Molecular Microbiology

Definition of Microbiology
Microbiology is the study of microorganisms, which are unicellular or cell-cluster microscopic organisms. This includes eukaryotes such as fungi and protists and
prokaryotes such as bacteria and certain algae. Viruses are also included. Microbiology subdivided into divisions including bacteriology, virology, mycology, parasitology
and others. A scientist who specializes in the area of microbiology is called a microbiologist. Microbiology can be divided into several subdisciplines, including:

Microbial physiology: The study of how the microbial cell functions biochemically. Includes the study of microbial growth, microbial metabolism and microbial cell
structure.
Microbial genetics: The study of how genes are organised and regulated in microbes in relation to their cellular functions. Closely related to the field of
molecular biology.
Molecular Microbiology: The study of the molecular biology and genomics of microorganisms.
Medical microbiology: The study of the role of microbes in human illness. Includes the study of microbial pathogenesis and epidemiology and is related to the
study of disease pathology and immunology.
Veterinary microbiology: The study of the role in microbes in veterinary medicine or animal taxonomy.
Environmental microbiology: The study of the function and diversity of microbes in their natural environments. Includes the study of microbial ecology,
microbially-mediated nutrient cycling, geomicrobiology, microbial diversity and bioremediation. Characterisation of key bacterial habitats such as the
rhizosphere and phyllosphere.
Evolutionary microbiology: The study of the evolution of microbes. Includes the study of bacterial systematics and taxonomy.
Industrial microbiology: The exploitation of microbes for use in industrial processes. Examples include industrial fermentation and wastewater treatment. Closely
linked to the biotechnology industry. This field also includes brewing, an important application of microbiology.
Aeromicrobiology: The study of airborne microorganisms.
Food Microbiology: The study of microorganisms causing food spoilage.
Pharmaceutical microbiology: the study of microorganisms causing pharmaceutical contamination and spoillage.
General Microbiology
Microbial Biodegradation, Bioremediation and Biotransformation Interest in the microbial biodegradation of pollutants has intensified in recent years as mankind
strives to find sustainable ways to cleanup contaminated environments. These bioremediation and biotransformation methods endeavour to harness the
astonishing, naturally occurring, microbial catabolic diversity to degrade, transform or accumulate a huge range of compounds.
Environmental Microbiology The study of the composition and physiology of microbial communities in the environment i.e. the soil, water, air and sediments
covering the planet. Can also include the microorganisms living on or in the animals and plants that inhabit these areas.
Oral Microbiology The study of the microorganisms that inhabit the mouth and in particular those involved in the two major dental diseases: caries and
periodontal disease. Oral bacteria include streptococci, lactobacilli, staphylococci, corynebacteria, and various anaerobes in particular bacteroides.
Plant Pathogenic Bacteria Bacteria pathogenic for plants are responsible for devastating losses in agriculture. Plant pathogenic bacteria impact innumerable
and valuable agricultural crops, causing hundreds of millions of dollars in damage each year. The use of antibiotics to control such infections is restricted in
many countries due to worries over the evolution and transmission of antibiotic resistance.
Microbiology Societies A list of societies relevant to microbiology
Bacteria
Acinetobacter The genus Acinetobacter is a group of Gram-negative, non-motile and non-fermentative bacteria belonging to the family Moraxellaceae. They are
important soil organisms where they contribute to the mineralisation of, for example, aromatic compounds. Acinetobacter are able to survive on various surfaces
(both moist and dry) in the hospital environment, thereby being an important source of infection in debilitated patients. These bacteria are innately resistant to
many classes of antibiotics. In addition, Acinetobacter is uniquely suited to exploitation for biotechnological purposes.
Bacillus Bacillus subtilis is one of the best understood prokaryotes in terms of molecular biology and cell biology. Its superb genetic amenability and relatively
large size have provided powerful tools to investigate a bacterium in all possible aspects. Recent improvements in technology have provided novel and amazing
insights into the dynamic structure of this single cell organism. The organism is a model for differentiation, gene/protein regulation and cell cycle events in
bacteria.
Clostridium The genus Clostridium comprises a heterogeneous group of anaerobic spore-forming bacteria, including prominent toxin-producing species, such
as C. difficile, C. botulinum, C. tetani and C. perfringens, in addition to well-known non-pathogens like solventogenic C. acetobutylicum. Clostridia produce a
range of different clostridial toxinsincluding two of the most potent biological toxins known to affect humans.
