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
Taxonomy (biology)
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Title page of
Systema Naturae, Leiden, 1735
Taxonomy (biology)
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Evolution of the
vertebrates at class level, width of spindles indicating number of families. Spindle diagrams are typical for
Evolutionary taxonomy
Taxonomy (biology)
–
The same relationship, expressed as a
cladogram typical for
cladistics
Taxonomy (biology)
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Type specimen for
Nepenthes smilesii, a tropical
pitcher plant.
2.
Bacterium
–
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
Bacterium
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Had'n
Bacterium
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A
biofilm of thermophilic bacteria in the outflow of
Mickey Hot Springs,
Oregon, approximately 20 mm thick.
Bacterium
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Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
Bacterium
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Bacillus anthracis (stained purple) growing in
cerebrospinal fluid
3.
Proteobacteria
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The Proteobacteria are a major phylum of Gram-negative bacteria. The name of the phylum has never been published as no type genus has been proposed. They include a variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia. Others are free-living, and include many of the responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the purple bacteria, the Alphaproteobacteria grow at very low levels of nutrients and have unusual morphology such as stalks and buds. They include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants, the type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The Betaproteobacteria are highly diverse and contain chemolithoautotrophs, photoautotrophs. The type order is the Burkholderiales, comprising a range of metabolic diversity. The Gammaproteobacteria are the largest class in terms of species with validly published names, the type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter. The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp, the Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp, the type order is the Oligoflexales, which contains the genus Oligoflexus. The Acidithiobacillia contain only sulfur-oxidising autotrophs, the type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp. All Proteobacteria are Gram-negative, though some may stain Gram-positive or Gram-variable in practice, many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the Myxobacteriales, an order of bacteria that can aggregate to form fruiting bodies. Also, a variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, Chemolithoautotrophic, and heterotrophic, a variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. Proteobacteria are associated with the imbalance of microbiota of the reproductive tract of women
Proteobacteria
–
Proteobacteria
4.
Alphaproteobacteria
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Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria. Its members are diverse and possess few commonalities, but nevertheless share a common ancestor. Like all Proteobacteria, its members are Gram-negative and some of its intracellular parasitic members lack peptidoglycan and are consequently gram variable. Moreover, the class includes the protomitochondrion, the bacterium that was engulfed by the ancestor and gave rise to the mitochondria. A species of technological interest is Rhizobium radiobacter, scientists use this species to transfer foreign DNA into plant genomes. There is some disagreement on the phylogeny of the orders, especially for the location of the Pelagibacterales and this issue stems form the large difference in gene content and the large difference in GC-richness between members of several order. Specifically, Pelagibacterales, Rickettsiales and Holosporales contains species with AT-rich genomes and it has been argued that it could be a case of convergent evolution that would result in an artefactual clustering. The basal group is Magnetococcidae, which is composed by a diversity of magnetotactic bacteria. The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales, the Caulobacteridae is composed of the Holosporales, Rhodospirillales, Sphingomonadales, Rhodobacterales, Caulobacterales, Kiloniellales, Kordiimonadales, Parvularculales and Sneathiellales. These molecular signatures provide novel means for the circumscription of these taxonomic groups, alphaproteobacteria at the US National Library of Medicine Medical Subject Headings Bacterial Phylogeny Webpage, Alpha Proteobacteria
Alphaproteobacteria
–
Alphaproteobacteria
5.
Rhizobiales
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The Rhizobiales are an order of Gram-negative Alphaproteobacteria. The rhizobia, which fix nitrogen and are symbiotic with plant roots, the four families Bradyrhizobiaceae, Hyphomicrobiaceae, Phyllobacteriaceae, and Rhizobiaceae contain at least six genera of nitrogen-fixing, legume-nodulating, microsymbiotic bacteria. Examples are the genera Bradyrhizobium and Rhizobium, species of the Methylocystaceae are methanotrophs, they use methanol or methane as their sole energy and carbon sources. Other important genera are Bartonella and Agrobacterium, natural genetic transformation has been reported in at least three Rhizobiales species, Agrobacterium tumefaciens, Methylobacterium organophilum, and Bradyrhizobium japonicum. Kuykendall, L. D. and Dazzo, F. B, in Brenner, Krieg, Staley and Garrity, The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology, 2nd. Vol.2, Springer, New York, NY, pp. 345–346, kuykendall, L. D.2005 Genus Azorhizobium. In Brenner, Krieg, Staley and Garrity, The Alpha-, Beta-, Delta- and Epsilonproteobacteria, The Proteobacteria, Part C, Bergey’s Manual of Systematic Bacteriology,2, Springer, New York, NY, pp. 505–506. In, Bergeys Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume, george Garrity, Springer–Verlag, New York, NY, pp. 438–443. Chen, W. X. E. T. Wang, in, Bergeys Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, Springer–Verlag, New York, NY, pp. 403–408, J. M. Young, E. Martínez-Romero, A. Kerr, and H. Sawada. Genus Rhizobium, a highly divergent genus in a revised family, in, Bergeys Manual of Systematic Bacteriology, 2nd Edition, 2nd Volume. George Garrity, Springer–Verlag, New York, NY, pp. 324–340
Rhizobiales
–
Rhizobiales
6.
Bartonellaceae
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Bartonella is a genus of Gram-negative bacteria. It is the genus in the family Bartonellaceae. Facultative intracellular parasites, Bartonella species can infect people, but are considered especially important as opportunistic pathogens. Bartonella species are transmitted by such as ticks, fleas, sand flies. At least eight Bartonella species or subspecies are known to infect humans, Bartonella henselae is the organism responsible for cat scratch disease. Bartonella species have been infecting humans for thousands of years, as demonstrated by Bartonella quintana DNA in a 4000-year-old tooth, the genus is named for Alberto Leonardo Barton Thompson, a Peruvian scientist born in Argentina. The currently accepted model explaining the infection cycle holds that the vectors are blood-sucking arthropods. Immediately after infection, the bacteria colonize a primary niche, the endothelial cells, every five days, some of the Bartonella bacteria in the endothelial cells are released into the blood stream, where they infect erythrocytes. The bacteria then invade a phagosomal membrane inside the erythrocytes, where they multiply until they reach a population density. At this point, they wait until they are taken up with the erythrocytes by a blood-sucking arthropod. Recent studies have shown a correlation between tick exposure and bartonellosis, including human bartonellosis. Bartonella bacteria are associated with disease, but a study in 2010 concluded. A history of a scratch or bite is not necessary for disease transmission. All current Bartonella species identified in canines are human pathogens, Bartonella infections are remarkable in the wide range of symptoms they can produce. The course of the diseases and the underlying pathologies are highly variable, treatment is dependent on which species or strain of Bartonella is found in a given patient. Immunocompromised patients should be treated with antibiotics because they are susceptible to systemic disease. Drugs of particular effectiveness include trimethoprim-sulfamethoxazole, gentamicin, ciprofloxacin, and rifampin, B. henselae is generally resistant to penicillin, amoxicillin, homeless intravenous drug users are at high risk for Bartonella infections, particularly B. elizabethae. B. elizabethae seropositivity rates in population range from 12. 5% in Los Angeles, to 33% in Baltimore, Maryland, 46% in New York City
Bartonellaceae
–
Bartonella
7.
