Molecular microbiology is the branch of microbiology devoted to the study of the molecular principles of the physiological processes involved in the life cycle of prokaryotic and eukaryotic microorganisms such as bacteria, viruses, unicellular algae, fungi, and protozoa. This includes gene expression and regulation, genetic transfer, the synthesis of macromolecules, sub-cellular organization, cell to cell communication, and molecular aspects of pathogenicity and virulence.
Molecular microbiology is primarily involved in the interactions between the various cell systems of microorganisms including the interrelationship of DNA, RNA and protein biosynthesis and the manner in which these interactions are regulated.
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, biotechnology, food microbiology and environmental microbiology.
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 rDNA 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
Viruses are important pathogens of humans and animals. 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.  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.  Other viruses such as Papillomavirus, Coronavirus, and Influenza virus 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. 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.  
Polymerase chain reaction (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. Real-time 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. The closely related technique of quantitative PCR (qPCR) permits the quantitative measurement of DNA or RNA molecules.
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 and western blotting are molecular techniques for detecting the presence of microbial DNA sequences (Southern), RNA sequences (northern) or protein molecules (western).
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.
DNA sequencing and genomics have been used for many decades in molecular microbiology studies. Due to their relatively small size, virus and bacterial 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.
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