Corynebacteria Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage,
skin, and cheese smear. Some are important pathogens while others are of immense industrial importance.
Cyanobacteria Cyanobacteria are a fascinating and versatile group of bacteria of immense biological importance. Thought to be amongst the first organisms to
colonize the earth, these bacteria are the photosynthetic ancestors of chloroplasts in eukaryotes such as plants and algae. In addition they can fix nitrogen,
survive in very hostile environments (e.g. down to -60C), are symbiotic, have circadian rhythms, exhibit gliding mobility, and can differentiate into specialized
cell types called heterocysts. This makes them ideal model systems for studying fundamental processes such as nitrogen fixation and photosynthesis.
Gram-positive Bacteria Gram-positive bacteria are generally divided into the Actinobacteria and the Firmicutes. The Actinobacteria include some of the most
common soil bacteria and some pathogens, such as Mycobacterium,Corynebacterium.
Helicobacter pylori Helicobacter pylori causes peptic ulcers, gastritis and gastric cancer. The bacterium infects up to 50% of the human population. H. pylori has
very unique characteristics, such as microaerophily and nitrogen metabolism.
Lactobacillus Lactobacillus is a genus of Gram-positive facultative anaerobic or microaerophilic bacteria. In humans they are symbiotic and are found in the gut
flora. Lactobacillus species are used for the production of yogurt, cheese, sauerkraut, pickles, beer, wine, cider, kimchi, chocolate and other fermented foods,
as well as animal feeds such as silage.
Legionella Legionella is the genus of bacterium that causes Legionnaires' Disease also known as Legionellosis. These bacteria are commonly found in aquatic
habitats where they can survive and multiply in different protozoa enabling the bacterium to be transmissible and pathogenic to humans.
Mycobacterium Mycobacterium is a genus of Actinobacteria, given its own family, the Mycobacteriaceae. The genus includes pathogens known to cause
serious diseases in mammals, including tuberculosis and leprosy. Mycobacteria are aerobic and nonmotile bacteria (except for the species Mycobacterium
marinum which has been shown to be motile within macrophages) that are characteristically acid-alcohol fast. Mycobacteria do not contain endospores or
capsules and are usually considered to be Gram-positive bacteria.
Pasteurellaceae The Pasteurellaceae family comprises a large and diverse family of Gram-negative bacteria with members ranging from important pathogens
such as Haemophilus influenzae to commensals of the animal and human mucosa. Members of the family Pasteurellaceae cause a wide variety of diseases in
humans and animals.
Pseudomonas The bacterial genus Pseudomonas includes the opportunistic human pathogen P. aeruginosa, plant pathogenic bacteria, plant beneficial
bacteria, ubiquitous soil bacteria with bioremediation capabilities and other species that cause spoilage of milk and dairy products. P. aeruginosa can cause
chronic opportunistic infections that have become increasingly apparent in immunocompromised patients and the ageing population of industrialised societies.
Staphylococcus Species of Staphylococcus are important pathogens that cause a variety of diseases in humans and animals. In particular, they cause hospital
acquired infections and antibiotic resistant strains (MRSA) cause major problems in hospitals.
Treponema Treponema pallidum is a gram-negative spirochaete bacterium. There are at least four known subspecies:T. pallidum pallidum, which causes
syphilis; T. pallidum pertenue, which causes yaws; T. pallidum carateum, which causes pinta; and T. pallidum endemicum, which causes bejel.
Vibrio cholerae Vibrio cholerae is the causative agent of cholera and belongs to a group of organisms whose natural habitats are the aquatic ecosystems. The
strains that cause cholera epidemics have evolved from non-pathogenic progenitor strains by acquisition of virulence genes, and V. cholerae represents a
paradigm for this evolutionary process.
Fungi
Candida Candida species are important human pathogens that are best known for causing opportunist infections in immunocompromised hosts (eg transplant
patients, AIDS sufferers, cancer patients). Infections are difficult to treat and can be very serious: 30-40% of systemic infections result in death. The sequencing
of the genome of C. albicans and those of several other medically-relevant Candida species has provided a major impetus for Candida comparative and
functional genomic analyses. These have provided a fascinating insight into the molecular and cellular biology of these fungi and these should pave the way for
the development of more sensitive diagnostic strategies and novel antifungal therapies.
Pathogenic Fungi Pathogenic fungi are fungi that cause disease in humans or other organisms. The study of pathogenic fungi is referred to as medical
mycology. Although fungi are eukaryotic organisms many pathogenic fungi are also microorganisms.
Viruses
Animal Viruses The study of animal viruses is important from a veterinary viewpoint and many of these viruses causes diseases that are economically
devastating. Many animal viruses are also important from a human medical perspective.