Bartonella
–
Bartonella is a genus of Gram-negative bacteria. It is the genus in the family Bartonellaceae. Facultative intracellular parasites, Bartonella species can infect people, but are considered especially important as opportunistic pathogens. Bartonella species are transmitted by such as ticks, fleas, sand flies. At least eight Bartonella species or subspecies are known to infect humans, Bartonella henselae is the organism responsible for cat scratch disease. Bartonella species have been infecting humans for thousands of years, as demonstrated by Bartonella quintana DNA in a 4000-year-old tooth, the genus is named for Alberto Leonardo Barton Thompson, a Peruvian scientist born in Argentina. The currently accepted model explaining the infection cycle holds that the vectors are blood-sucking arthropods. Immediately after infection, the bacteria colonize a primary niche, the endothelial cells, every five days, some of the Bartonella bacteria in the endothelial cells are released into the blood stream, where they infect erythrocytes. The bacteria then invade a phagosomal membrane inside the erythrocytes, where they multiply until they reach a population density. At this point, they wait until they are taken up with the erythrocytes by a blood-sucking arthropod. Recent studies have shown a correlation between tick exposure and bartonellosis, including human bartonellosis. Bartonella bacteria are associated with disease, but a study in 2010 concluded. A history of a scratch or bite is not necessary for disease transmission. All current Bartonella species identified in canines are human pathogens, Bartonella infections are remarkable in the wide range of symptoms they can produce. The course of the diseases and the underlying pathologies are highly variable, treatment is dependent on which species or strain of Bartonella is found in a given patient. Immunocompromised patients should be treated with antibiotics because they are susceptible to systemic disease. Drugs of particular effectiveness include trimethoprim-sulfamethoxazole, gentamicin, ciprofloxacin, and rifampin, B. henselae is generally resistant to penicillin, amoxicillin, homeless intravenous drug users are at high risk for Bartonella infections, particularly B. elizabethae. B. elizabethae seropositivity rates in population range from 12. 5% in Los Angeles, to 33% in Baltimore, Maryland, 46% in New York City
Bartonella
–
Bartonella
8.
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
Binomial nomenclature
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Carl Linnaeus (1707–1778), a Swedish botanist, invented the modern system of binomial nomenclature.
9.
Trimeric autotransporter adhesin
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In molecular biology, trimeric autotransporter adhesins, are proteins found on the outer membrane of Gram-negative bacteria. Bacteria use TAAs in order to infect their host cells via a process called cell adhesion, TAAs also go by another name, oligomeric coiled-coil adhesins, which is shortened to OCAs. In essence, they are virulence factors, factors that make the bacteria harmful, TAAs are just one of many methods bacteria use to infect their hosts, infection resulting in diseases such as pneumonia, sepsis, and meningitis. Most bacteria infect their host through a method named the secretion pathway, TAAs are part of the secretion pathway, to be more specific the type Vc secretion system. Trimeric autotransporter adhesins have a unique structure, the structure they hold is crucial to their function. They all appear to have a head-stalk-anchor structure, each TAA is made up of three identical proteins, hence the name trimeric. The head domain, once assembled, then adheres to an element of the host extracellular matrix, for example, collagen, fibronectin, most TAAs have a similar protein structure. When observed with microscopy, the structure has been described as a lollipop shape consisting of an N-terminal head domain, a stalk domain. Often, the literature refers to these as Passenger domain, containing the N-terminal, head, neck, and coiled-coil stalk, although all TAAs carry a membrane anchor in common, they may not all contain both a stalk and a head as well. In addition, all membrane anchor domains are of the left-handed parallel beta-roll type, the Extended Signal Peptide Region is found in the N-terminus of the signal peptides of proteins belonging to the Type V secretion systems. The function of the ESPR is to aid inner membrane translocation by acting as a temporary tether and this prevents the accumulation of misfolded proteins. The ESPR can be divided into regions, they are as follows, N1, H1, N2, H2. N1 and H1 form the ESPR and have strong conservation, function, There are several roles that the Extended Signal Peptide Region is thought to hold. First, biogenesis of proteins in the Type V Secretion System, second, it is thought to target the protein to the inner membrane to be translocated either by the signal recognition particle pathway or by twin arginine translocated. Third, it has observed and believed to regulate the rate of protein migration into the periplasm. Structure, This particular domain is a trimer of single-stranded, left-handed beta-helices and these associate to form a nine-coiled left-handed beta-roll. It contains sequence motifs, of which there is a similarity with other TAA heads. This indicates that there is a lot of similarity when comparing protein structure, the head domain is connected to the stalk by a short, highly conserved sequence, which is often called the neck, or occasionally named the connector
Trimeric autotransporter adhesin
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Figure 1
Trimeric autotransporter adhesin
–
Figure 3
Trimeric autotransporter adhesin
–
Figure 4
Trimeric autotransporter adhesin
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The beta barrel structure found in the C-terminus of the bacterial adhesin anchor domain, YadA
10.
Gram-negative
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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
Gram-negative
–
Microscopic image of gram-negative
Pseudomonas aeruginosa bacteria (pink-red rods)
11.
