Microbiology

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] Microbiology encompasses numerous sub-disciplines including virology, parasitology, mycology and bacteriology.

Eukaryotic microorganisms possess membrane-bound cell 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[2][3]. 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.[4] 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,[5] 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.

Agar plate with colonies
An agar plate streaked with microorganisms

History

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

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).[10]

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.[11]

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.[12][13][14][15]
Van Leeuwenhoek's microscopes by Henry Baker
Van Leeuwenhoek's microscopes by Henry Baker[16]
Mwb in lab
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.[17]

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.[18][1] He is considered a father of microbiology as he pioneered the use of simple single-lensed microscopes of his own design.[18] 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.[19] It has, however, been suggested that a Jesuit priest called Athanasius Kircher was the first to observe microorganisms.[20]

Kircher was among the first to design magic lanterns for projection purposes, so he must have been well acquainted with the properties of lenses.[20] 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.[20]

The birth of bacteriology

Albert Edelfelt - Louis Pasteur - 1885
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.[21] Louis Pasteur and Robert Koch were contemporaries of Cohn, and are often considered to be the father of microbiology[20] and medical microbiology, respectively.[22] 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.[23] One of his students, Adrien Certes, is considered the founder of marine microbiology.[24] Pasteur also designed methods for food preservation (pasteurization) and vaccines against several diseases such as anthrax, fowl cholera and rabies.[1] 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.[1]

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.[1] Beijerinck made two major contributions to microbiology: the discovery of viruses and the development of enrichment culture techniques.[25] 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.[26] He was responsible for the first isolation and description of both nitrifying and nitrogen-fixing bacteria.[1] French-Canadian microbiologist Felix d'Herelle co-discovered bacteriophages in 1917 and was one of the earliest applied microbiologists.[27]

Joseph Lister was the first to use phenol disinfectant on the open wounds of patients.[28]

Branches

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

The branches of microbiology can be classified into pure and 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[29][30] 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, reporter genes for use in other genetic systems and novel molecular biology techniques such as the yeast two-hybrid system.

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.[31] Since some bacteria have the ability to synthesize antibiotics, they are used for medicinal purposes, such as Streptomyces to make aminoglycoside antibiotics.[32]

Cuves de fermentations
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.[33]

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.[34]

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).[35][36] The ways the microbiome influences human and animal health, as well as methods to influence the microbiome are active areas of research.[37]

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.[38]

