Microbiology

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An agar plate streaked with microorganisms Agar plate with colonies.jpg
An agar plate streaked with microorganisms

Microbiology (from Ancient Greek μῑκρος (mīkros) 'small', βίος (bíos) ' life ',and -λογία ( -logía ) 'study of') is the scientific study of microorganisms, those being of unicellular (single-celled), multicellular (consisting of complex cells), or acellular (lacking cells). [1] [2] Microbiology encompasses numerous sub-disciplines including virology, bacteriology, protistology, mycology, immunology, and parasitology.

Contents

Eukaryotic microorganisms possess membrane-bound organelles and include fungi and protists, whereas prokaryotic organisms—all of which are microorganisms—are conventionally classified as lacking membrane-bound organelles and include Bacteria and Archaea. [3] [4] Microbiologists traditionally relied on culture, staining, and microscopy for the isolation and identification of microorganisms. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. [5] With the emergence of biotechnology, Microbiologists currently rely on molecular biology tools such as DNA sequence-based identification, for example, the 16S rRNA gene sequence used for bacterial identification.

Viruses have been variably classified as organisms [6] because they have been considered either very simple microorganisms or very complex molecules. Prions, never considered microorganisms, have been investigated by virologists; however, as the clinical effects traced to them were originally presumed due to chronic viral infections, virologists took a search—discovering "infectious proteins".

The existence of microorganisms was predicted many centuries before they were first observed, for example by the Jains in India and by Marcus Terentius Varro in ancient Rome. The first recorded microscope observation was of the fruiting bodies of moulds, by Robert Hooke in 1666, but the Jesuit priest Athanasius Kircher was likely the first to see microbes, which he mentioned observing in milk and putrid material in 1658. Antonie van Leeuwenhoek is considered a father of microbiology as he observed and experimented with microscopic organisms in the 1670s, using simple microscopes of his design. Scientific microbiology developed in the 19th century through the work of Louis Pasteur and in medical microbiology Robert Koch.

History

Avicenna postulated the existence of microorganisms. Avicenna TajikistanP17-20Somoni-1999 (cropped).png
Avicenna postulated the existence of microorganisms.

The existence of microorganisms was hypothesized for many centuries before their actual discovery. The existence of unseen microbiological life was postulated by Jainism which is based on Mahavira's teachings as early as 6th century BCE (599 BC - 527 BC). [7] :24 Paul Dundas notes that Mahavira asserted the existence of unseen microbiological creatures living in earth, water, air and fire. [7] :88 Jain scriptures describe nigodas which are sub-microscopic creatures living in large clusters and having a very short life, said to pervade every part of the universe, even in tissues of plants and flesh of animals. [8] The Roman Marcus Terentius Varro made references to microbes when he warned against locating a homestead in the vicinity of swamps "because there are bred certain minute creatures which cannot be seen by the eyes, which float in the air and enter the body through the mouth and nose and thereby cause serious diseases." [9]

Persian scientists hypothesized the existence of microorganisms, such as Avicenna in his book The Canon of Medicine , Ibn Zuhr (also known as Avenzoar) who discovered scabies mites, and Al-Razi who gave the earliest known description of smallpox in his book The Virtuous Life (al-Hawi). [10] The tenth-century Taoist Baoshengjing describes "countless micro organic worms" which resemble vegetable seeds, which prompted Dutch sinologist Kristofer Schipper to claim that "the existence of harmful bacteria was known to the Chinese of the time." [11]

In 1546, Girolamo Fracastoro proposed that epidemic diseases were caused by transferable seedlike entities that could transmit infection by direct or indirect contact, or vehicle transmission. [12]

Antonie van Leeuwenhoek (1632-1723) Anthonie van Leeuwenhoek (1632-1723). Natuurkundige te Delft Rijksmuseum SK-A-957.jpeg
Antonie van Leeuwenhoek (1632–1723)
Statue of Robert Koch, one of the founders of microbiology, in Berlin Statue of Robert Koch in Berlin.jpg
Statue of Robert Koch, one of the founders of microbiology, in Berlin
Martinus Beijerinck is often considered a founder of virology. Martinus Willem Beijerinck in his laboratory.jpg
Martinus Beijerinck is often considered a founder of virology.