Bacillus
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Bacillus is a genus of gram-positive, rod-shaped bacteria and a member of the phylum Firmicutes. Bacillus species can be obligate aerobes, or facultative anaerobes and they will test positive for the enzyme catalase when there has been oxygen used or present. Ubiquitous in nature, Bacillus includes both free-living and parasitic pathogenic species and these characteristics originally defined the genus, but not all such species are closely related, and many have been moved to other genera of the Firmicutes. Many species of Bacillus can produce copious amounts of enzymes which are use of in different industries. B. subtilis has proved a model for research. Other species of Bacillus are important pathogens, causing anthrax and food poisoning, many Bacillus species are able to secrete large quantities of enzymes. A portion of the Bacillus thuringiensis genome was incorporated into corn crops, the resulting GMOs are therefore resistant to some insect pests. Bacillus subtilis is one of the best understood prokaryotes, in terms of molecular and cellular biology and its superb genetic amenability and relatively large size have provided the powerful tools required to investigate a bacterium from all possible aspects. Recent improvements in fluorescent microscopy techniques have provided insight into the dynamic structure of a single cell organism. Bacillus species are almost ubiquitous in nature, e. g. in soil, B. thuringiensis produces a toxin that can kill insects and thus has been used as insecticide. Two Bacillus species are considered significant, B. anthracis, which causes anthrax, and B. cereus. A third species, B. thuringiensis, is an important insect pathogen, the type species is B. subtilis, an important model organism. It is also a notable food spoiler, causing ropiness in bread, some environmental and commercial strains of B. coagulans may play a role in food spoilage of highly acidic, tomato-based products. An easy way to isolate Bacillus species is by placing nonsterile soil in a test tube with water, shaking, placing in melted mannitol salt agar, colonies are usually large, spreading, and irregularly shaped. Under the microscope, the Bacillus cells appear as rods, the cell wall is composed of teichoic and teichuronic acids. The role of the cytoskeleton in shape generation and maintenance is important The genus Bacillus was named in 1835 by Christian Gottfried Ehrenberg and he had seven years earlier named the genus Bacterium. Bacillus was later amended by Ferdinand Cohn to further describe them as spore-forming, Gram-positive, like other genera associated with the early history of microbiology, such as Pseudomonas and Vibrio, the 266 species of Bacillus are ubiquitous. The genus has a very large ribosomal 16S diversity and is environmentally diverse, several studies have tried to reconstruct the phylogeny of the genus
Bacillus
–
Bacillus
Bacillus
–
Gram stain of a Bacillus species
12.
Warthin-Starry stain
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The Warthin–Starry stain is a silver nitrate-based staining method used in histology. It was first introduced in 1920 by American pathologists Aldred Scott Warthin and Allen Chronister Starry and it has been considered the best stain for detection of spirochetes, and is also used to stain Helicobacter pylori, Lawsonia intracellularis, Microsporidia, and particulates. It is also important for confirmation of Bartonella henselae, an organism in cat-scratch disease. Warthin–Starry stains organisms dark brown to black, and the background light golden brown/golden yellow, dieterle stain Warthin and Starry method at Who Named It
Warthin-Starry stain
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Helicobacter pylori colonized on the surface of regenerative epithelium, stained with the Warthin-Starry method.
Warthin-Starry stain
–
Clusters of
bacteria (arrow) shown on Warthin–Starry stain.
13.
Silver stain
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Silver staining is the use of silver to selectively alter the appearance of a target in microscopy of histological sections, in temperature gradient gel electrophoresis, and in polyacrylamide gels. Camillo Golgi perfected silver staining for the study of the nervous system, although the exact chemical mechanism by which this occurs is unknown, Golgis method stains a limited number of cells at random in their entirety. Silver staining was introduced by Kerenyi and Gallyas as a procedure to detect trace amounts of proteins in gels. The technique has been extended to the study of biological macromolecules that have been separated in a variety of supports. Classical Coomassie Brilliant Blue staining can usually detect a 50 ng protein band and these reduce silver solution to metallic silver after formalin fixation. These reduce silver solution to metallic silver after being exposed to the stain that contains a reductant, silver nitrate forms insoluble silver phosphate with phosphate ions, this method is known as the Von Kossa Stain. When subjected to an agent, usually hydroquinone, it forms black elementary silver. This is used for study of formation of calcium phosphate particles during bone growth, pseudomonas, Legionella, Leptospira, H. pylori, and fungi such as Pneumocystis and Candida are organisms that are stained with silver. Silver staining is used in karyotyping, silver nitrate stains the nucleolar organization region -associated protein, producing a dark region wherein the silver is deposited and denoting the activity of rRNA genes within the NOR. Human chromosomes 13,14,15,21, and 22 have NORs, silver staining is used to stain gels. Silver staining is also a technique in traditional stained glass to produce the yellow, brown and it is a technique that is often used for realistic hair colors. It was discovered in the 14th Century but was not originally used very frequently, there are several silver stains incorporating methenamine, including, Grocotts methenamine silver stain, used widely as a screen for fungal organisms. Jones stain, a methenamine silver-Periodic acid-Schiff that stains for basement membrane, medEd at Loyola Histo/practical/stains/hp2-55. html Hempelmann E. SDS-Protein PAGE and protein detection by silverstaining and immunoblotting of Plasmodium falciparum proteins. In, Moll K, Ljungström J, Perlmann H, Scherf A, Wahlgren M Methods in Malaria Research, 5th edition,2008, 263-266
Silver stain
–
A silver stain (
GMS) demonstrating the fungus
Histoplasma (black round balls) in a liver biopsy.
Silver stain
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A number of DNA samples from specimens of Littorina plena amplified using
PCR with primers targeting a variable
simple sequence repeat (SSR, a.k.a. microsatellite) locus. Samples have been run on a 5% polyacrylamide gel and visualized using silver staining.
Silver stain
–
RBC membrane proteins separated by
SDS-PAGE and silver-stained.
14.
Microbiologist
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The term microbiologist comes from the Greek mīkros meaning small βίος, and bios, meaning life -λογία, combined with -logia meaning one who studies. A microbiologist is a biological scientist who studies microscopic life forms, microbiologists investigate the growth, interactions and characteristics of microscopic organisms such as bacteria, algae, fungi, and some types of parasites and their vectors. They contribute much to the field by trying to understand and learn about the interaction between these microbes and the environment and also among themselves and other organisms, most microbiologists are qualified to work in offices and/or research facilities, such as a laboratory as well as in the academia. There, they conduct experiments that help them analyze microbes and their importance, a microbiologists work is often repeated or improved in order to establish accurate research. Most microbiologists specialize in environmental, food, agricultural, industrial or medical aspects of microbiology including, virology, immunology, bioinformatics, many microbiologists use biotechnology to advance the understanding of cell reproduction and human disease. Some microbiologists have contributed to knowledge of pathogens and disease-causing microbes, while others, study their interaction with the environment and their use as potential environmental pollution cleaners. Microbiology is a subset of science that often overlaps with other subjects surrounding biology. Nonetheless, the spectrum of fields, a microbiologists can work on is immense, there were 16,900 microbiologists employed in the United States in 2008, this number was projected to increase by over 12 percent in the next decade
Microbiologist
–
Microbiologists examining cultures on a
Petri dish.
15.