See also

Professional organizations
Journals

References

  1. ^ a b c d e f Madigan M, Martinko J (editors) (2006). Brock Biology of Microorganisms (13th ed.). Pearson Education. p. 1096. ISBN 978-0-321-73551-5.CS1 maint: Extra text: authors list (link)
  2. ^ Whitman, Whilliam B (2015). Bergey's Manual of Systematics of Archaea and Bacteria. John Wiley and Sons. CiteSeerX 10.1.1.737.4970. doi:10.1002/9781118960608. ISBN 9781118960608.
  3. ^ Pace, Norman R. (2006). "Time for a change". Nature. 441 (7091): 289. doi:10.1038/441289a. ISSN 0028-0836. PMID 16710401.
  4. ^ Nitesh RA, Ludwig W, Schleifer KH (2011). "Phylogenetic identification and in situ detection of individual microbial cells without cultivation". Microbiological Reviews. 59 (1): 143–169. PMC 239358. PMID 7535888.
  5. ^ Rice G (2007-03-27). "Are Viruses Alive?". Retrieved 2007-07-23.
  6. ^ Mahavira is dated 599 BC - 527 BC. See Dundas, Paul; John Hinnels ed. (2002). The Jain. London: Routledge. ISBN 978-0-415-26606-2.CS1 maint: Extra text: authors list (link) p. 24
  7. ^ Dundas, Paul (2002) p. 88
  8. ^ Jaini, Padmanabh (1998). The Jaina Path of Purification. New Delhi: Motilal Banarsidass. p. 109. ISBN 978-81-208-1578-0.
  9. ^ Marcus Terentius Varro. Varro on Agriculture 1, xii Loeb.
  10. ^ "فى الحضارة الإسلامية - ديوان العرب" [Microbiology in Islam]. Diwanalarab.com (in Arabic). Retrieved 14 April 2017.
  11. ^ Fracastoro, Girolamo (1546), De Contagione et Contagiosis Morbis transl. Wilmer Cave Wright (1930). New York: G.P. Putnam's
  12. ^ Dobell, Clifford (1932). Antony van Leeuwenhoek and His "Little Animals": being some account of the father of protozoology and bacteriology and his multifarious discoveries in these disciplines (Dover Publications ed.). New York: Harcourt, Brace and Company.
  13. ^ Corliss, John O (1975). "Three Centuries of Protozoology: A Brief Tribute to its Founding Father, A. van Leeuwenhoek of Delft". The Journal of Protozoology. 22 (1): 3–7. doi:10.1111/j.1550-7408.1975.tb00934.x. PMID 1090737.
  14. ^ Ford, Brian J. (1992). "From Dilettante to Diligent Experimenter: a Reappraisal of Leeuwenhoek as microscopist and investigator". Biology History. 5 (3).
  15. ^ Toledo-Pereyra, Luis H.: The Strange Little Animals of Antony van Leeuwenhoek — Surgical Revolution, in Surgical Revolutions: A Historical and Philosophical View. (World Scientific Publishing, 2008, ISBN 978-9814329620)
  16. ^ Chung, King-thom; Liu, Jong-kang: Pioneers in Microbiology: The Human Side of Science. (World Scientific Publishing, 2017, ISBN 978-9813202948). "We may fairly call Leeuwenhoek “The first microbiologist” because he was the first individual to actually culture, see, and describe a large array of microbial life. He actually measured the multiplication of the bugs. What is more amazing is that he published his discoveries."
  17. ^ Bennett, J.W. (1996). Martinus Willem Beijerinck: Dutch father of industrial microbiology. (SIM News 46(2):69–72)
  18. ^ a b Lane, Nick (6 March 2015). "The Unseen World: Reflections on Leeuwenhoek (1677) 'Concerning Little Animal'". Philos Trans R Soc Lond B Biol Sci. 370 (1666): 20140344. doi:10.1098/rstb.2014.0344. PMC 4360124. PMID 25750239.
  19. ^ Gest H (2005). "The remarkable vision of Robert Hooke (1635-1703): first observer of the microbial world". Perspect. Biol. Med. 48 (2): 266–72. doi:10.1353/pbm.2005.0053. PMID 15834198.