In 1676, Antonie van Leeuwenhoek, who lived most of his life in Delft, Netherlands, observed bacteria and other microorganisms using a single-lens microscope of his own design. [14] [2] He is considered a father of microbiology as he used simple single-lensed microscopes of his own design. [14] While Van Leeuwenhoek is often cited as the first to observe microbes, Robert Hooke made his first recorded microscopic observation, of the fruiting bodies of moulds, in 1665. [15] It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms. [16]

Kircher was among the first to design magic lanterns for projection purposes, and so he was well acquainted with the properties of lenses. [16] He wrote "Concerning the wonderful structure of things in nature, investigated by Microscope" in 1646, stating "who would believe that vinegar and milk abound with an innumerable multitude of worms." He also noted that putrid material is full of innumerable creeping animalcules. He published his Scrutinium Pestis (Examination of the Plague) in 1658, stating correctly that the disease was caused by microbes, though what he saw was most likely red or white blood cells rather than the plague agent itself. [16]

The birth of bacteriology

Innovative laboratory glassware and experimental methods developed by Louis Pasteur and other biologists contributed to the young field of bacteriology in the late 19th century. Albert Edelfelt - Louis Pasteur - 1885.jpg
Innovative laboratory glassware and experimental methods developed by Louis Pasteur and other biologists contributed to the young field of bacteriology in the late 19th century.

The field of bacteriology (later a subdiscipline of microbiology) was founded in the 19th century by Ferdinand Cohn, a botanist whose studies on algae and photosynthetic bacteria led him to describe several bacteria including Bacillus and Beggiatoa . Cohn was also the first to formulate a scheme for the taxonomic classification of bacteria, and to discover endospores. [17] Louis Pasteur and Robert Koch were contemporaries of Cohn, and are often considered to be the fathers of modern microbiology [16] and medical microbiology, respectively. [18] Pasteur is most famous for his series of experiments designed to disprove the then widely held theory of spontaneous generation, thereby solidifying microbiology's identity as a biological science. [19] One of his students, Adrien Certes, is considered the founder of marine microbiology. [20] Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies. [2] Koch is best known for his contributions to the germ theory of disease, proving that specific diseases were caused by specific pathogenic microorganisms. He developed a series of criteria that have become known as the Koch's postulates. Koch was one of the first scientists to focus on the isolation of bacteria in pure culture resulting in his description of several novel bacteria including Mycobacterium tuberculosis , the causative agent of tuberculosis. [2]

While Pasteur and Koch are often considered the founders of microbiology, their work did not accurately reflect the true diversity of the microbial world because of their exclusive focus on microorganisms having direct medical relevance. It was not until the late 19th century and the work of Martinus Beijerinck and Sergei Winogradsky that the true breadth of microbiology was revealed. [2] Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques. [21] While his work on the tobacco mosaic virus established the basic principles of virology, it was his development of enrichment culturing that had the most immediate impact on microbiology by allowing for the cultivation of a wide range of microbes with wildly different physiologies. Winogradsky was the first to develop the concept of chemolithotrophy and to thereby reveal the essential role played by microorganisms in geochemical processes. [22] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria. [2] French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages in 1917 and was one of the earliest applied microbiologists. [23]

Joseph Lister was the first to use phenol disinfectant on the open wounds of patients. [24]

Branches

A university food microbiology laboratory LUA, Faculty of Food Technology Food microbiology laboratory.jpg
A university food microbiology laboratory

The branches of microbiology can be classified into applied sciences, or divided according to taxonomy, as is the case with bacteriology, mycology, protozoology, virology, phycology, and microbial ecology. There is considerable overlap between the specific branches of microbiology with each other and with other disciplines, and certain aspects of these branches can extend beyond the traditional scope of microbiology [25] [26] A pure research branch of microbiology is termed cellular microbiology.

