Microbiology in the context of Eubacteria

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 the air, 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.

Like all animals, humans carry vast numbers (approximately 10 to 10) of bacteria. Most are in the gut, though there are many on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, and many are beneficial, particularly the ones in the gut. However, several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, tuberculosis, tetanus and bubonic plague. The most common fatal bacterial diseases are respiratory infections. Antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. 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 (biomining, bioleaching), as well as in biotechnology, and the manufacture of antibiotics and other chemicals.

Delft (Dutch pronunciation: [ˈdɛl(ə)ft] ) is a city and municipality in the province of South Holland, Netherlands. It is located between Rotterdam, to the southeast, and The Hague, to the northwest. Together with them, it is a part of both the Rotterdam–The Hague metropolitan area and the Randstad.

Delft is a popular tourist destination in the Netherlands, famous for its historical connections with the reigning House of Orange-Nassau, for its blue pottery, for being home to the painter Jan Vermeer, and for hosting Delft University of Technology (TU Delft). Historically, Delft played a highly influential role in the Dutch Golden Age. In terms of science and technology, thanks to the pioneering contributions of Antonie van Leeuwenhoek and Martinus Beijerinck, Delft can be considered to be the birthplace of microbiology.

A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea. Viruses are found in almost every ecosystem on Earth and are the most numerous type of biological entity. Since Dmitri Ivanovsky's 1892 article describing a non-bacterial pathogen infecting tobacco plants and the discovery of the tobacco mosaic virus by Martinus Beijerinck in 1898, more than 16,000 of the millions of virus species have been described in detail. The study of viruses is known as virology, a subspeciality of microbiology.

When infected, a host cell is often forced to rapidly produce thousands of copies of the original virus. When not inside an infected cell or in the process of infecting a cell, viruses exist in the form of independent viral particles, or virions, consisting of (i) genetic material, i.e., long molecules of DNA or RNA that encode the structure of the proteins by which the virus acts; (ii) a protein coat, the capsid, which surrounds and protects the genetic material; and in some cases (iii) an outside envelope of lipids. The shapes of these virus particles range from simple helical and icosahedral forms to more complex structures. Most virus species have virions too small to be seen with an optical microscope and are one-hundredth the size of most 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 non-microorganism 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.

Virology is the scientific study of biological viruses. It is a subfield of microbiology that focuses on their detection, structure, classification and evolution, their methods of infection and exploitation of host cells for reproduction, their interaction with host organism physiology and immunity, the diseases they cause, the techniques to isolate and culture them, and their use in research and therapy.

The identification of the causative agent of tobacco mosaic disease (TMV) as a novel pathogen by Martinus Beijerinck (1898) is now acknowledged as being the official beginning of the field of virology as a discipline distinct from bacteriology. He realized the source was neither a bacterial nor a fungal infection, but something completely different. Beijerinck used the word "virus" to describe the mysterious agent in his 'contagium vivum fluidum' ('contagious living fluid'). Rosalind Franklin proposed the full structure of the tobacco mosaic virus in 1955.

Semisynthesis, or partial chemical synthesis, is a type of chemical synthesis that uses chemical compounds isolated from natural sources (such as microbial cell cultures or plant material) as the starting materials to produce novel compounds with distinct chemical and medicinal properties. The novel compounds generally have a high molecular weight or a complex molecular structure, more so than those produced by total synthesis from simple starting materials. Semisynthesis is a means of preparing many medicines more cheaply than by total synthesis since fewer chemical steps are necessary.

Drugs derived from natural sources are commonly produced either by isolation from their natural source or, as described here, through semisynthesis of an isolated agent. From the perspective of chemical synthesis, living organisms act as highly efficient chemical factories, capable of producing structurally complex compounds through biosynthesis. In contrast, engineered chemical synthesis, although powerful, tends to be simpler and less chemically diverse than the complex biosynthetic pathways essential to life.

Antonie Philips van Leeuwenhoek FRS (/ˈɑːntəni vɑːn ˈleɪvənhuːk, -hʊk/ AHN-tə-nee vahn LAY-vən-hook, -⁠huuk; Dutch: [ˈɑntoːni vɑn ˈleːu.ə(n)ˌɦuk] ; 24 October 1632 – 26 August 1723) was a Dutch microbiologist and microscopist in the Golden Age of Dutch art, 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.

Raised in Delft, Dutch Republic, Van Leeuwenhoek worked as a draper in his youth and founded his own shop in 1654. He became well-recognized in municipal politics and developed an interest in lensmaking. In the 1670s, he started to explore microbial life with his microscope.