Bluetongue Virus Bluetongue virus (BTV), a member of Orbivirus genus within the Reoviridae family causes serious disease in livestock (sheep, goat, cattle).
Partly due to this 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.
Coronavirus Coronaviruses are positive-strand, enveloped RNA viruses that are important pathogens of mammals and birds. This group of viruses cause
enteric or respiratory tract infections in a variety of animals including humans, livestock and pets.
Bacteriophage The New Phage Biology from genomics to applications. Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and
diverse entities in the biosphere. From initial research defining the nature of viruses, to deciphering the fundamental principles of life, to the development of the
science of molecular biology, phages have been 'model organisms' for probing the basic chemistry of life. With more recent advances in technology, most
notably the ability to elucidate the genome sequences of phages and their bacterial hosts, there has been a resurgence of interest in phages as more
information is generated regarding their biology, ecology and diverse nature. Phage research in more recent years has revealed not only their abundance and
diversity of form, but also their dramatic impact on the ecology of our planet, their influence on the evolution of microbial populations, and their potential
applications. This review focuses on this new post-genomic era of phage biology, from information emerging from genomics and metagenomics approaches
through to applications in agriculture, human therapy and biotechnology.
Foot and Mouth Foot-and-mouth disease virus (FMDV) is the prototypic member of the Aphthovirus genus in the Picornaviridae family. This picornavirus is the
etiological agent of an acute systemic vesicular disease that affects cattle worldwide.
Cytomegalovirus Cytomegaloviruses are members of the herpesvirus group and can infect humans and other primates. Between 50-80% of adults in developed
countries and up to 100% in developing countries are infected with human cytomegalovirus. Infection causes problems in immunocompromised hosts including
AIDS victims or patients undergoing organ and stem cell transplantation and congenital infection can cause birth defects in the child. Development of an
effective vaccine has high priority.
Epstein-Barr Virus Epstein-Barr virus (EBV) is a human gamma herpes virus that remains one of the most successful viral parasites known to man. It is the
etiological agent of infectious mononucleosis and is the major biological cofactor contributing to a number of human cancers including B-cell neoplasms (e.g.
Burkitt's lymphoma, Hodgkin's disease and immunoblastic lymphomas), certain forms of T-cell lymphoma, and some epithelial tumours (e.g. nasopharyngeal
carcinomas and gastric carcinomas).
Papillomavirus Papillomaviruses are oncogenic DNA tumour viruses that infect humans and animals. Human papillomavirus is one of the most common causes
of sexually transmitted infection in the world and can also cause cancer. Papillomavirus research has been revolutionised in recent years with the advent of new
technologies such as organotypic raft cultures, virus-like particles and transgenic mice.
Bacteriophage
Phage Bacterial viruses, or bacteriophages, are estimated to be the most widely distributed and diverse entities in the biosphere. From initial research defining
the nature of viruses, to deciphering the fundamental principles of life, to the development of the science of molecular biology, phages have been 'model
organisms' for probing the basic chemistry of life. With more recent advances in technology, most notably the ability to elucidate the genome sequences of
phages and their bacterial hosts, there has been a resurgence of interest in phages as more information is generated regarding their biology, ecology and
diverse nature. Phage research in more recent years has revealed not only their abundance and diversity of form, but also their dramatic impact on the ecology
of our planet, their influence on the evolution of microbial populations, and their potential applications.
Gram-positive bacteria
Gram-positive Bacteria are generally divided into the Actinobacteria and the Firmicutes. The Actinobacteria include some of the most common soil bacteria and some
pathogens, including Mycobacterium, Corynebacterium, Bacillus, Staphylococcus.
Bacillus Bacillus subtilis is one of the best understood prokaryotes in terms of molecular biology and cell biology. Its superb genetic amenability and relatively
large size have provided powerful tools to investigate a bacterium in all possible aspects. Recent improvements in technology have provided novel and amazing
insights into the dynamic structure of this single cell organism. The organism is a model for differentiation, gene/protein regulation and cell cycle events in
bacteria.
Clostridium The genus Clostridium comprises a heterogeneous group of anaerobic spore-forming bacteria, including prominent toxin-producing species, such
as C. difficile, C. botulinum, C. tetani and C. perfringens, in addition to well-known non-pathogens like solventogenic C. acetobutylicum. Clostridia produce a
range of different clostridial toxinsincluding two of the most potent biological toxins known to affect humans.