Applications

While some people have fear of microbes due to the association of some microbes with various human diseases, many microbes are also responsible for numerous beneficial processes such as industrial fermentation (e.g. the production of alcohol, vinegar and dairy products), antibiotic production and act as molecular vehicles to transfer DNA to complex organisms such as plants and animals. Scientists have also exploited their knowledge of microbes to produce biotechnologically important enzymes such as Taq polymerase, [27] reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system. [28]

Bacteria can be used for the industrial production of amino acids. organic acids, vitamin, proteins, antibiotics and other commerically used metabolites with are produced by microorganisms. Corynebacterium glutamicum is one of the most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine. [29] Since some bacteria have the ability to synthesize antibiotics, they are used for medicinal purposes, such as Streptomyces to make aminoglycoside antibiotics. [30]

Fermenting tanks with yeast being used to brew beer Cuves de fermentations.jpg
Fermenting tanks with yeast being used to brew beer

A variety of biopolymers, such as polysaccharides, polyesters, and polyamides, are produced by microorganisms. Microorganisms are used for the biotechnological production of biopolymers with tailored properties suitable for high-value medical application such as tissue engineering and drug delivery. Microorganisms are for example used for the biosynthesis of xanthan, alginate, cellulose, cyanophycin, poly(gamma-glutamic acid), levan, hyaluronic acid, organic acids, oligosaccharides polysaccharide and polyhydroxyalkanoates. [31]

Microorganisms are beneficial for microbial biodegradation or bioremediation of domestic, agricultural and industrial wastes and subsurface pollution in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste depends on the nature of each contaminant. Since sites typically have multiple pollutant types, the most effective approach to microbial biodegradation is to use a mixture of bacterial and fungal species and strains, each specific to the biodegradation of one or more types of contaminants. [32]

Symbiotic microbial communities confer benefits to their human and animal hosts health including aiding digestion, producing beneficial vitamins and amino acids, and suppressing pathogenic microbes. Some benefit may be conferred by eating fermented foods, probiotics (bacteria potentially beneficial to the digestive system) or prebiotics (substances consumed to promote the growth of probiotic microorganisms). [33] [34] The ways the microbiome influences human and animal health, as well as methods to influence the microbiome are active areas of research. [35]

Research has suggested that microorganisms could be useful in the treatment of cancer. Various strains of non-pathogenic clostridia can infiltrate and replicate within solid tumors. Clostridial vectors can be safely administered and their potential to deliver therapeutic proteins has been demonstrated in a variety of preclinical models. [36]

Some bacteria are used to study fundamental mechanisms. An example of model bacteria used to study motility [37] or the production of polysaccharides and development is Myxococcus xanthus . [38]

See also

Professional organizations
Journals

Related Research Articles

<span class="mw-page-title-main">Microorganism</span> Microscopic living organism

A microorganism, or microbe, is an organism of microscopic size, which may exist in its single-celled form or as a colony of cells.

<span class="mw-page-title-main">Biofilm</span> Aggregation of bacteria or cells on a surface

A biofilm is a syntrophic community of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix that is composed of extracellular polymeric substances (EPSs). The cells within the biofilm produce the EPS components, which are typically a polymeric combination of extracellular polysaccharides, proteins, lipids and DNA. Because they have a three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes".

<span class="mw-page-title-main">Bacteriology</span> Subdiscipline of microbiology that studies bacteria

Bacteriology is the branch and specialty of biology that studies the morphology, ecology, genetics and biochemistry of bacteria as well as many other aspects related to them. This subdivision of microbiology involves the identification, classification, and characterization of bacterial species. Because of the similarity of thinking and working with microorganisms other than bacteria, such as protozoa, fungi, and viruses, there has been a tendency for the field of bacteriology to extend as microbiology. The terms were formerly often used interchangeably. However, bacteriology can be classified as a distinct science.

