1.
Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
2.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, 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, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only 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, 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 bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was 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—theyre extremely adaptable to conditions, 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 diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as 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 these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
3.
Biosafety level
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A biosafety level is a set of biocontainment precautions required to isolate dangerous biological agents in an enclosed laboratory facility. The levels of containment range from the lowest biosafety level 1 to the highest at level 4, in the United States, the Centers for Disease Control and Prevention have specified these levels. In the European Union, the same biosafety levels are defined in a directive, facilities with these designations are also sometimes given as P1 through P4, as in the term P3 laboratory. At the lowest level of biosafety, precautions may consist of regular hand-washing, kaempf was tired of his MP duties at Detrick and was able to transfer to the sheet metal department working with the contractor, the H. K. Ferguson Co. On 18 April 1955, fourteen representatives met at Camp Detrick in Frederick, because of the potential implication of the work conducted at biological warfare laboratories, the conferences were restricted to top level security clearances. Beginning in 1957, these conferences were planned to include non-classified sessions as well as classified sessions to enable sharing of biological safety information. It was not until 1964, however, that conferences were held in a government installation not associated with a biological warfare program, over the next ten years, the biological safety conferences grew to include representatives from all federal agencies that sponsored or conducted research with pathogenic microorganisms. By 1966 it began to include representatives from universities, private laboratories, hospitals, throughout the 1970s, participation in the conferences continued to expand and by 1983 discussions began regarding the creation of a formal organization. The American Biological Safety Association was officially established in 1984 and a constitution, as of 2008, ABSA includes some 1,600 members in its professional association. Biosafety level 1 is suitable for work with well-characterized agents which do not cause disease in healthy humans, in general, these agents should pose minimal potential hazard to laboratory personnel and the environment. At this level, precautions are limited relative to other levels, Laboratory personnel must wash their hands upon entering and exiting the lab. Research with these agents may be performed on standard open laboratory benches without the use of special containment equipment, however, eating and drinking are generally prohibited in laboratory areas. Potentially infectious material must be decontaminated before disposal, either by adding an appropriate disinfectant, personal protective equipment is only required for circumstances where personnel might be exposed to hazardous material. BSL-1 laboratories must have a door which can be locked to limit access to the lab, due to the relative ease and safety of maintaining a BSL-1 laboratory, these are the types of laboratories generally used as teaching spaces for high schools and colleges. At this level, all used at Biosafety Level 1 are followed. BSL-2 differs from BSL-1 in that, Laboratory personnel have specific training in handling pathogenic agents and are directed by scientists with advanced training, access to the laboratory is limited when work is being conducted. Extreme precautions are taken with contaminated sharp items, certain procedures in which infectious aerosols or splashes may be created are conducted in biological safety cabinets or other physical containment equipment. Biosafety level 2 is suitable for work involving agents of moderate potential hazard to personnel and this includes various microbes that cause mild disease to humans, or are difficult to contract via aerosol in a lab setting
4.
Eukaryote
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A eukaryote is any organism whose cells contain a nucleus and other organelles enclosed within membranes. Eukaryotes belong to the taxon Eukarya or Eukaryota, the presence of a nucleus gives eukaryotes their name, which comes from the Greek εὖ and κάρυον. Eukaryotic cells also contain other membrane-bound organelles such as mitochondria and the Golgi apparatus, in addition, plants and algae contain chloroplasts. Eukaryotic organisms may be unicellular or multicellular, only eukaryotes form multicellular organisms consisting of many kinds of tissue made up of different cell types. Eukaryotes can reproduce asexually through mitosis and sexually through meiosis and gamete fusion. In mitosis, one cell divides to produce two identical cells. In meiosis, DNA replication is followed by two rounds of division to produce four daughter cells each with half the number of chromosomes as the original parent cell. These act as sex cells resulting from genetic recombination during meiosis, the domain Eukaryota appears to be monophyletic, and so makes up one of the three domains of life. The two other domains, Bacteria and Archaea, are prokaryotes and have none of the above features, eukaryotes represent a tiny minority of all living things. However, due to their larger size, eukaryotes collective worldwide biomass is estimated at about equal to that of prokaryotes. Eukaryotes first developed approximately 1. 6–2.1 billion years ago, in 1905 and 1910, the Russian biologist Konstantin Mereschkowsky argued three things about the origin of nucleated cells. Firstly, plastids were reduced cyanobacteria in a symbiosis with a non-photosynthetic host, secondly, the host had earlier in evolution formed by symbiosis between an amoeba-like host and a bacteria-like cell that formed the nucleus. Thirdly, plants inherited photosynthesis from cyanobacteria, the split between the prokaryotes and eukaryotes was introduced in the 1960s. The concept of the eukaryote has been attributed to the French biologist Edouard Chatton, the terms prokaryote and eukaryote were more definitively reintroduced by the Canadian microbiologist Roger Stanier and the Dutch-American microbiologist C. B. van Niel in 1962. In his 1938 work Titres et Travaux Scientifiques, Chatton had proposed the two terms, calling the bacteria prokaryotes and organisms with nuclei in their cells eukaryotes. However he mentioned this in one paragraph, and the idea was effectively ignored until Chattons statement was rediscovered by Stanier. In 1967, Lynn Margulis provided microbiological evidence for endosymbiosis as the origin of chloroplasts and mitochondria in cells in her paper. In the 1970s, Carl Woese explored microbial phylogenetics, studying variations in 16S ribosomal RNA and this helped to uncover the origin of the eukaryotes and the symbiogenesis of two important eukaryote organelles, mitochondria and chloroplasts
5.