  20. ^ a b c d Wainwright, Milton (2003). An Alternative View of the Early History of Microbiology. Advances in Applied Microbiology. 52. pp. 333–55. doi:10.1016/S0065-2164(03)01013-X. ISBN 978-0-12-002654-8. PMID 12964250.
  21. ^ Drews, G. (1999). "Ferdinand Cohn, among the Founder of Microbiology". ASM News. 65 (8): 547.
  22. ^ Ryan, K.J.; Ray, C.G., eds. (2004). Sherris Medical Microbiology (4th ed.). McGraw Hill. ISBN 978-0-8385-8529-0.
  23. ^ Bordenave, G. (2003). "Louis Pasteur (1822-1895)". Microbes Infect. 5 (6): 553–60. doi:10.1016/S1286-4579(03)00075-3. PMID 12758285.
  24. ^ Adler, Antony; Dücker, Erik (2017-04-05). "When Pasteurian Science Went to Sea: The Birth of Marine Microbiology". Journal of the History of Biology. 51 (1): 107–133. doi:10.1007/s10739-017-9477-8. PMID 28382585.
  25. ^ Johnson, J. (2001) [1998]. "Martinus Willem Beijerinck". APSnet. American Phytopathological Society. Archived from the original on 2010-06-20. Retrieved May 2, 2010. Retrieved from Internet Archive January 12, 2014.
  26. ^ Paustian T, Roberts G (2009). "Beijerinck and Winogradsky Initiate the Field of Environmental Microbiology". Through the Microscope: A Look at All Things Small (3rd ed.). Textbook Consortia. § 1–14.
  27. ^ Keen, E.C. (2012). "Felix d'Herelle and Our Microbial Future". Future Microbiology. 7 (12): 1337–1339. doi:10.2217/fmb.12.115. PMID 23231482.
  28. ^ Lister, Joseph (2010-08-01). "The Classic: On the Antiseptic Principle in the Practice of Surgery". Clinical Orthopaedics and Related Research. 468 (8): 2012–2016. doi:10.1007/s11999-010-1320-x. PMC 2895849. PMID 20361283.
  29. ^ "Branches of Microbiology". General MicroScience. 2017-01-13. Retrieved 2017-12-10.
  30. ^ Brock Biology of Microorganisms (14th ed.). ISBN 978-0321897398.
  31. ^ Burkovski A (editor). (2008). Corynebacteria: Genomics and Molecular Biology. Caister Academic Press. ISBN 978-1-904455-30-1. Retrieved 2016-03-25.
  32. ^ Fourmy, Dominique; Recht, Michael I.; Blanchard, Scott C; Puglisi, Joseph D. (1996). "Structure of the A site of Escherichia coli 16S ribosomal RNA complexed with an Aminoglycoside Antibiotic" (PDF). Science. 274 (5291): 1367–1371. Bibcode:1996Sci...274.1367F. doi:10.1126/science.274.5291.1367. PMID 8910275. Retrieved 2016-04-05.
  33. ^ Rehm BHA (editor). (2008). Microbial Production of Biopolymers and Polymer Precursors: Applications and Perspectives. Caister Academic Press. ISBN 978-1-904455-36-3. Retrieved 2016-03-25.
  34. ^ Diaz E (editor). (2008). Microbial Biodegradation: Genomics and Molecular Biology (1st ed.). Caister Academic Press. ISBN 978-1-904455-17-2. Retrieved 2016-03-25.
  35. ^ MacFarlane, GT; Cummings, JH (1999). "Probiotics and prebiotics: Can regulating the activities of intestinal bacteria benefit health?". BMJ: British Medical Journal. 318 (7189): 999–1003. doi:10.1136/bmj.318.7189.999. PMC 1115424. PMID 10195977.
  36. ^ Tannock GW, ed. (2005). Probiotics and Prebiotics: Scientific Aspects. Caister Academic Press. ISBN 978-1-904455-01-1. Retrieved 2016-03-25.
  37. ^ Wenner, Melinda (30 November 2007). "Humans Carry More Bacterial Cells than Human Ones". Scientific American. Retrieved 14 April 2017.
  38. ^ Mengesha; et al. (2009). "Clostridia in Anti-tumor Therapy". Clostridia: Molecular Biology in the Post-genomic Era. Caister Academic Press. ISBN 978-1-904455-38-7.

