Molecular microbiology

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For the scientific journal, see Molecular Microbiology (journal).

Molecular microbiology is the branch of microbiology devoted to the study of the molecular basis of the physiological processes that occur in microorganisms.


Mainly because of their relative simplicity, ease of manipulation and growth in vitro, and importance in medicine, bacteria were instrumental in the development of molecular biology. The complete genome sequence for a large number of bacterial species is now available. A list of sequenced prokaryotic genomes is available. Molecular microbiology techniques are currently being used in the development of new genetically engineered vaccines, in bioremediation,[1] biotechnology, food microbiology,[2] probiotic research,[3] antibacterial development[4] and environmental microbiology.[5]

Many bacteria have become model organisms for molecular studies.

Molecular techniques have had a direct influence on the clinical practice of medical microbiology. In many cases where traditional phenotypic methods of microbial identification and typing are insufficient or time-consuming, molecular techniques can provide rapid and accurate data, potentially improving clinical outcomes. Specific examples include:

  • 16s rRNA sequencing to provide bacterial identifications
  • Pulsed Field Gel Electrophoresis for strain typing of epidemiologically related organisms.
  • Direct detection of genes related to resistance mechanisms, such as mecA gene in Staphylococcus aureus


Bacteria possess diverse proteins and RNA that can sense changes to their intracellular and extracellular environment. The signals received by these macromolecules are transmitted to key genes or proteins, which alter their activities to suit the new conditions.[6]


Viruses are important pathogens of humans and animals.[7] Their genomes are relatively small. For these reasons they were among the first organisms to be fully sequenced. The complete DNA sequence of the Epstein-Barr virus was completed in 1984.[8][9] Bluetongue virus (BTV) has been in the forefront of molecular studies for last three decades and now represents one of the best understood viruses at the molecular and structural levels.[10] Other viruses such as Papillomavirus,[11] Coronavirus,[12] Caliciviruses,[13] Paramyxoviruses[14] and Influenza virus[15][16] have also been extensively studied at the molecular level.

Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and diverse entities in the biosphere. Bacteriophages, or "phage", have been fundamental in the development of the science of molecular biology and became "model organisms" for probing the basic chemistry of life.[17] The first DNA-genome project to be completed was the phage Φ-X174 in 1977. Φ29 phage, a phage of Bacillus, is a paradigm for the study of several molecular mechanisms of general biological processes, including DNA replication and regulation of transcription.[17][18]

Gene Therapy[edit]

Some viruses are used as vectors for gene therapy. Virus vectors have been developed that mediate stable genetic modification of treated cells by chromosomal integration of the transferred vector genomes. Gammaretroviral and lentiviral vectors, for example, can be utilized in clinical gene therapy aimed at the long-term correction of genetic defects, e.g., in stem and progenitor cells. Gammaretroviral and lentiviral vectors have so far been used in more than 300 clinical trials, addressing treatment options for various diseases.[19][20]


Yeasts and molds are eukaryotic microorganisms classified in the kingdom Fungi.


Polymerase chain reaction[21] (PCR) is used in microbiology to amplify (replicate many times) a single DNA sequence. If required, the sequence can also be altered in predetermined ways. Quantitative PCR is used for the rapid detection of microorganisms and is currently employed in diagnostic clinical microbiology laboratories, environmental analysis, food microbiology, and many other fields.[22] The closely related technique of quantitative PCR permits the quantitative measurement of DNA or RNA molecules and is used to estimate the densities of the reference pathogens in food, water and environmental samples. Quantitative PCR provides both specificity and quantification of target microorganisms.[23]

Gel electrophoresis is used routinely in microbiology to separate DNA, RNA, or protein molecules using an electric field by virtue of their size, shape or electric charge.

Southern blotting, northern blotting, western blotting and Eastern blotting are molecular techniques for detecting the presence of microbial DNA sequences (Southern), RNA sequences (northern), protein molecules (western) or protein modifications (Eastern).

DNA microarrays are used in microbiology as the modern alternative to the "blotting" techniques. Microarrays permit the exploration of thousands of sequences at one time. This technique is used in molecular microbiology to detect the presence of pathogens in a sample (air, water, organ tissue, etc.). It is also used to determine the genetic differences between two microbial strains.[24]

DNA sequencing and genomics have been used for many decades in molecular microbiology studies. Due to their relatively small size, viral genomes were the first to be completely analysed by DNA sequencing. A huge range of sequence and genomic data is now available for a number of species and strains of microorganisms.