Corynebacteria Corynebacteria are a diverse group of Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage,
skin, and cheese smear. Some are important pathogens while others are of immense industrial importance.
Lactobacillus Lactobacillus is a genus of Gram-positive facultative anaerobic or microaerophilic bacteria. In humans they are symbiotic and are found in the gut
flora. Lactobacillus species are used for the production of yogurt, cheese, sauerkraut, pickles, beer, wine, cider, kimchi, chocolate and other fermented foods,
as well as animal feeds such as silage.
Mycobacterium Mycobacterium is a genus of Actinobacteria, given its own family, the Mycobacteriaceae. The genus includes pathogens known to cause
serious diseases in mammals, including tuberculosis and leprosy. Mycobacteria are aerobic and nonmotile bacteria (except for the species Mycobacterium
marinum which has been shown to be motile within macrophages) that are characteristically acid-alcohol fast. Mycobacteria do not contain endospores or
capsules and are usually considered to be Gram-positive bacteria.
Staphylococcus Species of Staphylococcus are important pathogens that cause a variety of diseases in humans and animals. In particular, they cause hospital
acquired infections and antibiotic resistant strains (MRSA) cause major problems in hospitals.
Gram-negative bacteria
Many species of Gram-negative bacteria are pathogenic. Medically relevant Gram-negative include Acinetobacter, Helicobacter
pylori, Legionella, Pasteurellaceae, Pseudomonas, Treponema, Vibrio cholerae.
Acinetobacter The genus Acinetobacter is a group of Gram-negative, non-motile and non-fermentative bacteria belonging to the family Moraxellaceae. They are
important soil organisms where they contribute to the mineralisation of, for example, aromatic compounds. Acinetobacter are able to survive on various surfaces
(both moist and dry) in the hospital environment, thereby being an important source of infection in debilitated patients. These bacteria are innately resistant to
many classes of antibiotics. In addition, Acinetobacter is uniquely suited to exploitation for biotechnological purposes.
Cyanobacteria Cyanobacteria are a fascinating and versatile group of bacteria of immense biological importance. Thought to be amongst the first organisms to
colonize the earth, these bacteria are the photosynthetic ancestors of chloroplasts in eukaryotes such as plants and algae. In addition they can fix nitrogen,
survive in very hostile environments (e.g. down to -60C), are symbiotic, have circadian rhythms, exhibit gliding mobility, and can differentiate into specialized
cell types called heterocysts. This makes them ideal model systems for studying fundamental processes such as nitrogen fixation and photosynthesis.
Helicobacter pylori Helicobacter pylori causes peptic ulcers, gastritis and gastric cancer. The bacterium infects up to 50% of the human population. H. pylori has
very unique characteristics, such as microaerophily and nitrogen metabolism.
Legionella Legionella is the genus of bacterium that causes Legionnaires' Disease also known as Legionellosis. These bacteria are commonly found in aquatic
habitats where they can survive and multiply in different protozoa enabling the bacterium to be transmissible and pathogenic to humans.
Pasteurellaceae The Pasteurellaceae family comprises a large and diverse family of Gram-negative bacteria with members ranging from important pathogens
such as Haemophilus influenzae to commensals of the animal and human mucosa. Members of the family Pasteurellaceae cause a wide variety of diseases in
humans and animals.
Pseudomonas The bacterial genus Pseudomonas includes the opportunistic human pathogen P. aeruginosa, plant pathogenic bacteria, plant beneficial
bacteria, ubiquitous soil bacteria with bioremediation capabilities and other species that cause spoilage of milk and dairy products. P. aeruginosa can cause
chronic opportunistic infections that have become increasingly apparent in immunocompromised patients and the ageing population of industrialised societies.
Treponema Treponema pallidum is a gram-negative spirochaete bacterium. There are at least four known subspecies:T. pallidum pallidum, which causes
syphilis; T. pallidum pertenue, which causes yaws; T. pallidum carateum, which causes pinta; and T. pallidum endemicum, which causes bejel.
Vibrio cholerae Vibrio cholerae is the causative agent of cholera and belongs to a group of organisms whose natural habitats are the aquatic ecosystems. The
strains that cause cholera epidemics have evolved from non-pathogenic progenitor strains by acquisition of virulence genes, and V. cholerae represents a
paradigm for this evolutionary process.
Borrelia The genus Borrelia, in the spirochete phylum, is not closely related to any other bacteria and has a highly unusual genome composed of a linear
chromosome and multiple circular and linear plasmids that appear to be in a constant state of rearrangement, recombination, and deletion. The determination of
the genome sequence of Borreliastrains has facilitated tremendous advances in understanding this genus at the molecular and cellular level as well as the
pathogenesis of Lyme disease and relapsing fever.