External links

Aerobic organism

An aerobic organism or aerobe is an organism that can survive and grow in an oxygenated environment. In contrast, an anaerobic organism (anaerobe) is any organism that does not require oxygen for growth. Some anaerobes react negatively or even die if oxygen is present.

American Society for Microbiology

The American Society for Microbiology (ASM), originally the Society of American Bacteriologists, is a professional organization for scientists who study viruses, bacteria, fungi, algae, and protozoa as well as other aspects of microbiology. Founded in 1899, ASM has grown into the largest life science professional organization in the world. The Society publishes a variety of scientific journals, textbooks, and other educational materials related to microbiology and infectious diseases. Additionally, ASM organizes several large annual meetings, as well as workshops and professional development opportunities for its members.

Anaerobic organism

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.)

An anaerobic organism may be unicellular (e.g. protozoans, bacteria) or multicellular. For practical purposes, there are three categories of anaerobe: obligate anaerobes, which are harmed by the presence of oxygen; aerotolerant organisms, which cannot use oxygen for growth but tolerate its presence; and facultative anaerobes, which can grow without oxygen but use oxygen if it is present.

Archaea

Archaea ( (listen) or ar-KEE-ə or ar-KAY-ə) constitute a domain of single-celled microorganisms. These microbes (archaea; singular archaeon) are prokaryotes, meaning they have no cell nucleus.

Archaea were initially classified as bacteria, receiving the name archaebacteria (in the Archaebacteria kingdom), but this classification is outdated.Archaeal cells have unique properties separating them from the other two domains of life, Bacteria and Eukarya. Archaea are further divided into multiple recognized phyla. Classification is difficult because most have not been isolated in the laboratory and were only detected by analysis of their nucleic acids in samples from their environment.

Archaea and bacteria are generally similar in size and shape, although a few archaea have shapes quite unlike that of bacteria, such as the flat and square-shaped cells of Haloquadratum walsbyi. Despite this morphological similarity to bacteria, archaea possess genes and several metabolic pathways that are more closely related to those of eukaryotes, notably for the enzymes involved in transcription and translation. Other aspects of archaeal biochemistry are unique, such as their reliance on ether lipids in their cell membranes, including archaeols. Archaea use more energy sources than eukaryotes: these range from organic compounds, such as sugars, to ammonia, metal ions or even hydrogen gas. Salt-tolerant archaea (the Haloarchaea) use sunlight as an energy source, and other species of archaea fix carbon, but unlike plants and cyanobacteria, no known species of archaea does both. Archaea reproduce asexually by binary fission, fragmentation, or budding; unlike bacteria and eukaryotes, no known species forms spores.

The first observed archaea were living in harsh environments such as hot springs and salt lakes with no other organisms, but improved detection tools led to the discovery of archaea in almost every habitat, including soils, oceans, and marshlands. They are also part of the human microbiota in the gut, mouth, and skin. Archaea are particularly numerous in the oceans, and the archaea in plankton may be one of the most abundant groups of organisms on the planet. Archaea are a major part of Earth's life and may play roles in the carbon cycle and the nitrogen cycle. No clear examples of archaeal pathogens or parasites are known, but they are often mutualists or commensals. One example is the methane producing strains that inhabit human and ruminant guts, where their vast numbers aid digestion. Methanogens are also used in biogas production and sewage treatment, and biotechnology exploits enzymes from extremophile archaea that can endure high temperatures and organic solvents.

Asepsis

Asepsis is the state of being free from disease-causing micro-organisms (such as pathogenic bacteria, viruses, pathogenic fungi, and parasites). The term often refers to those practices used to promote or induce asepsis in an operative field of surgery or medicine to prevent infection.

The goal of asepsis is to eliminate infection, not to achieve sterility. Ideally, a surgical field is sterile, meaning it is free of all biological contaminants (e.g. fungi, bacteria, viruses), not just those that can cause disease, putrefaction, or fermentation. At present, there is no method to safely eliminate all of a patient's contaminants without causing significant tissue damage.

Bacteria

Bacteria ( (listen); common noun bacteria, singular bacterium) are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. 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 portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants and animals. Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as 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. Data reported by researchers in October 2012 and published in March 2013 suggested that bacteria thrive in the Mariana Trench, which, with a depth of up to 11 kilometres, is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, "You can find microbes everywhere—they're extremely adaptable to conditions, and survive wherever they are."The famous notion that bacterial cells in the human body outnumber human cells by a factor of 10:1 has been debunked. There are approximately 39 trillion bacterial cells in the human microbiota as personified by a "reference" 70 kg male 170 cm tall, whereas there are 30 trillion human cells in the body. This means that although they do have the upper hand in actual numbers, it is only by 30%, and not 900%.The largest number exist in the gut flora, and a large number on the skin. The vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial, particularly in the gut flora. However several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, and bubonic plague. The most common fatal bacterial diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year, mostly in sub-Saharan Africa. In developed countries, antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. In industry, bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector, as well as in biotechnology, and the manufacture of antibiotics and other chemicals.Once regarded as plants constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and rarely harbour membrane-bound organelles. Although the term bacteria traditionally included all prokaryotes, the scientific classification changed after the discovery in the 1990s that prokaryotes consist of two very different groups of organisms that evolved from an ancient common ancestor. These evolutionary domains are called Bacteria and Archaea.