RNA interference (RNAi) was discovered as a cellular gene regulation mechanism in 1998, but several RNAi-based applications for gene silencing have already made it into clinical trials. RNA interference (RNAi) technology has formed the basis of novel tools for biological research and drug discovery.[25]

See also[edit]


  1. ^ Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-17-2. 
  2. ^ Fratamico PM and Bayles DO (editor). (2005). Foodborne Pathogens: Microbiology and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-00-4. 
  3. ^ Mayo, B; van Sinderen, D (editor) (2010). Bifidobacteria: Genomics and Molecular Aspects. Caister Academic Press. ISBN 978-1-904455-68-4. 
  4. ^ Miller, AA; Miller, PF (editor) (2011). Emerging Trends in Antibacterial Discovery: Answering the Call to Arms. Caister Academic Press. ISBN 978-1-904455-89-9. 
  5. ^ Sen, K; Ashbolt, NK (editor) (2010). Environmental Microbiology: Current Technology and Water Applications. Caister Academic Press. ISBN 978-1-904455-70-7. 
  6. ^ Kramer, R; Jung, K (editor) (2010). Bacterial Signaling. Caister Academic Press. ISBN 978-3-527-32365-4. 
  7. ^ Mettenleiter TC and Sobrino F (editors). (2008). Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. 
  8. ^ Baer; et al. (1984). "DNA sequence and expression of the B95-8 Epstein—Barr virus genome". Nature. 310 (5974): 207–211. doi:10.1038/310207a0. PMID 6087149. 
  9. ^ Robertson ES (editor). (2005). Epstein-Barr Virus. Caister Academic Press. ISBN 978-1-904455-03-5. 
  10. ^ Roy P (2008). "Molecular Dissection of Bluetongue Virus". Animal Viruses: Molecular Biology. Caister Academic Press. ISBN 978-1-904455-22-6. 
  11. ^ Campo MS (editor). (2006). Papillomavirus Research: From Natural History To Vaccines and Beyond. Caister Academic Press. ISBN 978-1-904455-04-2. 
  12. ^ Thiel V (editor). (2007). Coronaviruses: Molecular and Cellular Biology. Caister Academic Press. ISBN 978-1-904455-16-5. 
  13. ^ Hansman, GS (editor) (2010). Caliciviruses: Molecular and Cellular Virology. Caister Academic Press. ISBN 978-1-904455-63-9. 
  14. ^ Samal, SK (editor) (2011). The Biology of Paramyxoviruses. Caister Academic Press. ISBN 978-1-904455-85-1. 
  15. ^ Kawaoka Y (editor). (2006). Influenza Virology: Current Topics. Caister Academic Press. ISBN 978-1-904455-06-6. 
  16. ^ Wang, Q; Tao, YJ (editors) (2010). Influenza: Molecular Virology. Caister Academic Press. ISBN 978-1-904455-57-8. 
  17. ^ a b Mc Grath S and van Sinderen D (editors). (2007). Bacteriophage: Genetics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-14-1. 
  18. ^ Graumann P (editor). (2007). Bacillus: Cellular and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-12-7. 
  19. ^ Kurth, R; Bannert, N (editors) (2010). Retroviruses: Molecular Biology, Genomics and Pathogenesis. Caister Academic Press. ISBN 978-1-904455-55-4. 
  20. ^ Desport, M (editors) (2010). Lentiviruses and Macrophages: Molecular and Cellular Interactions. Caister Academic Press. ISBN 978-1-904455-60-8. 
  21. ^ Kennedy, S; Oswald, N (editor) (2011). PCR Troubleshooting and Optimization: The Essential Guide. Caister Academic Press. ISBN 978-1-904455-72-1. 
  22. ^ Mackay IM (editor). (2007). Real-Time PCR in Microbiology: From Diagnosis to Characterization. Caister Academic Press. ISBN 978-1-904455-18-9. 
  23. ^ Filion, M (editor) (2012). Quantitative Real-time PCR in Applied Microbiology. Caister Academic Press. ISBN 978-1-908230-01-0. 
  24. ^ Herold, KE; Rasooly, A (editor) (2009). Lab-on-a-Chip Technology: Biomolecular Separation and Analysis. Caister Academic Press. ISBN 978-1-904455-47-9. 
  25. ^ Morris, KV (editor) (2008). RNA and the Regulation of Gene Expression: A Hidden Layer of Complexity. Caister Academic Press. ISBN 978-1-904455-25-7. 

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