Microbes, Germs and Antibiotics
This article gives a brief overview of the different types of microbes (germs) that can cause infections and a brief overview of the use of antibiotics.

What are microbes?
Healthcare professionals classify microbes or 'germs' into different groups. The most common groups of microbes that cause illness are described
below.

Bacteria
There are many different types of bacteria. Some are helpful and protective to humans. Some flourish naturally in our bodies - particularly in the
bowel and vagina - and help to protect the body from infections. However, infections with certain bacteria can cause serious illnesses such as
meningitis, pneumonia, tuberculosis, etc. A bacterial infection may be treated with a course of antibiotics.

Viruses
These are smaller and different to bacteria. Many different types exist. Most of the common 'minor' illnesses are caused by viruses. For example,
colds, coughs, sore throats, chickenpox and some other rashes. Most common infections in the community are due to a viral infection.
Viral infections are much more common than bacterial and fungal infections.
For many viral infections there are no effective antiviral drugs (unlike antibiotics for bacteria). Fortunately, the immune system in the body usually
fights off most viral infections within a few days. Taking 'symptomatic' treatments for fever or catarrh, such as paracetamol and/or ibuprofen, resting
and drinking plenty are usually all that needs to be done to get better.
However, some viruses are not fought off and can be very serious. The HIV virus is a good example. There are some antiviral medicines that are
used for certain infections - such as antiretroviral medicines used to treat HIV. Another example is aciclovir and related medicines which are used to
treat certain herpes virus infections. As a rule, antiviral medicines do not clear the virus from the body. They usually work by stopping the virus from
multiplying and so 'control' the virus and the infection that it causes.

Fungi
Many types of fungi exist and cause problems in humans, animals and plants. Fungal infections commonly affect the skin and nails in humans. They
can cause ringworm, athlete's foot, other localised skin rashes and infections in and around nails. Modern creams usually work well to clear a local
fungal rash quickly. However, nail infections can be rather stubborn and may need long-term treatment of antifungal medicines taken by mouth.
Most fungi are free-living in the environment and few of these are capable of causing infection in an otherwise healthy person. However, they can
cause serious infections in patients with weakened immune systems (for example, those who have recently received chemotherapy for cancer).

