krieg NR (1984) Seriology and chemotaxonomy. In: Krieg NR, Holt JC (eds) Bergey’s manual of systematic bacteriology. Williams and Wilkins, Baltimore, pp 15–18Google Scholar
  35. Keller AP, Beggs ML, Amthor B, Bruns F, Meissner P, Haas WH (2002) Evidence of the presence of IS1245 and IS1311 or closely related insertion elements in nontuberculous mycobacteria outside of the Mycobacterium avium complex. J Clin Microbiol 40:1869–1872PubMedCrossRefGoogle Scholar
  36. Knezevich V, Koren O, Ron EZ, Rosenberg E (2006) Petroleum bioremediation in seawater using guano as the fertilizer. Bioremed J 10:83–91CrossRefGoogle Scholar
  37. Koneman EW, Allen SD, Janda WM, Schreckenberger PC, Winn WC Jr (1992) Diagnostic microbiology. 4th ed. Philadelphia: JB LippincottGoogle Scholar
  38. Koren O, Knezvic V, Ron EZ, Rosenberg E (2003) Petroleum bioremediation using water insoluble uric acid as the nitrogen source. Appl Environ Microbiol 69:6337–6339PubMedCrossRefGoogle Scholar
  39. Kreig NR (1981) Enrichment and isolation. In: Gerhardt P (ed) Manual of methods for general bacteriology. ASM, Washington, DC, pp 112–142Google Scholar
  40. Kumar R (1995) Recombinant hemoglobins as blood substitutes: a biotechnology perspective. Proc Soc Exp Biol 208:150–158PubMedCrossRefGoogle Scholar
  41. Kumaravel S, Hema R, Lakshmi R (2010) Production of polyhydroxybutyrate (bioplastic) and its biodegradation by Pseudomonas lemoignei and Aspergillus niger. E-J Chem 7(S1):S536–S542CrossRefGoogle Scholar
  42. Lawrence S (2006) Biotech blockbusters consolidate markets. Nat Biotechnol 24:1466PubMedCrossRefGoogle Scholar
  43. Leiberman DG, Fink R, Schaffer F (1986) Biosafety in biotechnology. In: Demain AL, Solomon NA (eds) Industrial microbiology and biotechnology. ASM, Washington, DC, pp 402–409Google Scholar
  44. Ley RE, Turnbaugh PJ, Klein S, Gordon JI (2006) Human gut microbes associated with obesity. Nature 444:1022–1023PubMedCrossRefGoogle Scholar
  45. Lloyd A (1998) High-throughput screening. Drug Discov Today 3:566–569CrossRefGoogle Scholar
  46. Mai V, Ukhanova M, Baer DJ (2010) Understanding the extent and sources of variation in gut microbiota studies; a prerequisite for establishing associations with disease. Diversity 2:1085–1096CrossRefGoogle Scholar
  47. McDaniel R, Ebert-Khosla S, Hopwood DA, Khosla C (1993) Engineered biosynthesis of novel polyketides. Science 262:1546–1550PubMedCrossRefGoogle Scholar
  48. O’Hara AM, Shanahan F (2006) The gut flora as a forgotten organ. EMBO Rep 7:688–693PubMedCrossRefGoogle Scholar
  49. Prescott SC, Dunn CG (1940) Industrial microbiology. McGraw-Hill, New YorkGoogle Scholar
  50. Price KE, Buck RE, Lein J (1964) System for detecting inducers of lysogenic Escherichia coli W1709 (gamma) and its applicability as a screen for antineoplastic antibiotics. Appl Microbiol 12:428–435PubMedGoogle Scholar
  51. Queener SW, Lively DH (1986) Screening and selection for strain improvement. In: Demain AL, Solomon NA (eds) Industrial microbiology and biotechnology. ASM, Washington, DC, pp 155–169Google Scholar
  52. Reineke W (1998) Development of hybrid strains for the mineralization of chloroaromatics by patchwork assembly. Annu Rev Microbiol 52:287–332PubMedCrossRefGoogle Scholar
  53. Reisman HB (1993) Problems in scale-up of biotechnology production processes. Crit Rev Biotechnol 13:195–253PubMedCrossRefGoogle Scholar
  54. Relman DA, Schmidt TM, MacDermott RP, Falkow S (1992) Identification of the uncultured bacillus of Whipple’s disease. N Eng J Med 327:293–301CrossRefGoogle Scholar
  55. Ron EZ, Rosenberg E (2009) Role of biosurfactants. In: Timmis KN (ed) Handbook of hydrocarbon and lipid microbiology. Springer, HeidelbergGoogle Scholar
  56. Rosenberg E (1991) Hydrocarbon-oxidizing bacteria. In: Balows A, Truper HG, Dworkin M, Harder W, Schleifer K-H (eds) The prokaryotes, 2nd edn. Springer, New York, pp 446–459Google Scholar
