Molecular microbiology
Encyclopedia
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 microorganism
s such as bacteria
, virus
es, 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.
, 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
, probiotic
research, antibacterial development 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:
in response to signals in the intracellular and extracellular environment. Key to this are the diverse macromolecules (proteins or RNA) that sense change through direct interactions with chemical or physical stimuli.
, whooping cough and typhoid fever, are still a major cause of global mortality. In recent decades the development of molecular biology and genetic tools has led to extensive studies on the molecular and cellular aspects of the virulence properties of pathogenic bacteria.
is advancing rapidly due to improvements in analytical methodologies and the development of new and innovative approaches for glycan isolation, characterization and synthesis. Research in bacterial glycomics could lead to the development of novel drugs, bioactive glycans and glycoconjugate vaccines.
s 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
, Caliciviruses
, Paramyxovirus
es and Influenza virus have also been extensively studied at the molecular level.
Bacterial viruses, or bacteriophage
s, 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.
. 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.
is emerging as a powerful modality for battling some of the most notoriously challenging viral clinical targets. In particular, this technology is being developed as a new therapeutic tool for fighting specific viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV) and respiratory viruses.
(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.
Loop-mediated isothermal amplification
(LAMP) is a relatively new DNA amplification technique that is simple, rugged and low cost. In LAMP, the target sequence is amplified at a constant temperature using either two or three sets of primers and a polymerase with high strand displacement activity. LAMP is used in organizations engaged in combating infectious diseases such as tuberculosis
, malaria
, and sleeping sickness in developing regions and has been proposed for the detection of waterborne pathogens.
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 microarray
s 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.
Lab-on-a-chip
(LOC) devices integrate and scale down laboratory functions and processes to a miniaturized chip format. Many LOC devices are used in a wide array of biomedical and other analytical applications including rapid pathogen detection, clinical diagnosis, forensic science, electrophoresis, flow cytometry, blood chemistry analysis, protein and DNA analysis. LOC devices can be fabricated from many types of material including various polymers, glass, or silicon, or combinations of these materials. A broad variety of fabrication technologies are used for LOC device fabrication. LOC systems have several common features including microfluidics and sensing capabilities. Microfluidics deals with fluid flow in tiny channels using flow control devices (e.g. channels, pumps, mixers and valves). Sensing capabilities, usually optical or electrochemical sensors, can also be integrated into the chip.
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.
Nanotechnology
, the engineering and art of manipulating matter at the nanoscale (1-100 nm), offers the potential of novel nanomaterials with applications in microbiology, in particular environmental microbiology.
Microbiology
Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
devoted to the study of the molecular principles of the physiological processes involved in the life cycle of prokaryotic and eukaryotic microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s such as bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
, virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...
es, unicellular algae
Algae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
, fungi, and protozoa
Protozoa
Protozoa are a diverse group of single-cells eukaryotic organisms, many of which are motile. Throughout history, protozoa have been defined as single-cell protists with animal-like behavior, e.g., movement...
. 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
DNA
Deoxyribonucleic acid is a nucleic acid that contains the genetic instructions used in the development and functioning of all known living organisms . The DNA segments that carry this genetic information are called genes, but other DNA sequences have structural purposes, or are involved in...
, RNA
RNA
Ribonucleic acid , or RNA, is one of the three major macromolecules that are essential for all known forms of life....
and protein biosynthesis
Protein biosynthesis
Protein biosynthesis is the process in which cells build or manufacture proteins. The term is sometimes used to refer only to protein translation but more often it refers to a multi-step process, beginning with amino acid synthesis and transcription of nuclear DNA into messenger RNA, which is then...
and the manner in which these interactions are regulated.
Bacteria
Mainly because of their relative simplicity, ease of manipulation and growth in vitroIn vitro
In vitro refers to studies in experimental biology that are conducted using components of an organism that have been isolated from their usual biological context in order to permit a more detailed or more convenient analysis than can be done with whole organisms. Colloquially, these experiments...
, 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
Microbial biodegradation
Interest in the microbial biodegradation of pollutants has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments...
, biotechnology
Biotechnology
Biotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Biotechnology also utilizes these products for manufacturing purpose...
, food microbiology
Food microbiology
Food microbiology is the study of the microorganisms that inhabit, create, or contaminate food. Of major importance is the study of microorganisms causing food spoilage. "Good" bacteria, however, such as probiotics, are becoming increasingly important in food science...
, probiotic
Probiotic
Probiotics are live microorganisms thought to be beneficial to the host organism. According to the currently adopted definition by FAO/WHO, probiotics are: "Live microorganisms which when administered in adequate amounts confer a health benefit on the host"...
research, antibacterial development and environmental microbiology
Environmental microbiology
Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
.