Bacteriology

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.

Food microbiology

Food microbiology is the study of the microorganisms that inhibit, create, or contaminate food, including the study of microorganisms causing food spoilage, 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, and those with other useful roles such as producing probiotics.

Gram-positive bacteria

Gram-positive bacteria are bacteria that give a positive result in the Gram stain test, which is traditionally used to quickly classify bacteria into two broad categories according to their cell wall.

Gram-positive bacteria take up the crystal violet stain used in the test, and then appear to be purple-coloured when seen through a microscope. This is because the thick peptidoglycan layer in the bacterial cell wall retains the stain after it is washed away from the rest of the sample, in the decolorization stage of the test.

Gram-negative bacteria cannot retain the violet stain after the decolorization step; alcohol used in this stage degrades the outer membrane of gram-negative cells, making the cell wall more porous and incapable of retaining the crystal violet stain. Their peptidoglycan layer is much thinner and sandwiched between an inner cell membrane and a bacterial outer membrane, causing them to take up the counterstain (safranin or fuchsine) and appear red or pink.

Despite their thicker peptidoglycan layer, gram-positive bacteria are more receptive to certain cell wall targeting antibiotics than gram-negative bacteria, due to the absence of the outer membrane.

Halophile

Halophiles are organisms that thrive in high salt concentrations. They are a type of extremophile organism. The name comes from the Greek word for "salt-loving". While most halophiles are classified into the Archaea domain, there are also bacterial halophiles and some eukaryota, such as the alga Dunaliella salina or fungus Wallemia ichthyophaga. Some well-known species give off a red color from carotenoid compounds, notably bacteriorhodopsin. Halophiles can be found anywhere with a concentration of salt five times greater than the salt concentration of the ocean, such as the Great Salt Lake in Utah, Owens Lake in California, the Dead Sea, and in evaporation ponds.

Medical microbiology

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.

A medical microbiologist studies the characteristics of pathogens, their modes of transmission, mechanisms of infection and growth. Using this information, a treatment can be devised. Medical microbiologists often serve as consultants for physicians, providing identification of pathogens and suggesting treatment options.

Other tasks may include the identification of potential health risks to the community or monitoring the evolution of potentially virulent or resistant strains of microbes, educating the community and assisting in the design of health practices. They may also assist in preventing or controlling epidemics and outbreaks of disease.

Not all medical microbiologists study microbial pathology; some study common, non-pathogenic species to determine whether their properties can be used to develop antibiotics or other treatment methods.

Epidemiology, the study of the patterns, causes, and effects of health and disease conditions in populations, is an important part of medical microbiology, although the clinical aspect of the field primarily focuses on the presence and growth of microbial infections in individuals, their effects on the human body, and the methods of treating those infections. In this respect the entire field, as an applied science, can be conceptually subdivided into academic and clinical subspecialties, although in reality there is a fluid continuum between public health microbiology and clinical microbiology, just as the state of the art in clinical laboratories depends on continual improvements in academic medicine and research laboratories.