Oklahoma
–
Oklahoma is a state located in the South Central United States. Oklahoma is the 20th-most extensive and the 28th-most populous of the 50 United States, the states name is derived from the Choctaw words okla and humma, meaning red people. The name was settled upon statehood, Oklahoma Territory and Indian Territory were merged, on November 16,1907, Oklahoma became the 46th state to enter the union. Its residents are known as Oklahomans, or informally Okies, and its capital, a major producer of natural gas, oil, and agricultural products, Oklahoma relies on an economic base of aviation, energy, telecommunications, and biotechnology. In 2007, it had one of the economies in the United States, ranking among the top states in per capita income growth. Oklahoma City and Tulsa serve as Oklahomas primary economic anchors, with nearly two-thirds of Oklahomans living within their metropolitan statistical areas. With small mountain ranges, prairie, mesas, and eastern forests, most of Oklahoma lies in the Great Plains, Cross Timbers, interior Highlands—a region especially prone to severe weather. The name Oklahoma comes from the Choctaw phrase okla humma, literally meaning red people, equivalent to the English word Indian, okla humma was a phrase in the Choctaw language used to describe Native American people as a whole. Oklahoma later became the de facto name for Oklahoma Territory, and it was approved in 1890. Oklahoma is the 20th-largest state in the United States, covering an area of 69,898 square miles and it is one of six states on the Frontier Strip and lies partly in the Great Plains near the geographical center of the 48 contiguous states. It is bounded on the east by Arkansas and Missouri, on the north by Kansas, on the northwest by Colorado, on the far west by New Mexico, much of its border with Texas lies along the Southern Oklahoma Aulacogen, a failed continental rift. The geologic figure defines the placement of the Red River, the Oklahoma panhandles Western edge is out of alignment with its Texas border. The Oklahoma/New Mexico border is actually 2.1 to 2.2 miles east of the Texas line, the border between Texas and New Mexico was set first as a result of a survey by Spain in 1819. It was then set along the 103rd Meridian, in the 1890s, when Oklahoma was formally surveyed using more accurate surveying equipment and techniques, it was discovered the Texas line was not set along the 103rd Meridian. Surveying techniques were not as accurate in 1819, and the actual 103rd Meridian was approximately 2.2 miles to the east and it was much easier to leave the mistake than for Texas to cede land to New Mexico to correct the surveying error. The placement of the Oklahoma/New Mexico border represents the true 103rd Meridian, cimarron County in Oklahomas panhandle is the only county in the United States that touches four other states, New Mexico, Texas, Colorado and Kansas. Its highest and lowest points follow this trend, with its highest peak, Black Mesa, at 4,973 feet above sea level, situated near its far northwest corner in the Oklahoma Panhandle. The states lowest point is on the Little River near its far southeastern boundary near the town of Idabel, Oklahoma, which dips to 289 feet above sea level
Oklahoma
–
State rock (
rose rock) specimens from Cleveland County, with a
US quarter for size reference.
Oklahoma
–
Flag
Oklahoma
–
The state's high plains stretch behind a greeting sign in the
Oklahoma Panhandle.
Oklahoma
–
A view of
Mt Scott
16.
PubMed Identifier
–
PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
PubMed Identifier
–
PubMed
17.
Rickettsiales
–
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
Rickettsiales
–
Rickettsias
18.
Rickettsia rickettsii
–
Rickettsia rickettsii is a gram-negative, intracellular, coccobacillus bacterium that is around 0.8 to 2.0 micrometers long. R. rickettsi is the agent of Rocky Mountain spotted fever. R. rickettsii is one of the most pathogenic Rickettsia strains known to humans and affects a large majority of the Western Hemisphere, Rocky Mountain spotted fever first emerged in the Idaho Valley in 1896. At that time, not much information was known about the disease, the first clinical description of Rocky Mountain Spotted Fever was reported in 1899 by Edward E. Maxey. Howard Ricketts, a professor of pathology at the University of Chicago in 1902, was the first to identify. At this time, the trademark rash now began to emerge in the western Montana area. His research entailed interviewing victims of the disease and collecting and studying infected animals and he was also known to inject himself with pathogens to measure their effects. Unfortunately, his research was cut short after his death from an insect bite. S. Burt Wolbach is credited for the first detailed description of the agent that causes R. rickettsii in 1919. He clearly recognized it as a bacterium which was seen most frequently in endothelial cells. The most common hosts for the R. rickettsii bacteria are ticks, ticks that carry R. rickettsia fall into the family of Ixodidae ticks, also known as hard bodied ticks. Ticks are vectors, reservoirs and amplifiers of this disease, there are currently three known tick specifics that commonly carry R. rickettsii. American dog tick Rocky Mountain Wood Tick Brown dog tick, ticks can contract R. rickettsii by many means. Once a tick becomes infected with this pathogen, they are infected for life, in addition, an infected male tick can transmit the organism to an uninfected female during mating. Once infected, the tick can transmit the infection to her offspring. Due to its confinement in the midgut and small intestine, Rickettsia rickettsii can be transmitted to mammals, transmission to mammals can occur in multiple ways. One way of contraction is through the contact of infected host feces to an uninfected host, if infected host feces comes into contact with an open skin wound, it is possible for the disease to be transmitted. Additionally, an uninfected host can become infected with R. rickettsii when eating food that contains the feces of the infected vector, another way of contraction is by the bite of an infected tick
Rickettsia rickettsii
–
Rickettsia rickettsii
Rickettsia rickettsii
–
Early-stage lesions of RMSF
19.
Mite
–
Mites, along with ticks, are small arthropods belonging to the subclass Acari and the class Arachnida. The scientific discipline devoted to the study of ticks and mites is called acarology, in soil ecosystems, mites are favored by high organic matter content and by moist conditions, wherein they actively engage in the fragmentation and mixing of organic matter. Mites are among the most diverse and successful of all the invertebrate groups and they have exploited an incredible array of habitats, and because of their small size, go largely unnoticed. Many live freely in the soil or water, but there are also a number of species that live as parasites on plants, animals. It is estimated that 48,200 species of mites have been described, mites occupy a wide range of ecological niches. For example, Oribatida mites are important decomposers and occur in many habitats and they eat a wide variety of material including living and dead plant and fungal material, lichens and carrion, some are even predatory, though no species of Oribatida mite are parasites. Many mites which have well studied are parasitic on plants. One family of mites Pyroglyphidae, or nest mites, live primarily in the nests of birds and these mites are largely parasitic and consume blood, skin and keratin. Dust mites, which feed mostly on dead skin and hair shed from humans instead of consuming them from the organism directly, insects may also be infested by parasitic mites. Examples are Varroa destructor, which attaches to the body of the bee, and Acarapis woodi. There are hundreds of species of associated with other bee species. They attach to the bees in a variety of ways, for example, Trigona corvina workers have been found with mites attached to the outer face of their hind tibiae. Some are thought to be parasites, while others are beneficial symbionts, mites also parasitize some ant species, such as Eciton burchellii. Some of the plant pests include the spider mites, thread-footed mites. Among the species that attack animals are members of the sarcoptic mange mites, demodex mites are parasites that live in or near the hair follicles of mammals, including humans. Acari are mites, except for the three families of ticks, mites also hold the record speed, for its length, Paratarsotomus macropalpis is the fastest animal on Earth. The majority of species are harmless to humans, but a few species of mites can colonize humans directly, act as vectors for disease transmission. Mites which colonize human skin are the cause of several types of skin rashes, such as grain itch, grocers itch
Mite
–
Mite
Mite
–
The microscopic mite
Lorryia formosa (
Tydeidae)
Mite
–
Lime nail galls on
Tilia × europaea, caused by the mite
Eriophyes tiliae
Mite
–
Sarcoptes scabiei, the cause of
scabies
20.