Many bacteria have become model organisms for molecular studies.
Molecular techniques have had a direct influence on the clinical practice of medical microbiology
Medical microbiology
Medical microbiology is both a branch of medicine and microbiology which deals with the study of microorganisms including bacteria, viruses, fungi and parasites which are of medical importance and are capable of causing infectious diseases in human beings...
. 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
Gene expression and regulation
Bacteria have evolved abilities to regulate gene expressionGene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
in response to signals in the intracellular and extracellular environment. Key to this are the diverse macromolecules (proteins or RNA) that sense change through direct interactions with chemical or physical stimuli.
Bacterial pathogenesis
New infectious diseases are emerging and bacteria-induced illnesses, such as tuberculosisTuberculosis
Tuberculosis, MTB, or TB is a common, and in many cases lethal, infectious disease caused by various strains of mycobacteria, usually Mycobacterium tuberculosis. Tuberculosis usually attacks the lungs but can also affect other parts of the body...
, whooping cough and typhoid fever, are still a major cause of global mortality. In recent decades the development of molecular biology and genetic tools has led to extensive studies on the molecular and cellular aspects of the virulence properties of pathogenic bacteria.
Bacterial glycomics
Glycans play diverse roles in bacterial physiology. Progress in the study of bacterial glycomicsGlycomics
Glycomics is the comprehensive study of glycomes , including genetic, physiologic, pathologic, and other aspects. Glycomics "is the systematic study of all glycan structures of a given cell type or organism" and is a subset of glycobiology...
is advancing rapidly due to improvements in analytical methodologies and the development of new and innovative approaches for glycan isolation, characterization and synthesis. Research in bacterial glycomics could lead to the development of novel drugs, bioactive glycans and glycoconjugate vaccines.
Viruses
Viruses are important pathogens of humanHuman
Humans are the only living species in the Homo genus...
s 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
Epstein-Barr virus
The Epstein–Barr virus , also called human herpesvirus 4 , is a virus of the herpes family and is one of the most common viruses in humans. It is best known as the cause of infectious mononucleosis...
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
Papillomavirus
Papillomaviridae is an ancient taxonomic family of non-enveloped DNA viruses, collectively known as papillomaviruses. Several hundred species of papillomaviruses, traditionally referred to as "types", have been identified infecting all carefully inspected birds and mammals, but also a small number...
, Coronavirus
Coronavirus
Coronaviruses are species in the genera of virus belonging to the subfamily Coronavirinae in the family Coronaviridae. Coronaviruses are enveloped viruses with a positive-sense single-stranded RNA genome and a helical symmetry. The genomic size of coronaviruses ranges from approximately 16 to 31...
, Caliciviruses
Caliciviridae
The Caliciviridae family are a family of viruses, members of Class IV of the Baltimore scheme. They are positive-sense, single stranded RNA which is non-segmented. The caliciviruses have been found in a number of organisms such as humans, cattle, pigs, cats, chickens, reptiles, dolphins and...
, Paramyxovirus
Paramyxovirus
Paramyxoviruses are viruses of the Paramyxoviridae family of the Mononegavirales order; they are negative-sense single-stranded RNA viruses responsible for a number of human and animal diseases.-Genera:*Subfamily Paramyxovirinae**Genus Avulavirus Paramyxoviruses (from Greek para-, beyond, -myxo-,...
es and Influenza virus have also been extensively studied at the molecular level.
Bacterial viruses, or bacteriophage
Bacteriophage
A bacteriophage is any one of a number of viruses that infect bacteria. They do this by injecting genetic material, which they carry enclosed in an outer protein capsid...
s, 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
Bacillus
Bacillus is a genus of Gram-positive, rod-shaped bacteria and a member of the division Firmicutes. Bacillus species can be obligate aerobes or facultative anaerobes, and test positive for the enzyme catalase. Ubiquitous in nature, Bacillus includes both free-living and pathogenic species...
, is a paradigm for the study of several molecular mechanisms of general biological processes, including DNA replication and regulation of transcription.
Gene Therapy
Some viruses are used as vectors for gene therapyGene therapy
Gene therapy is the insertion, alteration, or removal of genes within an individual's cells and biological tissues to treat disease. It is a technique for correcting defective genes that are responsible for disease development...
. 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.
