Microbiology

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

Microbiology (from Greek μῑκρος, mīkros, "small"; βίος, bios, "life"; and -λογία, -logia ) is the study of microorganisms, those being unicellular (single cell), multicellular (cell colony), or acellular (lacking cells). [1] [2] Microbiology encompasses numerous sub-disciplines including virology, parasitology, mycology and bacteriology.

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. However, less than 1% of the microorganisms present in common environments can be cultured in isolation using current means. [5] Microbiologists often rely on molecular biology tools such as DNA sequence based identification, for example 16s rRNA gene sequence used for bacteria identification.

Viruses have been variably classified as organisms, [6] as they have been considered either as very simple microorganisms or very complex molecules. Prions, never considered as microorganisms, have been investigated by virologists, however, as the clinical effects traced to them were originally presumed due to chronic viral infections, and virologists took 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 1676, using simple microscopes of his own design. Scientific microbiology developed in the 19th century through the work of Louis Pasteur and in medical microbiology Robert Koch.

History

Avicenna hypothesized the existence of microorganisms. Avicenna TajikistanP17-20Somoni-1999 (cropped).png
Avicenna hypothesized 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. [7] Paul Dundas notes that Mahavira asserted the existence of unseen microbiological creatures living in earth, water, air and fire. [8] 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. [9] 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." [10]

In the golden age of Islamic civilization, Iranian 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). [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, often cited as the first to experiment with microorganisms. Anthonie van Leeuwenhoek (1632-1723). Natuurkundige te Delft Rijksmuseum SK-A-957.jpeg
Antonie van Leeuwenhoek, often cited as the first to experiment with microorganisms.
Van Leeuwenhoek's microscopes by Henry Baker Van Leeuwenhoek's microscopes by Henry Baker.jpg
Van Leeuwenhoek's microscopes by Henry Baker
Martinus Beijerinck, the founding father of the Delft School of Microbiology, in his laboratory. Beijerinck is often considered as a founder of virology, environmental microbiology, and industrial microbiology. Martinus Willem Beijerinck in his laboratory.jpg
Martinus Beijerinck, the founding father of the Delft School of Microbiology, in his laboratory. Beijerinck is often considered as a founder of virology, environmental microbiology, and industrial microbiology.

In 1676, Antonie van Leeuwenhoek, who lived most of his life in Delft, Holland, observed bacteria and other microorganisms using a single-lens microscope of his own design. [19] [2] He is considered a father of microbiology as he pioneered the use of simple single-lensed microscopes of his own design. [19] 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. [20] It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms. [21]

Kircher was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses. [21] 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. [21]

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. [22] Louis Pasteur and Robert Koch were contemporaries of Cohn, and are often considered to be the father of microbiology [21] and medical microbiology, respectively. [23] 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. [24] One of his students, Adrien Certes, is considered the founder of marine microbiology. [25] 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. [26] 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. [27] 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. [28]

Joseph Lister was the first to use phenol disinfectant on the open wounds of patients. [29]

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, and phycology. 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 [30] [31] A pure research branch of microbiology is termed cellular microbiology.

Applications

While some fear 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, [32] reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system.[ citation needed ]

Bacteria can be used for the industrial production of amino acids. 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. [33] Since some bacteria have the ability to synthesize antibiotics, they are used for medicinal purposes, such as Streptomyces to make aminoglycoside antibiotics. [34]

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. [35]

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. [36]

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). [37] [38] The ways the microbiome influences human and animal health, as well as methods to influence the microbiome are active areas of research. [39]

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. [40]

See also

Professional organizations
Journals

Related Research Articles

Microorganism Microscopic living organism

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

Antonie van Leeuwenhoek Dutch tradesman and scientist

Antonie Philips van Leeuwenhoek was a Dutch businessman and scientist in the Golden Age of Dutch science and technology. A largely self-taught man in science, he is commonly known as "the Father of Microbiology", and one of the first microscopists and microbiologists. Van Leeuwenhoek is best known for his pioneering work in microscopy and for his contributions toward the establishment of microbiology as a scientific discipline.

Bacteriology study of 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.

An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It may react negatively or even die if free oxygen is present. In contrast, an aerobic organism (aerobe) is an organism that requires an oxygenated environment. Anaerobes may be unicellular or multicellular.

Kochs postulates Four criteria showing a causal relationship between a causative microbe and a disease

Koch's postulates are four criteria designed to establish a causative relationship between a microbe and a disease. The postulates were formulated by Robert Koch and Friedrich Loeffler in 1884, based on earlier concepts described by Jakob Henle, and refined and published by Koch in 1890. Koch applied the postulates to describe the etiology of cholera and tuberculosis, but they have been controversially generalized to other diseases. These postulates were generated prior to understanding of modern concepts in microbial pathogenesis that cannot be examined using Koch's postulates, including viruses and asymptomatic carriers. They have largely been supplanted by other criteria such as the Bradford Hill criteria for infectious disease causality in modern public health.