Orientia tsutsugamushi
–
Orientia tsutsugamushi is the causative organism of scrub typhus, and the natural vector and reservoir is probably trombiculid mites. The organism is an intracellular pathogen, which needs to infect eukaryotic cells in order to multiply. The envelope is similar to that of Gram negative bacteria, but it is not easily stained with Gram stain, genetic methods have revealed even greater complexity than had been previously described. Infection with one serotype does not confer immunity to other serotypes, repeated infection in the same individual is therefore possible, and this complicates vaccine design. The bacterium was initially categorised in the genus Rickettsia, but is now classed in a genus, Orientia. It is 0.5 µm wide and 1.2 to 3.0 µm long, the organism is highly virulent and should only be handled in a laboratory with biosafety level 3 facilities. O. tsutsugamushi is sensitive in vitro to doxycycline, rifampicin and azithromycin and it is innately resistant to all β-lactam antibiotics because it lacks a classical peptidoglycan cell wall. Aminoglycosides are also ineffective in human infection because the organism is intracellular, there are currently no licensed scrub typhus vaccines available. It is now known there is enormous antigenic variation in Orientia tsutsugamushi strains. Any scrub typhus vaccine should give protection to all the strains present locally, a vaccine developed for one locality may not be protective in another locality, because of antigenic variation. This complexity continues to hamper efforts to produce a viable vaccine
Orientia tsutsugamushi
–
Orientia
21.
Flea
–
Fleas are small flightless insects that form the order Siphonaptera. As external parasites of mammals and birds, they live by consuming the blood of their hosts, adults are up to about 3 mm long and usually brown. Bodies flattened sideways enable them to move through their hosts fur or feathers and they lack wings, and have mouthparts adapted for piercing skin and sucking blood and hind legs adapted for jumping. The latter enable them to leap a distance of some 50 times their body length, larvae are worm-like with no limbs, they have chewing mouthparts and feed on organic debris. Over 2,500 species of fleas have been described worldwide, the Siphonaptera are most closely related to the snow scorpionflies, placing them within the endopterygote insect order Mecoptera. Fleas arose in the early Cretaceous, most likely as ectoparasites of mammals and marsupials, each species of flea is more or less a specialist on its host animal species, many species never breed on any other host, though some are less selective. The oriental rat flea, Xenopsylla cheopis, is a vector of Yersinia pestis, the disease was spread by rodents such as the black rat, which were bitten by fleas that then infected humans. Major outbreaks included the Plague of Justinian and the Black Death, both of which killed a sizeable fraction of the worlds population. Fleas appear in human culture in such forms as flea circuses, poems like John Donnes erotic The Flea, works of music such as by Modest Mussorgsky. Flea legs end in strong claws that are designed to grasp a host, unlike other insects, fleas do not possess compound eyes but instead only have simple eyespots with a single biconvex lens, some species lack eyes altogether. Their bodies are compressed, permitting easy movement through the hairs or feathers on the hosts body. The flea body is covered with hard plates called sclerites and these sclerites are covered with many hairs and short spines directed backward, which also assist its movements on the host. The tough body is able to withstand great pressure, likely an adaptation to survive attempts to eliminate them by scratching, fleas lay tiny, white, oval eggs. The larvae are small and pale, have bristles covering their bodies, lack eyes. The larvae feed on organic matter, especially the feces of mature fleas, adults feed only on fresh blood. Immediately before the jump, muscles contract and deform the resilin pad, to prevent premature release of energy or motions of the leg, the flea employs a catch mechanism. Early in the jump, the tendon of the primary jumping muscle passes slightly behind the coxa-trochanter joint, generating a torque which holds the joint closed with the leg close to the body. To trigger jumping, another muscle pulls the tendon forward until it passes the joint axis, generating the opposite torque to extend the leg, the actual take off has been shown by high-speed video to be from the tibiae and tarsi rather than from the trochantera
Flea
Flea
–
A
Cat flea under an optical microscope, x35
Flea
–
Hooke's drawing of a flea in
Micrographia
Flea
–
Flea bites on the back of a human
22.
Anaplasma phagocytophilum
–
Anaplasma phagocytophilum is a gram-negative bacterium that is unusual in its tropism to neutrophils. It causes anaplasmosis in sheep and cattle, also known as fever and pasture fever. Anaplasma phagocytophilum is a Gram-negative, obligate bacterium of neutrophils and it causes human granulocytic anaplasmosis, which is a tick-borne rickettsial disease. Because this bacterium invades neutrophils, it has a unique adaptation, anaplasma phagocytophilum is a small, obligate, intracellular bacterium with a Gram-negative cell wall. It is 0. 2–1.0 μm and lacks a lipopolysaccharide biosynthetic machinery, the bacterium first resides in an early endosome, where it acquires nutrients for binary fission and grows into small groups called morulae. This bacterium prefers to grow within myeloid or granulocytic cells, anaplasma phagocytophilum causes human granulocytic anaplasmosis. This disease was first identified in 1990, although this pathogen was known to cause veterinary disease since 1932, since 1990, incidence of this disease has increased, and it is now recognized in Europe. This disease was first identified due to a Wisconsin patient who died with a severe illness two weeks after a tick bite. During the last stage of the infection, a group of bacteria were seen within the neutrophils in the blood. Other symptoms include fever, headache, absence of skin rash, leucopenia, thrombocytopenia, the disease is multisystemic, but the most severe changes are anaemia and leukopenia. This organism causes lameness which can be confused with symptoms of Lyme disease and it is a vector borne zoonotic disease whose morula can be visualized within neutrophils from the peripheral blood and synovial fluid. It can cause lethargy, ataxia, loss of appetite, anaplasma phagocytophilum binds to fucosylated and sialylated scaffold proteins on neutrophil and granulocyte surfaces. A type IV secretion apparatus is known to help in the transfer of molecules between the bacterium and the host, the most studied ligand is PSGL-1. The bacterium adheres to PSGL-1 through 44-kDa major surface protein-2, after the bacterium enters the cell, the endosome stops maturation and does not accumulate markers of late endosomes or phagolysosomes. Because of this, the vacuole does not become acidified or fused to lysosomes, a. phagocytophilum then divides until cell lysis or when the bacteria leave to infect other cells. This bacterium has the ability to affect neutrophils by altering the function of the host cell and it can survive the first encounter with the host cell by detoxifying superoxide produced by neutrophil phagocyte oxidase assembly. It also disrupts normal neutrophil function, such as cell adhesion, transmigration, motility, degranulation, respiratory burst. It causes an increase in the secretion of IL-8, a chemoattractant that increases the phagocytosis of neutrophils, the purpose of this is to increase bacterial dissemination into the neutrophil
Anaplasma phagocytophilum
–
Light micrograph of Anaplasma phagocytophilum cultured in human promyelocytic cell line HL-60, showing A. phagocytophilum morulae as basophilic and intracytoplasmic inclusions (arrows). Wright–Giemsa stain, original magnification x1,000.