RNAi and viruses
The new technology of RNAiRNAI
RNAI is a non-coding RNA that is an antisense repressor of the replication of some E. coli plasmids, including ColE1. Plasmid replication is usually initiated by RNAII, which acts as a primer by binding to its template DNA. The complementary RNAI binds RNAII prohibiting it from its initiation role...
is emerging as a powerful modality for battling some of the most notoriously challenging viral clinical targets. In particular, this technology is being developed as a new therapeutic tool for fighting specific viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV) and respiratory viruses.
Technology
Polymerase chain reactionPolymerase chain reaction
The polymerase chain reaction is a scientific technique in molecular biology to amplify a single or a few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence....
(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.
Loop-mediated isothermal amplification
Loop-mediated isothermal amplification
Loop mediated isothermal amplification is a single tube technique for the amplification of DNA. This may be of use in future as a low cost alternative to detect certain diseases...
(LAMP) is a relatively new DNA amplification technique that is simple, rugged and low cost. In LAMP, the target sequence is amplified at a constant temperature using either two or three sets of primers and a polymerase with high strand displacement activity. LAMP is used in organizations engaged in combating infectious diseases such as tuberculosis
Tuberculosis
Tuberculosis, MTB, or TB is a common, and in many cases lethal, infectious disease caused by various strains of mycobacteria, usually Mycobacterium tuberculosis. Tuberculosis usually attacks the lungs but can also affect other parts of the body...
, malaria
Malaria
Malaria is a mosquito-borne infectious disease of humans and other animals caused by eukaryotic protists of the genus Plasmodium. The disease results from the multiplication of Plasmodium parasites within red blood cells, causing symptoms that typically include fever and headache, in severe cases...
, and sleeping sickness in developing regions and has been proposed for the detection of waterborne pathogens.
Gel electrophoresis
Gel electrophoresis
Gel electrophoresis is a method used in clinical chemistry to separate proteins by charge and or size and in biochemistry and molecular biology to separate a mixed population of DNA and RNA fragments by length, to estimate the size of DNA and RNA fragments or to separate proteins by charge...
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
Eastern blotting
Eastern blotting is a biochemical technique used to analyze protein post translational modifications such as lipids and glycoconjugates. It is most often used to detect carbohydrate epitopes. Thus, Eastern blotting can be considered an extension of the biochemical technique of Western blotting...
are molecular techniques for detecting the presence of microbial DNA sequences (Southern), RNA sequences (northern), protein molecules (western) or protein modifications (Eastern).
DNA microarray
DNA microarray
A DNA microarray is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome...
s 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
DNA sequencing
DNA sequencing includes several methods and technologies that are used for determining the order of the nucleotide bases—adenine, guanine, cytosine, and thymine—in a molecule of DNA....
and genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
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.
Lab-on-a-chip
Lab-on-a-chip
A lab-on-a-chip is a device that integrates one or several laboratory functions on a single chip of only millimeters to a few square centimeters in size. LOCs deal with the handling of extremely small fluid volumes down to less than pico liters. Lab-on-a-chip devices are a subset of MEMS devices...
(LOC) devices integrate and scale down laboratory functions and processes to a miniaturized chip format. Many LOC devices are used in a wide array of biomedical and other analytical applications including rapid pathogen detection, clinical diagnosis, forensic science, electrophoresis, flow cytometry, blood chemistry analysis, protein and DNA analysis. LOC devices can be fabricated from many types of material including various polymers, glass, or silicon, or combinations of these materials. A broad variety of fabrication technologies are used for LOC device fabrication. LOC systems have several common features including microfluidics and sensing capabilities. Microfluidics deals with fluid flow in tiny channels using flow control devices (e.g. channels, pumps, mixers and valves). Sensing capabilities, usually optical or electrochemical sensors, can also be integrated into the chip.
RNA interference
RNA interference
RNA interference is a process within living cells that moderates the activity of their genes. Historically, it was known by other names, including co-suppression, post transcriptional gene silencing , and quelling. Only after these apparently unrelated processes were fully understood did it become...
(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.
Nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
, the engineering and art of manipulating matter at the nanoscale (1-100 nm), offers the potential of novel nanomaterials with applications in microbiology, in particular environmental microbiology.
See also
- MicrobiologyMicrobiologyMicrobiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
- Environmental microbiologyEnvironmental microbiologyEnvironmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
- Food microbiologyFood microbiologyFood microbiology is the study of the microorganisms that inhabit, create, or contaminate food. Of major importance is the study of microorganisms causing food spoilage. "Good" bacteria, however, such as probiotics, are becoming increasingly important in food science...
- Biofilms
- Industrial microbiologyIndustrial microbiologyIndustrial microbiology or microbial biotechnology encompasses the use of microorganisms in the manufacture of food or industrial products. The use of microorganisms for the production of food, either human or animal, is often considered a branch of food microbiology...