Martinus Beijerinck Dutch microbiologist

Martinus Willem Beijerinck was a Dutch microbiologist and botanist. He is often considered one of the founders of virology and environmental microbiology. In spite of his numerous pioneering and seminal contributions to science in general, he was never awarded the Nobel Prize.

Microbial ecology 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.

Geobacter is a genus of Proteobacteria. Geobacter species are anaerobic respiration bacterial species which have capabilities that make them useful in bioremediation. Geobacter was found to be the first organism with the ability to oxidize organic compounds and metals, including iron, radioactive metals, and petroleum compounds into environmentally benign carbon dioxide while using iron oxide or other available metals as electron acceptors. Geobacter species are also found to be able to respire upon a graphite electrode. They have been found in anaerobic conditions in soils and aquatic sediment.

Sergei Winogradsky Ukrainian-Russian microbiologist

Sergei Nikolaievich Winogradsky was a Russian microbiologist, ecologist and soil scientist who pioneered the cycle-of-life concept.

Lactic acid bacteria order of gram-positive, low-GC, acid-tolerant, generally nonsporulating, nonrespiring, either rod-shaped or spherical bacteria

Lactic acid bacteria (LAB) 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. This trait has, throughout history, linked LAB with food fermentations, as acidification inhibits the growth of spoilage agents. Proteinaceous bacteriocins are produced by several LAB strains and provide an additional hurdle for spoilage and pathogenic microorganisms. Furthermore, lactic acid and other metabolic products contribute to the organoleptic and textural profile of a food item. The industrial importance of the LAB is further evidenced by their generally recognized as safe (GRAS) status, due to their ubiquitous appearance in food and their contribution to the healthy microbiota of animal and human mucosal surfaces. The genera that comprise the LAB are at its core Lactobacillus, Leuconostoc, Pediococcus, Lactococcus, and Streptococcus, as well as the more peripheral Aerococcus, Carnobacterium, Enterococcus, Oenococcus, Sporolactobacillus, Tetragenococcus, Vagococcus, and Weissella; these belong to the order Lactobacillales.

Food microbiology study of the microorganisms that inhibit, create, or contaminate food

Food microbiology is the study of the microorganisms that inhibit, create, or contaminate food. This includes the study of microorganisms causing food spoilage; as well as, pathogens that may cause disease especially if food is improperly cooked or stored. Those used to produce fermented foods such as cheese, yogurt, bread, beer, and wine. Then those researchers with other useful roles such as producing probiotics.

Medical microbiology medical specialty

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.

Biotransformation is the chemical modification (or modifications) made by an organism on a chemical compound. If this modification ends in mineral compounds like CO2, NH4+, or H2O, the biotransformation is called mineralisation.

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.

Oral microbiology community of microorganisms in the mouth

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.

<i>Bifidobacterium</i> genus of bacteria

Bifidobacterium is a genus of gram-positive, nonmotile, often branched anaerobic bacteria. They are ubiquitous inhabitants of the gastrointestinal tract, vagina and mouth of mammals, including humans. Bifidobacteria are one of the major genera of bacteria that make up the gastrointestinal tract microbiota in mammals. Some bifidobacteria are used as probiotics.

Microbial phylogenetics is the study of the manner in which various groups of microorganisms are genetically related. This helps to trace their evolution. To study these relationships biologists rely on comparative genomics, as physiology and comparative anatomy are not possible methods.

Petroleum microbiology is a branch of microbiology that deals with the study of microorganisms that can metabolize or alter crude or refined petroleum products. These microorganisms, also called hydrocarbonoclastic microorganisms, can degrade hydrocarbons and, include a wide distribution of bacteria, methanogenic archaea, and some fungi. Not all hydrocarbonoclasic microbes depend on hydrocarbons to survive, but instead may use petroleum products as alternative carbon and energy sources. Interest in this field is growing due to the increasing role of bioremediation in oil spill cleanup.

Human interactions with microbes

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.

Branches of microbiology

The branches of microbiology can be classified into pure and applied sciences. Microbiology can be also classified based on taxonomy, in the cases of bacteriology, mycology, protozoology, and phycology. 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 In general the field of microbiology can be divided in the more fundamental branch and the applied microbiology (biotechnology). In the more fundamental field the organisms are studied as the subject itself on a deeper (theoretical) level. Applied microbiology refers to the fields where the micro-organisms are applied in certain processes such as brewing or fermentation. The organisms itself are often not studied as such, but applied to sustain certain processes.

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