Metabolite

A metabolite is the intermediate end product of metabolism. The term metabolite is usually restricted to small molecules. Metabolites have various functions, including fuel, structure, signaling, stimulatory and inhibitory effects on enzymes, catalytic activity of their own (usually as a cofactor to an enzyme), defense, and interactions with other organisms (e.g. pigments, odorants, and pheromones). A primary metabolite is directly involved in normal "growth", development, and reproduction. Ethylene is an example of a primary metabolite produced in large-scale by industrial microbiology. A secondary metabolite is not directly involved in those processes, but usually has an important ecological function. Examples include antibiotics and pigments such as resins and terpenes etc. Some antibiotics use primary metabolites as precursors, such as actinomycin which is created from the primary metabolite, tryptophan. Some sugars are metabolites, such as fructose or glucose, which are both present in the metabolic pathways.

Examples of primary metabolites produced by industrial microbiology:

The metabolome forms a large network of metabolic reactions, where outputs from one enzymatic chemical reaction are inputs to other chemical reactions.

Metabolites from chemical compounds, whether inherent or pharmaceutical, are formed as part of the natural biochemical process of degrading and eliminating the compounds. The rate of degradation of a compound is an important determinant of the duration and intensity of its action. Profiling metabolites of pharmaceutical compounds, drug metabolism, is an important part of drug discovery, leading to an understanding of any undesirable side effects.

Microbial ecology

Microbial ecology (or environmental microbiology) 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.Microorganisms, by their omnipresence, impact the entire biosphere. Microbial life plays a primary role in regulating biogeochemical systems in virtually all of our planet's environments, including some of the most extreme, from frozen environments and acidic lakes, to hydrothermal vents at the bottom of deepest oceans, and some of the most familiar, such as the human small intestine. As a consequence of the quantitative magnitude of microbial life (Whitman and coworkers calculated 5.0×1030 cells, eight orders of magnitude greater than the number of stars in the observable universe) microbes, by virtue of their biomass alone, constitute a significant carbon sink. Aside from carbon fixation, microorganisms' key collective metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) control global biogeochemical cycling. The immensity of microorganisms' production is such that, even in the total absence of eukaryotic life, these processes would likely continue unchanged.

Microbiological culture

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 extensively as a research tool in molecular biology.

Microbial cultures are used to determine the type of organism, its abundance in the sample being tested, or both. It is one of the primary diagnostic methods of microbiology and used as a tool to determine the cause of infectious disease by letting the agent multiply in a predetermined medium. For example, a throat culture is taken by scraping the lining of tissue in the back of the throat and blotting the sample into a medium to be able to screen for harmful microorganisms, such as Streptococcus pyogenes, the causative agent of strep throat. Furthermore, the term culture is more generally used informally to refer to "selectively growing" a specific kind of microorganism in the lab.

It is often essential to isolate a pure culture of microorganisms. A pure (or axenic) culture is a population of cells or multicellular organisms growing in the absence of other species or types. A pure culture may originate from a single cell or single organism, in which case the cells are genetic clones of one another. For the purpose of gelling the microbial culture, the medium of agarose gel (agar) is used. Agar is a gelatinous substance derived from seaweed. A cheap substitute for agar is guar gum, which can be used for the isolation and maintenance of thermophiles.

Microbiologist

A microbiologist (from Greek μῑκρος) is a scientist who studies microscopic life forms and processes. This includes study of the growth, interactions and characteristics of microscopic organisms such as bacteria, algae, fungi, and some types of parasites and their vectors. Most microbiologists work in offices and/or research facilities, both in private biotechnology companies as well as in academia. Most microbiologists specialize in a given topic within microbiology such as bacteriology, parasitology, virology, or immunology.

Microbiota

A microbiota is an "ecological community of commensal, symbiotic and pathogenic microorganisms" found in and on all multicellular organisms studied to date from plants to animals. A microbiota includes bacteria, archaea, protists, fungi and viruses. Microbiota have been found to be crucial for immunologic, hormonal and metabolic homeostasis of their host.