Anaplasma phagocytophilum
–
Doxycycline
23.
Ehrlichia chaffeensis
–
Ehrlichia chaffeensis is an obligate intracellular gram-negative species of rickettsiales bacteria. It is a zoonotic pathogen transmitted to humans by the lone star tick and it is the causative agent of human monocytic ehrlichiosis. ATP production in the rickettsia is biochemically identical to that in mammalian mitochondria, human monocytic ehrlichiosis caused by E. chaffeensis is known to spread through tick infection primarily in the southern, southcentral and mid-Atlantic regions of the United States. In recent years the lone star tick has expanded its range up the East Coast to New England and it is named for Fort Chaffee where the bacteria was first discovered in blood samples of infected patients. E. chaffeensis is maintained in nature through a complex zoonotic relationship, the white-tailed deer is known to be the main competent reservoir for E. chaffeensis and the lone star tick is the principal vector for human transmission. There is some evidence that other organisms may serve as reservoirs for the bacteria such as goats, domestic dogs, raccoons. E. chaffeensis can be transmitted to non-infected tick larvae feeding on the blood from an infected host. The infection is then maintained and can be transmitted to an organism or humans at the nymphal stage. Adult ticks can maintain the infection or be infected from feeding on the blood of a reservoir organism. Transovarial transmission is not known to occur so eggs and unfed larvae are not believed to be infected, E. chaffeensis causes human monocytic ehrlichiosis and is known to infect monocytes. It has also known to infect other cell types such as lymphocytes, atypical lymphocytes, myelocytes, and neutrophils. E. chaffeensis has also shown to infect canines both naturally and articifially. Symptoms in canine infections are hard to differentiate between E. chaffeensis infection and Ehrlichia canis, which is the species of Ehrlichia that most commonly affects canines, patients display early symptoms within 1 to 2 weeks after tick infection. Early symptoms include fever, headache, malaise, low-back pain, some patients may also have myalgias, arthralgias, and an estimated 10–40% of patients may develop coughing, pharyngitis, diarrhea, vomiting, abdominal pain, and changes in mental status. A variety of procedures have been used to detect E. chaffeensis in humans, most commonly serologic testing and PCR amplification are used. E. chaffeensis is susceptible to tetracyclines, doxycycline treatment is suggested for any patients presenting symptoms of an Ehrlichia infection during the appropriate season and potential tick exposure
Ehrlichia chaffeensis
–
Ehrlichia chaffeensis
24.
Bartonella quintana
–
Bartonella quintana, originally known as Rochalimaea quintana, and Rickettsia quintana, is a microorganism transmitted by the human body louse. This microorganism is the agent of trench fever. This bacterium resulted in over 1 million soldiers in Europe during World War I being infected with trench fever, B. quintana has an estimated genome size of 1,700 to 2,174 kb. B. quintana is a fastidious, aerobic, Gram-negative, rod-shaped bacterium. The infection caused by this microorganism, trench fever, was first documented in soldiers during World War I, but has now been seen Europe, Asia and its primary vector is known to be Pediculus humanus variety corporis, also known as the human body louse. It was first isolated in culture by J. W. Vinson in 1960. He then followed Kochs postulates, infecting volunteers with the bacterium, showing consistent symptoms, the medium best for growing this bacterium is blood-enriched in an atmosphere containing 5% carbon dioxide. Humans are the known animal host for this bacterium in vivo. It infects endothelial cells and can infect erythrocytes by binding and entering with a large vacuole, once inside, they begin to proliferate and cause nuclear atypia. This leads to apoptosis being suppressed, proinflammatory cytokines are released, all of these processes result in patients possessing systemic symptoms, bacteremia, and lymphatic enlargement. A major role in B. quintana infection is its lipopolysaccharide covering which is an antagonist of the toll-like receptor 4, the reason this infection might persist is because this organism also results in monocytes overproducing interleukin-10, thus weakening the immune response. B. quintana also induces lesions seen in bacillary angiomatosis that protrude into vascular lumina, the enhanced growth of these cells is believed to be due to the secretion of angiogenic factors, thus inducing neovascularization. Release of a particle,40 nm in length, has been detected in cultures of B. quintanas close relative. This particle contains a 14-kb linear DNA segment, but its function in Bartonella pathophysiology is still unknown, in trench fever or B. quintana-induced endocarditis patients, bacillary angiomatosis lesions are also seen. Notably, endocarditis is a new manifestation of the infection, not seen in World War I troops, B. quintana infection has subsequently been seen in every continent except Antarctica. Local infections have been associated with factors such as poverty, alcoholism. Serological evidence of B. quintana infection showed, of hospitalized patients, 16% were infected, as opposed to 1. 8% of nonhospitalized homeless persons. Lice have been demonstrated, as of recently, to be the key component in transmitting B. quintana and this has been attributed to living in unsanitary conditions and crowded areas, where the risk of coming into contact with other individuals carrying B. quintana and ectoparasites is increased. Also noteworthy, the increasing migration worldwide may also play a role in spreading trench fever, recent concern is the possibility of the emergence of new strains of B. quintana through horizontal gene transfer, which could result in the acquisition of other virulence factors
Bartonella quintana
–
B. quintana and
Mycobacterium avium complex coinfecting an AIDS patient
25.