  57. Rosenberg E, Ron EZ (1996) Bioremediation of petroleum contamination. In: Crawford RL, Crawford DL (eds) Bioremediation: principles and applications. Cambridge University Press, New York, pp 100–124CrossRefGoogle Scholar
  58. Rosenberg E, Legmann R, Kushmaro A, Adler E, Abir H, Ron EZ (1996) Oil bioremediation using insoluble nitrogen source. J Biotechnol 51:273–278PubMedCrossRefGoogle Scholar
  59. Saliwanchik R (1986) Legal protection for biotechnology. In: Demain AL, Solomon NA (eds) Industrial microbiology and biotechnology. ASM, Washington, DC, pp 389–401Google Scholar
  60. Schmid I, Sattler I, Grabley S et al (1999) Natural products in high throughput screening: automatic high-quality sample preparation. J Biomol Screen 4:15–25PubMedCrossRefGoogle Scholar
  61. Silverman L, Campbell R, Broach JR (1998) New assay technologies for high-throughput screening. Curr Opin Chem Biol 2:397–403PubMedCrossRefGoogle Scholar
  62. Song HG, Bartha R (1990) Effects of jet fuel spills on the microbial community in soil. Appl Environ Microbiol 56:646–651PubMedGoogle Scholar
  63. Stappenbeck TS, Hooper LV, Gordon JI (2002) Developmental regulation of intestinal angiogenesis by Peneth cells. Proc Natl Acad Sci USA 99:15451–15455PubMedCrossRefGoogle Scholar
  64. Steele DB, Stowers MD (1991) Techniques for selection of industrially important microorganisms. Annu Rev Microbiol 45:89–106PubMedCrossRefGoogle Scholar
  65. Tang YW, Stratton CW (2011) Advanced techniques in diagnostic microbiology overview. Springer, New YorkGoogle Scholar
  66. Timmis KW, Steffan RJ, Unterman R (1994) Designing microorganisms for the treatment of toxic wastes. Annu Rev Microbiol 48:525–557PubMedCrossRefGoogle Scholar
  67. Trilli A (1981) Scale-up of fermentation. In: Demain AL, Solomon NA (eds) Industrial microbiology and biotechnology. ASM, Washington, DC, pp 277–307Google Scholar
  68. Turnbaugh PJ, Ley RE, Mahowald MA et al (2006) An obesity-associated gut microbiome with increased capacity for energy harvest. Nature 444:1027–1031PubMedCrossRefGoogle Scholar
  69. Veldamp H (1970) Enrichment cultures of prokaryotic organisms. In: Noris JR, Ribbons DW (eds) Methods in microbiology, vol 6. Academic, New York, p 305Google Scholar
  70. Wang HY (1981) Bioinstrumentation and computer control of fermentation processes. In: Demain AL, Solomon NA (eds) Industrial microbiology and biotechnology. ASM, Washington, DC, pp 308–320Google Scholar
  71. Whelen AC, Persing DH (1996) The role of nucleic acid amplification and detection in the clinical microbiology laboratory. Annu Rev Microbiol 50:349–373PubMedCrossRefGoogle Scholar
  72. Whitcombe D, Newton CR, Little S (1998) DNA-based diagnostics. Curr Opin Biotechnol 9:602–608PubMedCrossRefGoogle Scholar
  73. White RJ, Maiese WM, Greenstein M (1986) In: Demain AL, Solomon NA (eds) Industrial microbiology and biotechnology. ASM Press, Washington, DC, pp 24–31Google Scholar
  74. Zhang XHD (2011) Optimal high-throughput screening: practical experimental design and data analysis for genome-scale RNAi research. Cambridge University Press, CambridgeCrossRefGoogle Scholar
  75. Zhang YX, Perry K, Vinci VA et al (2002) Genome shuffling leads to rapid phenotype improvement in bacteria. Nature 415:644–646PubMedCrossRefGoogle Scholar
  76. Zilber-Rosenberg I, Rosenberg E (2008) Role of microorganisms in the evolution of animals and plants: the hologenome theory of evolution. FEMS Microbiol Rev 32:723–735PubMedCrossRefGoogle Scholar
  77. Zilber-Rosenberg I, Rosenberg E (2011) Prebiotics and probiotics within the framework of the hologenome concept. J Microbial Biochem, doi:10.4172/1948-5948.S1-001Google Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.Department of Molecular Microbiology and BiotechnologyTel Aviv UniversityTel AvivIsrael

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