<span class="mw-page-title-main">Germ theory of disease</span> Prevailing theory about diseases

The germ theory of disease is the currently accepted scientific theory for many diseases. It states that microorganisms known as pathogens or "germs" can cause disease. These small organisms, too small to be seen without magnification, invade humans, other animals, and other living hosts. Their growth and reproduction within their hosts can cause disease. "Germ" refers to not just a bacterium but to any type of microorganism, such as protists or fungi, or other pathogens that can cause disease, such as viruses, prions, or viroids. Diseases caused by pathogens are called infectious diseases. Even when a pathogen is the principal cause of a disease, environmental and hereditary factors often influence the severity of the disease, and whether a potential host individual becomes infected when exposed to the pathogen. Pathogens are disease-carrying agents that can pass from one individual to another, both in humans and animals. Infectious diseases are caused by biological agents such as pathogenic microorganisms as well as parasites.

<i>Lactobacillus</i> Genus of bacteria

Lactobacillus is a genus of gram-positive, aerotolerant anaerobes or microaerophilic, rod-shaped, non-spore-forming bacteria. Until 2020, the genus Lactobacillus comprised over 260 phylogenetically, ecologically, and metabolically diverse species; a taxonomic revision of the genus assigned lactobacilli to 25 genera.

<span class="mw-page-title-main">Microbiological culture</span> Method of allowing microorganisms to multiply in a controlled medium

A microbiological culture, or microbial culture, is a method of multiplying microbial organisms by letting them reproduce in predetermined culture medium under controlled laboratory conditions. Microbial cultures are foundational and basic diagnostic methods used as research tools in molecular biology.

<span class="mw-page-title-main">Probiotic</span> Microorganisms said to provide health benefits when consumed

Probiotics are live microorganisms promoted with claims that they provide health benefits when consumed, generally by improving or restoring the gut microbiota. Probiotics are considered generally safe to consume, but may cause bacteria-host interactions and unwanted side effects in rare cases. There is some evidence that probiotics are beneficial for some conditions, but there is little evidence for many of the health benefits claimed for them.

<span class="mw-page-title-main">Microbial ecology</span> Study of the relationship of microorganisms with their environment

Microbial ecology is the ecology of microorganisms: their relationship with one another and with their environment. It concerns the three major domains of life—Eukaryota, Archaea, and Bacteria—as well as viruses.

<i>Staphylococcus epidermidis</i> Species of bacterium

Staphylococcus epidermidis is a Gram-positive bacterium, and one of over 40 species belonging to the genus Staphylococcus. It is part of the normal human microbiota, typically the skin microbiota, and less commonly the mucosal microbiota and also found in marine sponges. It is a facultative anaerobic bacteria. Although S. epidermidis is not usually pathogenic, patients with compromised immune systems are at risk of developing infection. These infections are generally hospital-acquired. S. epidermidis is a particular concern for people with catheters or other surgical implants because it is known to form biofilms that grow on these devices. Being part of the normal skin microbiota, S. epidermidis is a frequent contaminant of specimens sent to the diagnostic laboratory.

<span class="mw-page-title-main">Lactic acid bacteria</span> Order of bacteria

Lactobacillales are an order of gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod-shaped (bacilli) or spherical (cocci) bacteria that share common metabolic and physiological characteristics. These bacteria, usually found in decomposing plants and milk products, produce lactic acid as the major metabolic end product of carbohydrate fermentation, giving them the common name lactic acid bacteria (LAB).

<span class="mw-page-title-main">Food microbiology</span> Study of the microorganisms that inhibit, create, or contaminate food

Food microbiology is the study of the microorganisms that inhabit, create, or contaminate food. This includes the study of microorganisms causing food spoilage; pathogens that may cause disease ; microbes used to produce fermented foods such as cheese, yogurt, bread, beer, and wine; and microbes with other useful roles, such as producing probiotics.