Bartonella bacilliformis
–
Bartonella bacilliformis is a proteobacterium, Gram negative aerobic, pleomorphic, flagellated, motile, coccobacillary, 2–3 μm long,0. 2–0.5 μm wide, and a facultative intracellular bacterium. The bacterium was discovered by Peruvian microbiologist Alberto Barton in 1905, Barton originally identified them as endoglobular structures, which actually were the bacteria living inside red blood cells. Until 1993, the Bartonella genus contained only one species, there are now more than 23 identified species, Bartonella bacilliformis is found only in Peru, Ecuador, and Colombia. It is endemic in some areas of Peru, with outbreaks of the disease occurring in new epidemic areas, the bacterium is transmitted by sandflies of the genus Lutzomyia. For its isolation, special cultures are required, containing complemental soy agar, proteases, peptones, some amino acids. The optimum growing temperature is 19–29 °C, colonies grow in Columbia blood agar supplemented with 10% defibrinated bovine blood incubated at 19–25 °C for 2 weeks. As the sandflies bite, the bacteria are inoculated into the capillaries and this phase is a potentially life-threatening infection, and it is associated with high fever, anemia, and transient immunosuppression. The acute phase typically lasts two to four weeks, peripheral blood smears show anisomacrocytosis with many coccobacilli adhered to red blood cells. Thrombocytopenia is also seen and can be severe, neurological involvement is sometimes seen and the prognosis in this case is poor. The most feared complications are super-infections, mainly by enterobacteria such as Salmonella, or parasites such as Toxoplasma gondii, when the bacterium invades endothelial cells, it produces the chronic manifestation of the disease known as verruga peruana. This phase consists of a skin eruption with raised, reddish-purple nodules. Visualization of the bacteria is possible using silver stain on biopsies, Bartonella bacilliformis is the etiologic agent of Carrions disease or Oroya fever, and verruga peruana or Peruvian wart. The acute phase of the disease is a disease characterized by massive invasion of Bartonella to human red blood cells and consequently acute hemolysis. If the infection is not treated, the fatality rate is 40 to 85% Patients in this phase of the infection can be complicated by overwhelming infections, primarily by enterobacteria. The chronic phase is characterized by benign eruptive lesions that are pruritic and bleeding, Bartonella can be isolated from blood cultures and secretion of the lesions in people from endemic areas. Before the antibiotic era, the treatment for the acute phase was blood transfusion, but the effectiveness of this treatment was poor. Later, with the discovering of new antibiotics, penicillin, chloramphenicol, tetracycline, however, because of the risk of overwhelming infections by enterobacteria, quinolones are preferred. So, the drug of choice is ciprofloxacin, in the chronic phase, the treatment used traditionally has been streptomycin for 10 days
Bartonella bacilliformis
–
thin blood film
26.
Neisseriaceae
–
The Neisseriaceae are a family of Proteobacteria, within the Neisseriales order. As a group, the Neisseriaceae are strictly aerobic and Gram-negative, occur mainly in pairs, bacteria of Medical Importance in Todars Online Textbook of Bacteriology. CS1 maint, Multiple names, authors list Ryan KJ, Ray CG
Neisseriaceae
–
Neisseriaceae
27.
Maltose
–
Maltose, also known as maltobiose or malt sugar, is a disaccharide formed from two units of glucose joined with an α bond, formed from a condensation reaction. The isomer isomaltose has two glucose molecules linked through an α bond, maltose is the second member of an important biochemical series of glucose chains. Maltose is the disaccharide produced when amylase breaks down starch and it is found in germinating seeds as they break down their starch stores to use for food, which is why it was named after malt. It is also produced when glucose is caramelized, maltose was discovered by Irish chemist and brewer Cornelius OSullivan in 1872. Its name comes from malt, from Old English mealt, of Germanic origin, and the suffix –ose, maltose is a biomolecule that belongs to the group of carbohydrates within the division of biomolecules into the three main groups, carbohydrates, lipids and proteins. Carbohydrates are composed of carbon, oxygen and hydrogen C, O, H and are either polyhydroxyaldehydes or polyhydroxyketones, as a group, they are generally divided into monosaccharides, oligosaccharides, and polysaccharides depending on the number of sugar subunits. Maltose is an oligosaccharide, specifically a disaccharide, formed by the union of two glucose units, glucose is classified as a hexose because it is composed of six carbons. The link is characterized as α due to the O-glycosidic bond to the anomeric carbon being in the plane from the CH 2OH substituent in the same ring. If the O-glycosidic bond to the carbon was in the same plane as the CH 2OH substituent, it would be classified as a β bond. Due to O-glycosidic link, maltose is a disaccharide that can reduce Fehlings reagent, furthermore, maltose can be obtained by hydrolysis of glycogen or starch, polymers of linked maltoses in position α and branching in position α. These are very abundant and form a number of branches. Amylase enzymes produce maltose and limit dextrin and these can be further degraded by maltase enzyme to hydrolyze maltoses as glucoses and they are ready to be degrade and obtain energy in form of ATP. An isomer of maltose is isomaltose and this is similar to maltose but instead of bonds in position α, the linkage is formed in position α, therefore, glycogen branching is defined by isomaltose. maltose, isomaltose is also a reducing sugar. Maltose has the ability to reduce the Fehling’s solution, due to its free aldehyde, the aldehyde group is oxidized giving a positive result, which means that the maltose is a reducing sugar. Maltose in aqueous solution exhibit mutarotation, due to its anomeric carbon which can form α and β isomers, in aqueous solutions, it is in equilibrium between its α and β forms. It is sometimes water-soluble and sometimes crystalline, homopolysaccharides of glucose are broken down by maltase and isomaltase to produce glucose. The lack of the Sucrase-Isomaltase enzyme, one of the four integral glycoproteins and this congenital disorder is most prominent in infancy but can develop later in life. It is caused by an autosomal mutation
Maltose
–
Maltose syrup
Maltose
–
α-Maltose
Maltose
–
Chemistry
28.