Yeasts
Yeasts are actually a type of fungus. There are different yeasts which cause various infections. The most common yeast infection is thrush. This is
due to a yeast called candida which thrives in moist, airless, warm areas of the body. It can cause infections in the vagina; it can be a case of nappy
rash in babies, and it can also sometimes infect other areas of the body. Treatment of yeast infections usually works well with anti-yeast creams and
medicines.

Parasites
A parasite is a type of germ that needs to live on or in another living being (host) to survive. It gets its food from its host. Parasites are not as
common as the other types of germs although they can cause some types of diseases in humans.
Parasites are usually found in contaminated water or food. They can also get into the body by insect bites or by sexual contact. Parasitic infections
are more common in the tropics and subtropics. They can occur in the UK but are more typically seen in people who have weakened immune
systems (for example, those with HIV or those people taking chemotherapy for types of cancer).
Examples of diseases caused by parasites are malaria, amoebic dysentery and giardia. Hookworms and tapeworms are also parasites.

Antibiotics
Antibiotics are no 'cure all' for infections. Antibiotics will only clear infections caused by bacteria and some parasites. They do not work when an
infection is caused by viruses, fungi or yeasts. As mentioned, most common infections are caused by viruses when an antibioti c will not be of use.
Even if you have a bacterial infection, the immune system can clear most bacterial infections. This means that antibiotics are not needed for minor
infections (for example, an ear or throat infection in an otherwise fit person).
However, you do need antibiotics if you have certain serious infections caused by bacteria, such as meningitis, pneumonia or kidney infections. In
these situations, antibiotics are often life-saving. When you are ill, doctors are skilled at checking you over to rule out serious illness and to advise if
an antibiotic is needed.

How do antibiotics work?
Some work by killing the bacteria. This is often done by interfering with the structure of the cell wall of the bacteria. Some work by stopping the
bacteria from multiplying.

Some possible problems with antibiotics

Antibiotics are not without problems. This is why it is not usually good practice to take antibiotics 'just in case' an infection is bacterial, but to take
them only when they are really needed. For example:

Antibiotics can cause side-effects such as allergies, diarrhoea, rashes and nausea. Side-effects are quite common. Most side-effects are not serious,
but some people have died from a severe allergic reaction to an antibiotic. Antibiotics can kill off normal 'defence' bacteria which live in the bowel and
vagina. This may then allow other infections - for example, thrush - to develop. Overuse of antibiotics has led to some bacteria mutating and
becoming resistant to some antibiotics which may then not work when really needed. For example, meticillin-resistant Staphylococcus aureus
(MRSA) is a bacterium that has become resistant to many different antibiotics and is often very difficult to treat. The more antibiotics are used, the
greater the problem of antibiotic resistance. When antibiotics are appropriately prescribed, it is important to take them as directed on your
prescription and to complete the full course of treatment. That often means continuing to take the antibiotics as directed when you feel better. Failing
to finish a course of treatment or failing to take the antibiotics as prescribed, can actually result in the growth of resistant antibiotics. Some antibiotics
may interact with other medicines that you might take. This may cause reactions, or reduce the effectiveness of one or other of the treatments. Food
and drink affect the absorption of some antibiotics - so follow the instructions on how to take a course of antibiotics. In summary

Doctors are skilled in diagnosing which conditions are in need of antibiotics. So do not be surprised if a doctor does not recommend an antibiotic for
conditions caused by viruses or non-bacterial infections, or even for a mild bacterial infection.

Most simple coughs, colds, sore throats and influenza are caused by viruses and an antibiotic will not work.

Occasionally, a viral infection or minor bacterial infection develops into a more serious 'secondary' bacterial infection. You should see a doctor to
review the situation if an illness appears to change, becomes worse, does not go after a few days or if you are worried about any new symptom that
develops.