<i>Streptococcus thermophilus</i> Species of bacterium

Streptococcus thermophilus formerly known as Streptococcus salivarius subsp. thermophilus is a gram-positive bacterium, and a fermentative facultative anaerobe, of the viridans group. It tests negative for cytochrome, oxidase, and catalase, and positive for alpha-hemolytic activity. It is non-motile and does not form endospores. S. thermophilus is fimbriated.

<span class="mw-page-title-main">Bacteria</span> Domain of microorganisms

Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in mutualistic, commensal and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

<span class="mw-page-title-main">Medical microbiology</span> Branch of medical science

Medical microbiology, the large subset of microbiology that is applied to medicine, is a branch of medical science concerned with the prevention, diagnosis and treatment of infectious diseases. In addition, this field of science studies various clinical applications of microbes for the improvement of health. There are four kinds of microorganisms that cause infectious disease: bacteria, fungi, parasites and viruses, and one type of infectious protein called prion.

Microbial biodegradation is the use of bioremediation and biotransformation methods to harness the naturally occurring ability of microbial xenobiotic metabolism to degrade, transform or accumulate environmental pollutants, including hydrocarbons, polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds, pharmaceutical substances, radionuclides and metals.

<span class="mw-page-title-main">Extracellular polymeric substance</span> Gluey polymers secreted by microorganisms to form biofilms

Extracellular polymeric substances (EPSs) are natural polymers of high molecular weight secreted by microorganisms into their environment. EPSs establish the functional and structural integrity of biofilms, and are considered the fundamental component that determines the physicochemical properties of a biofilm. EPS in the matrix of biofilms provides compositional support and protection of microbial communities from the harsh environments. Components of EPS can be of different classes of polysaccharides, lipids, nucleic acids, proteins, lipopolysaccharides, and minerals. This chemical formula is (C135H217N15Na2O74P10).

<span class="mw-page-title-main">Oral microbiology</span>

Oral microbiology is the study of the microorganisms (microbiota) of the oral cavity and their interactions between oral microorganisms or with the host. The environment present in the human mouth is suited to the growth of characteristic microorganisms found there. It provides a source of water and nutrients, as well as a moderate temperature. Resident microbes of the mouth adhere to the teeth and gums to resist mechanical flushing from the mouth to stomach where acid-sensitive microbes are destroyed by hydrochloric acid.

Oral ecology is the microbial ecology of the microorganisms found in mouths. Oral ecology, like all forms of ecology, involves the study of the living things found in oral cavities as well as their interactions with each other and with their environment. Oral ecology is frequently investigated from the perspective of oral disease prevention, often focusing on conditions such as dental caries, candidiasis ("thrush"), gingivitis, periodontal disease, and others. However, many of the interactions between the microbiota and oral environment protect from disease and support a healthy oral cavity. Interactions between microbes and their environment can result in the stabilization or destabilization of the oral microbiome, with destabilization believed to result in disease states. Destabilization of the microbiome can be influenced by several factors, including diet changes, drugs or immune system disorders.

<span class="mw-page-title-main">Bacteriologist</span> Professional trained in bacteriology

A bacteriologist is a microbiologist, or similarly trained professional, in bacteriology— a subdivision of microbiology that studies bacteria, typically pathogenic ones. Bacteriologists are interested in studying and learning about bacteria, as well as using their skills in clinical settings. This includes investigating properties of bacteria such as morphology, ecology, genetics and biochemistry, phylogenetics, genomics and many other areas related to bacteria like disease diagnostic testing. Alongside human and animal healthcare providers, they may carry out various functions as medical scientists, veterinary scientists, pathologists, or diagnostic technicians in locations like clinics, blood banks, hospitals, laboratories and animal hospitals. Bacteriologists working in public health or biomedical research help develop vaccines for public use as well as public health guidelines for restaurants and businesses.

<span class="mw-page-title-main">Human interactions with microbes</span> Overview of human–microbe interactions

Human interactions with microbes include both practical and symbolic uses of microbes, and negative interactions in the form of human, domestic animal, and crop diseases.

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Further reading