Louis Pasteur ForMemRS (/ˈluːi pæˈstɜːr/, French: [lwi pastœʁ] ; 27 December 1822 – 28 September 1895) was a French chemist, pharmacist, and microbiologist renowned for his discoveries of the principles of vaccination, microbial fermentation, and pasteurization, the last of which was named after him. His research in chemistry led to remarkable breakthroughs in the understanding of the causes and preventions of diseases, which laid down the foundations of hygiene, public health and much of modern medicine. Pasteur's works are credited with saving millions of lives through the developments of vaccines for rabies and anthrax. He is regarded as one of the founders of modern bacteriology and has been honored as the "father of bacteriology" and the "father of microbiology" (together with Robert Koch; the latter epithet also attributed to Antonie van Leeuwenhoek).

Pasteur was responsible for disproving the doctrine of spontaneous generation. Under the auspices of the French Academy of Sciences, his experiment demonstrated that in sterilized and sealed flasks, nothing ever developed; conversely, in sterilized but open flasks, microorganisms could grow. For this experiment, the academy awarded him the Alhumbert Prize carrying 2,500 francs in 1862.

In biology, a pathogen (Greek: πάθος, pathos "suffering", "passion" and -γενής, -genēs "producer of"), in the oldest and broadest sense, is any organism or agent that can produce disease. A pathogen may also be referred to as an infectious agent, or simply a germ.

The term pathogen came into use in the 1880s. Typically, the term pathogen is used to describe an infectious microorganism or agent, such as a virus, bacterium, protozoan, prion, viroid, or fungus. Small animals, such as helminths and insects, can also cause or transmit disease. However, these animals are usually referred to as parasites rather than pathogens. The scientific study of microscopic organisms, including microscopic pathogenic organisms, is called microbiology, while parasitology refers to the scientific study of parasites and the organisms that host them.

In biology, a strain is a genetic variant, a subtype or a culture within a biological species. Strains are often seen as inherently artificial concepts, characterized by a specific intent for genetic isolation. This is most easily observed in microbiology where strains are derived from a single cell colony and are typically quarantined by the physical constraints of a Petri dish. Strains are also commonly referred to within virology, botany, and with rodents used in experimental studies.

A heterotroph (/ˈhɛtərəˌtroʊf, -ˌtrɒf/; from Ancient Greek ἕτερος (héteros), meaning "other", and τροφή (trophḗ), meaning "nourishment") is an organism that cannot produce its own food, instead taking nutrition from other sources of organic carbon, mainly matter from other organisms. In the food chain, heterotrophs are primary, secondary and tertiary consumers, but not producers. Living organisms that are heterotrophic include most animals, all fungi, some bacteria and protists, and many parasitic plants. The term heterotroph arose in microbiology in 1946 as part of a classification of microorganisms based on their type of nutrition. The term is now used in many fields, such as ecology, in describing the food chain. Heterotrophs occupy the second and third trophic levels of the food chain while autotrophs occupy the first trophic level.

Heterotrophs may be subdivided according to their energy source. If the heterotroph uses chemical energy, it is a chemoheterotroph (e.g., humans and mushrooms). If it uses light for energy, then it is a photoheterotroph (e.g., haloquadratum walsbyi and green non-sulfur bacteria).

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. The academic qualification as a clinical/Medical Microbiologist in a hospital or medical research centre generally requires a Bachelors degree while in some countries a Masters in Microbiology along with Ph.D. in any of the life-sciences (Biochem, Micro, Biotech, Genetics, etc.). Medical microbiologists often serve as consultants for physicians, providing identification of pathogens and suggesting treatment options. Using this information, a treatment can be devised.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.

Environmental engineering is a professional engineering discipline related to environmental science. It encompasses broad scientific topics like chemistry, biology, ecology, geology, hydraulics, hydrology, microbiology, and mathematics to create solutions that will protect and also improve the health of living organisms and improve the quality of the environment. Environmental engineering is a sub-discipline of civil engineering and chemical engineering. While on the part of civil engineering, the Environmental Engineering is focused mainly on Sanitary Engineering.

Environmental engineering applies scientific and engineering principles to improve and maintain the environment to protect human health, protect nature's beneficial ecosystems, and improve environmental-related enhancement of the quality of human life.Environmental engineers devise solutions for wastewater management, water and air pollution control, recycling, waste disposal, and public health. They design municipal water supply and industrial wastewater treatment systems, and design plans to prevent waterborne diseases and improve sanitation in urban, rural and recreational areas. They evaluate hazardous-waste management systems to evaluate the severity of such hazards, advise on treatment and containment, and develop regulations to prevent mishaps. They implement environmental engineering law, as in assessing the environmental impact of proposed construction projects.

Alexandre Émile John Yersin (22 September 1863 – 1 March 1943) was a Swiss-French physician and bacteriologist. He is remembered for his work as a pioneer in microbiology and immunology. Yersin is the co-discoverer of both the Diphtheria and Tetanus toxins (1890 with Émile Roux) and of the bacillus responsible for the bubonic plague or pest (1894, with Kitasato Shibasaburō). The bacteria was later named in his honour: Yersinia pestis. Yersin also demonstrated for the first time that the same bacillus was present in the rodent as well as in the human disease, thus underlining the possible means of transmission.