The synonymous term microbiome describes either the collective genomes of the microorganisms that reside in an environmental niche or the microorganisms themselves.The microbiome and host emerged during evolution as a synergistic unit from epigenetics and genetic characteristics, sometimes collectively referred to as a holobiont.

Microorganism

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

The possible existence of unseen microbial life was suspected from ancient times, such as in Jain scriptures from 6th century BC India and the 1st century BC book On Agriculture by Marcus Terentius Varro. Microbiology, the scientific study of microorganisms, began with their observation under the microscope in the 1670s by Antonie van Leeuwenhoek. In the 1850s, Louis Pasteur found that microorganisms caused food spoilage, debunking the theory of spontaneous generation. In the 1880s, Robert Koch discovered that microorganisms caused the diseases tuberculosis, cholera and anthrax.

Microorganisms include all unicellular organisms and so are extremely diverse. Of the three domains of life identified by Carl Woese, all of the Archaea and Bacteria are microorganisms. These were previously grouped together in the two domain system as Prokaryotes, the other being the eukaryotes. The third domain Eukaryota includes all multicellular organisms and many unicellular protists and protozoans. Some protists are related to animals and some to green plants. Many of the multicellular organisms are microscopic, namely micro-animals, some fungi and some algae, but these are not discussed here.

They live in almost every habitat from the poles to the equator, deserts, geysers, rocks and the deep sea. Some are adapted to extremes such as very hot or very cold conditions, others to high pressure and a few such as Deinococcus radiodurans to high radiation environments. Microorganisms also make up the microbiota found in and on all multicellular organisms. A December 2017 report stated that 3.45-billion-year-old Australian rocks once contained microorganisms, the earliest direct evidence of life on Earth.Microbes are important in human culture and health in many ways, serving to ferment foods, treat sewage, produce fuel, enzymes and other bioactive compounds. They are essential tools in biology as model organisms and have been put to use in biological warfare and bioterrorism. They are a vital component of fertile soils. In the human body microorganisms make up the human microbiota including the essential gut flora. They are the pathogens responsible for many infectious diseases and as such are the target of hygiene measures.

Molecular biology

Molecular biology is a branch of biology that concerns the molecular basis of biological activity between biomolecules in the various systems of a cell, including the interactions between DNA, RNA, proteins and their biosynthesis, as well as the regulation of these interactions. Writing in Nature in 1961, William Astbury described molecular biology as:

...not so much a technique as an approach, an approach from the viewpoint of the so-called basic sciences with the leading idea of searching below the large-scale manifestations of classical biology for the corresponding molecular plan. It is concerned particularly with the forms of biological molecules and [...] is predominantly three-dimensional and structural – which does not mean, however, that it is merely a refinement of morphology. It must at the same time inquire into genesis and function.

Sterilization (microbiology)

Sterilization (or sterilization or sterilization) refers to any process that eliminates, removes, kills, or deactivates all forms of life and other biological agents (such as fungi, bacteria, viruses, spore forms, prions, unicellular eukaryotic organisms such as Plasmodium, etc.) present in a specified region, such as a surface, a volume of fluid, medication, or in a compound such as biological culture media. Sterilization can be achieved through various means, including: heat, chemicals, irradiation, high pressure, and filtration. Sterilization is distinct from disinfection, sanitization, and pasteurization, in that sterilization kills, deactivates, or eliminates all forms of life and other biological agents which are present.

Branches of life science and biology
Microbiology: Bacteria
Medical
microbiology
Biochemistry
and ecology
Shape
Structure
Taxonomy
Microbiology: Fungus
Branch
Structure
Growth patterns
List
Microbiology: Protistology: Protists
Former
classifications
Morphology
Ecology and
physiology
Microbiology: Virus
Components
Viral life cycle
Genetics
By host
Other
Groups
Microbiology
Ecology
Techniques
Marine
Human related
Other
Microscopic discoveries 1
General topics
Related people
Recognitions

This page is based on a Wikipedia article written by authors (here).
Text is available under the CC BY-SA 3.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.