Gram stain
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Gram staining or Gram stain, also called Grams method, is a method of staining used to differentiate bacterial species into two large groups. The name comes from the Danish bacteriologist Hans Christian Gram, who developed the technique, Gram staining differentiates bacteria by the chemical and physical properties of their cell walls by detecting peptidoglycan, which is present in the cell wall of Gram-positive bacteria. Both Gram-positive bacteria and Gram-negative bacteria pick up the counterstain, the counterstain, however, is unseen on Gram-positive bacteria because of the darker crystal violet stain. The Gram stain is almost always the first step in the identification of a bacterial organism. While Gram staining is a diagnostic tool in both clinical and research settings, not all bacteria can be definitively classified by this technique. This gives rise to gram-variable and gram-indeterminate groups, the method is named after its inventor, the Danish scientist Hans Christian Gram, who developed the technique while working with Carl Friedländer in the morgue of the city hospital in Berlin in 1884. Gram devised his technique not for the purpose of distinguishing one type of bacterium from another and he published his method in 1884, and included in his short report the observation that the typhus bacillus did not retain the stain. Gram staining is a laboratory technique used to differentiate bacterial species into two large groups based on the physical properties of their cell walls. Gram staining is not used to classify archaea, formerly archaeabacteria, the Gram stain is not an infallible tool for diagnosis, identification, or phylogeny, and it is of extremely limited use in environmental microbiology. It is used mainly to make a preliminary morphologic identification or to establish that there are significant numbers of bacteria in a clinical specimen. It cannot identify bacteria to the level, and for most medical conditions. In clinical microbiology laboratories, it is used in combination with other traditional, some organisms are gram-variable, some are not stained with either dye used in the Gram technique and are not seen. Gram staining has been suggested to be as effective a tool as PCR in one primary research report regarding gonococcal urethritis. Gram stains are performed on body fluid or biopsy when infection is suspected, there are four basic steps of the Gram stain, Applying a primary stain to a heat-fixed smear of a bacterial culture. Carbol fuchsin is sometimes substituted for safranin since it more intensely stains anaerobic bacteria, crystal violet dissociates in aqueous solutions into CV+ and chloride ions. These ions penetrate through the wall and cell membrane of both gram-positive and gram-negative cells. The CV+ ion interacts with negatively charged components of bacterial cells, iodide interacts with CV+ and forms large complexes of crystal violet and iodine within the inner and outer layers of the cell. Iodine is often referred to as a mordant, but is an agent that prevents the removal of the CV–I complex and, therefore
6.
Beta-lactam
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A beta-lactam ring is a four-membered lactam. It is named as such because the atom is attached to the β-carbon atom relative to the carbonyl. The simplest β-lactam possible is 2-azetidinone, nearly all of these antibiotics work by inhibiting bacterial cell wall biosynthesis. This has an effect on bacteria. Bacteria do, however, contain within their populations, in smaller quantities and they do this by expressing one of many β-lactamase genes. More than 1,800 different β-lactamase enzymes have been documented in species of bacteria. These enzymes vary widely in their structure and catalytic efficiencies. When bacterial populations have these resistant subgroups, treatment with β-lactam can result in the resistant strain becoming more prevalent and this strain is further increased by fusion to a second ring, as found in most β-lactam antibiotics. This trend is due to the character of the β-lactam being reduced by the aplanarity of the system. The nitrogen atom of an amide is sp2-hybridized due to resonance. As a pyramidal bond geometry is forced upon the nitrogen atom by the strain, the resonance of the amide bond is reduced. Nobel laureate Robert Burns Woodward described a parameter h as a measure of the height of the trigonal pyramid defined by the nitrogen, H corresponds to the strength of the β-lactam bond with lower numbers being stronger and less reactive. Monobactams have h values between 0.05 and 0.10 angstroms, cephems have h values in of 0. 20–0.25 Å. Penams have values in the range 0. 40–0.50 Å, while carbapenems and clavams have values of 0. 50–0.60 Å, a new study has suggested that β-lactams can undergo ring-opening polymerization to form amide bonds, to become nylon-3 polymers. The backbones of these polymers are identical to peptides, which offer them biofunctionality and these nylon-3 polymers can either mimic host defense peptides or act as signals to stimulate 3T3 stem cell function. Antiproliferative agents that target tubulin with β-lactams in their structure have also been reported
7.
Gram-negative bacteria
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Gram-negative bacteria are a group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are spread worldwide, in all environments that support life. Several classes of antibiotics target gram-negative bacteria specifically, including aminoglycosides, historically, the kingdom Monera was divided into four divisions based on Gram staining, Firmacutes, Gracillicutes, Mollicutes and Mendocutes. Since 1987, the monophyly of the bacteria has been disproven with molecular studies. However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon, bacteria are traditionally divided into the two groups, gram-positive and gram-negative, based on their Gram stain retention. These groups are thought of as lineages, with gram-negative bacteria more closely related to one another than to gram-positive bacteria. While this is true, the classification system breaks down in some cases. A given bacterias Gram stain result, bacterial membrane organization, as such, the Gram stain cannot be reliably used to assess familial relationships of bacteria. That said, Gram staining does often give information about the composition of the cell membrane. Of these two distinct groups of prokaryotic organisms, monoderm prokaryotes are indicated to be ancestral. In addition, a number of taxa that are either part of the phylum Firmicutes or branches in its proximity are also found to possess a diderm cell structure. Other notable groups of bacteria include the cyanobacteria, spirochaetes, green sulfur. Medically relevant gram-negative cocci include the four types that cause a sexually transmitted disease, a meningitis, medically relevant gram-negative bacilli include a multitude of species. Some of them cause primarily respiratory problems, primarily urinary problems, transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. One of the unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this comprises a complex lipopolysaccharide whose lipid portion acts as an endotoxin
8.
Rickettsiales
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The Rickettsiales, also called rickettsias, are an order of small proteobacteria. Most of those described survive only as endosymbionts of other cells, some are notable pathogens, including Rickettsia, which causes a variety of diseases in humans. On the other end of the scale, genetic studies support the theory according to which mitochondria. Some have also speculated that viruses might have developed from them, the Rickettsiales are among the most mysterious groups of Proteobacteria, owing largely to difficulties in cultivating them. The group includes all obligate endosymbiont bacteria, however, a number of species have been removed, such as Coxiella burnetii, the cause of Q fever. The Rickettsiales has an order the Pelagibacterales, which is composed of free living bacteria with extremely streamlined genomes. The relation between the two order is retained in the subclass, the Rickettsidae, which include the Rickettsiales, the Pelagibacteriales and the extinct protomitochondrion
9.
Orientia
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Orientia is a genus of bacteria in family Rickettsiaceae. They are obligate intracellular, Gram-negative bacteria found in insects and mammals and they are spread through the bites or feces of infected insects. The genus comprises the species Orientia tsutsugamushi and Orientia chuto, which both cause scrub typhus in humans
10.
Binomial nomenclature
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Such a name is called a binomial name, a binomen, binominal name or a scientific name, more informally it is also called a Latin name. The first part of the name identifies the genus to which the species belongs, for example, humans belong to the genus Homo and within this genus to the species Homo sapiens. The formal introduction of system of naming species is credited to Carl Linnaeus. But Gaspard Bauhin, in as early as 1623, had introduced in his book Pinax theatri botanici many names of genera that were adopted by Linnaeus. Although the general principles underlying binomial nomenclature are common to these two codes, there are differences, both in the terminology they use and in their precise rules. Similarly, both parts are italicized when a binomial name occurs in normal text, thus the binomial name of the annual phlox is now written as Phlox drummondii. In scientific works, the authority for a name is usually given, at least when it is first mentioned. In zoology Patella vulgata Linnaeus,1758, the original name given by Linnaeus was Fringilla domestica, the parentheses indicate that the species is now considered to belong in a different genus. The ICZN does not require that the name of the person who changed the genus be given, nor the date on which the change was made, in botany Amaranthus retroflexus L. – L. is the standard abbreviation used in botany for Linnaeus. – Linnaeus first named this bluebell species Scilla italica, Rothmaler transferred it to the genus Hyacinthoides, the ICN does not require that the dates of either publication be specified. Prior to the adoption of the binomial system of naming species. Together they formed a system of polynomial nomenclature and these names had two separate functions. First, to designate or label the species, and second, to be a diagnosis or description, such polynomial names may sometimes look like binomials, but are significantly different. For example, Gerards herbal describes various kinds of spiderwort, The first is called Phalangium ramosum, Branched Spiderwort, is aptly termed Phalangium Ephemerum Virginianum, Soon-Fading Spiderwort of Virginia. The Latin phrases are short descriptions, rather than identifying labels, the Bauhins, in particular Caspar Bauhin, took some important steps towards the binomial system, by pruning the Latin descriptions, in many cases to two words. The adoption by biologists of a system of binomial nomenclature is due to Swedish botanist and physician Carl von Linné. It was in his 1753 Species Plantarum that he first began using a one-word trivial name together with a generic name in a system of binomial nomenclature. This trivial name is what is now known as an epithet or specific name
11.
Peptidoglycan
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Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine, attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a role in the bacterial cell wall, giving structural strength. Peptidoglycan is also involved in binary fission during bacterial cell reproduction, the peptidoglycan layer is substantially thicker in gram-positive bacteria than in gram-negative bacteria, with the attachment of the S-layer. Peptidoglycan forms around 90% of the dry weight of gram-positive bacteria, thus, presence of high levels of peptidoglycan is the primary determinant of the characterisation of bacteria as gram-positive. In gram-positive strains, it is important in attachment roles and serotyping purposes, for both gram-positive and gram-negative bacteria, particles of approximately 2 nm can pass through the peptidoglycan. The peptidoglycan layer in the cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars, namely N-acetylglucosamine and N-acetylmuramic acid. The alternating sugars are connected by a β--glycosidic bond, peptidoglycan is one of the most important sources of D-amino acids in nature. Cross-linking between amino acids in different linear amino sugar chains occurs with the help of the enzyme DD-transpeptidase and results in a 3-dimensional structure that is strong, the specific amino acid sequence and molecular structure vary with the bacterial species. The peptidoglycan monomers are synthesized in the cytosol and are attached to a membrane carrier bactoprenol. Bactoprenol transports peptidoglycan monomers across the membrane where they are inserted into the existing peptidoglycan. In the first step of peptidoglycan synthesis, the glutamine, which is an acid, donates an amino group to a sugar. This turns fructose 6-phosphate into glucosamine-6-phosphate, in step two, an acetyl group is transferred from acetyl CoA to the amino group on the glucosamine-6-phosphate creating N-acetyl-glucosamine-6-phosphate. In step three of the process, the N-acetyl-glucosamine-6-phosphate is isomerized, which will change N-acetyl-glucosamine-6-phosphate to N-acetyl-glucosamine-1-phosphate. In step 4, the N-acetyl-glucosamine-1-phosphate, which is now a monophosphate, uridine triphosphate, which is a pyrimidine nucleotide, has the ability to act as an energy source. In this particular reaction, after the monophosphate has attacked the UTP and this initial stage, is used to create the precursor for the NAG in peptidoglycan. In step 5, some of the UDP-N-acetylglucosamine is converted to UDP-MurNAc by the addition of a group to the glucosamine
12.
Serotype
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A serotype or serovar is a distinct variation within a species of bacteria or virus or among immune cells of different individuals. These microorganisms, viruses, or cells are classified based on their cell surface antigens. A group of serovars with common antigens is called a serogroup or sometimes serocomplex, serotyping often plays an essential role in determining species and subspecies. Vibrio cholerae, the species of bacteria that causes cholera, has over 200 serotypes, only two of them have been observed to produce the potent enterotoxin that results in cholera,0,1 and 0,139. Serotypes were discovered by the American microbiologist Rebecca Lancefield in 1933, the immune system is capable of discerning a cell as being self or non-self according to that cells serotype. In humans, that serotype is determined by human leukocyte antigen. Cells determined to be non-self are usually recognized by the system as foreign, causing an immune response. For this reason, transplants between genetically non-identical humans often induce an immune response in the recipient, leading to transplant rejection. In some situations this effect can be reduced by serotyping both recipient and potential donors to determine the closest HLA match, the Kauffman–White classification scheme is the basis for naming the manifold serovars of Salmonella. To date, more than 2600 different serotypes have been identified, a Salmonella serotype is determined by the unique combination of reactions of cell surface antigens. The O antigen is determined by the outermost portion of the Lipopolysaccharide, there are two species of Salmonella, Salmonella bongori and Salmonella enterica. Salmonella enterica can be subdivided into six subspecies, the process to identify the serovar of the bacterium consists of finding the formula of cell antigens which represent the variations of the bacteria. First of all, the use of the method on slides is required in order to get the antigen formula. The agglutination between the antigen and the antibody is made with a specific antisera, which reacts with the antigen to produce a mass. The antigen O is tested with a suspension from an agar plate whereas the antigen H is tested with a bacterial suspension from a broth culture. The scheme is used to classify the serovar depending on its antigen formula obtained with the reaction of the agglutination, biovar Morphovar HLA Allele and Haplotype Frequency Database
. PMID 23316486.