Neisseria meningitidis
–
The bacterium is referred to as a coccus because it is round, and more specifically, diplococcus because of its tendency to form pairs. About 10% of adults are carriers of the bacteria in their nasopharynx, as an exclusively human pathogen it is the main cause of bacterial meningitis in children and young adults, causing developmental impairment and death in about 10% of cases. It causes the form of bacterial meningitis known to occur epidemically, mainly Africa. It occurs worldwide in both epidemic and endemic form, N. meningitidis is spread through saliva and respiratory secretions during coughing, sneezing, kissing, chewing on toys and even freshwater. It infects the cell by sticking to it with long thin extensions called pili, meningococcus can cause meningitis and other forms of meningococcal disease. It initially produces general symptoms like fatigue, fever, and headache and can progress to neck stiffness, coma. Symptoms of meningococcal meningitis are easily confused with those caused by bacteria, such as Hemophilus influenzae. Suspicion of meningitis is an emergency and immediate medical assessment is recommended. Current guidance in the United Kingdom is that if a case of meningitis or septicaemia is suspected intravenous antibiotics should be given. This means that laboratory tests may be likely to confirm the presence of Neisseria meningitidis as the antibiotics will dramatically lower the number of bacteria in the body. The UK guidance is based on the idea that the ability to identify the bacteria is outweighed by reduced chance of death. Septicaemia caused by Neisseria meningitidis has received less public attention than meningococcal meningitis even though septicaemia has been linked to infant deaths. Meningococcal septicaemia typically causes a rash, that does not lose its color when pressed with a glass. This means the condition may be ignored by those not aware of the significance of the rash, septicaemia carries an approximate 50% mortality rate over a few hours from initial onset. N. meningitidis is a Gram-negative bacterium since it has an outer and inner membranes with a layer of peptidoglycan in between. It tests positive for the cytochrome c oxidase. N. meningitidis is a part of the normal flora in the nasopharynx of up to 5–15% of adults. It colonizes and infects only humans, and has never been isolated from other animals and this is thought to stem from the bacteriums inability to get iron sources other than human transferrin and lactoferrin
Neisseria meningitidis
–
The growth of Neisseria meningitidis colonies on New York City Medium Agar
Neisseria meningitidis
–
Neisseria meningitidis
29.
Neisseria gonorrhoeae
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Neisseria gonorrhoeae, also known as gonococci, or gonococcus, is a species of Gram-negative coffee bean-shaped diplococci bacteria responsible for the sexually transmitted infection gonorrhea. N. gonorrhoeae was first described by Albert Neisser in 1879, Neisseria species are fastidious Gram-negative cocci that require nutrient supplementation to grow in laboratory cultures. To be specific, they grow on agar with carbon dioxide. These cocci are facultatively intracellular and typically appear in pairs, in the shape of coffee beans, of the 11 species of Neisseria that colonize humans, only two are pathogens. N. gonorrhoeae is the agent of gonorrhea and is transmitted via sexual contact. Further testing to differentiate the species includes testing for oxidase and the carbohydrates maltose, sucrose, N. gonorrhoeae possess many dynamic polymeric protein filaments called type IV pili, which allow the bacteria to adhere and move along surfaces. The bacterial movement is mediated by twitching motility powered by the extension and retraction of the type IV pilus, pili extend and attach to a substrate that signals the pilus to retract, dragging the cell forward. N. gonorrhoeae is able to pull 100,000 times its own weight, the pulling of type IV pilus is powered by a set of ATPases proteins, Pil F and Pil T. The type IV pilus in N. gonorrhoeae adhesive properties also play a role in microcolony aggregation, N. gonorrhoeae is naturally competent for DNA exchange, which is also dependent on type IV pilus dynamics, specifically proteins Pil Q and Pil T. These processes allow for the DNA of N. gonorrhoeae to acquire or spread new genes, especially dangerous from the aspect of healthcare is the ability to conjugate, since this can lead to antibiotic resistance. N. gonorrhoeae has surface proteins called Opa proteins, which bind to receptors on immune cells, in so doing, N. gonorrhoeae is able to prevent an immune response. The host is unable to develop an immunological memory against N. gonorrhoeae – which means that future reinfection is possible. The many permutations of proteins make it more difficult for immune cells to recognize N. gonorrhoeae. The genomes of several strains of N. gonorrhoeae have been sequenced, most of them are about 2.1 Mb in size and encode 2,100 to 2,600 proteins. For instance, strain NCCP11945 consists of one circular chromosome encoding 2,662 predicted ORFs, the estimated coding density over the entire genome is 87%, and the average G+C content is 52. 4%, values that are similar to those of strain FA1090. The NCCP11945 genome encodes 54 tRNAs and four copies of 16S-23S-5S rRNA operons, N. gonorrhoeae is transmitted from person to person during sexual relations. Traditionally, the bacteria was thought to move attached to spermatozoon, a recent study suggests that rather than “surf” on wiggling sperm, N. gonorrhoeae bacteria uses hairlike structures called pili to anchor onto proteins in the sperm and move through coital liquid. It can also be transmitted to the fetus in utero and afterward become apparent as a neonatal infection, symptoms of infection with N. gonorrhoeae differ, depending on the site of infection
Neisseria gonorrhoeae
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The growth of Neisseria gonorrhoeae colonies on New York City medium agar, a specialised and selective media for Gonococci
Neisseria gonorrhoeae
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Neisseria gonorrhoeae
30.
Chromobacterium violaceum
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Chromobacterium violaceum is a Gram-negative, facultative anaerobic, non-sporing coccobacillus. It is motile with the help of a single flagellum which is located at the pole of the coccobacillus, usually, there are one or two more lateral flagella as well. It is part of the flora of water and soil of tropical and sub-tropical regions of the world. It produces a natural antibiotic called violacein, which may be useful for the treatment of colon and it grows readily on nutrient agar, producing distinctive smooth low convex colonies with a dark violet metallic sheen. Some strains of the bacteria which do not produce this pigment have also been reported and it has the ability to break down tarballs. C. violaceum ferments glucose, trehalose, N-acetylglucosamine and gluconate but not L-arabinose, D-galactose, Bacterial isolates in many cases can show high level resistance to a range of antibiotics. C. violaceum rarely infects humans, but when it does it causes skin lesions, sepsis, the first reported case of chromobacterium violaceum infection in humans in literature is from Malaysia in 1927. Only 150 cases have reported in literature since then. To date, cases have reported from Argentina, Australia, Brazil, Cuba, India, Japan, Nigeria, Singapore, Sri Lanka, Taiwan, United States. The commonest mode of entry of the bacteria into the body is through the skin coming in contact with soil or water containing the bacteria. Other reported pathologies include chronic granulomatosis, osteomyelitis, cellulitis, diarrhoea, septic spondylitis, conjunctivitis, periorbital, care must be taken because Burkholderia pseudomallei is commonly misidentified as C. violaceum by many common identification methods. The two are distinguished because B. pseudomallei produces large wrinkled colonies, whereas C. violaceum produces a distinctive violet pigment. C. violaceum produces a number of antibiotics, Aztreonam is a monobactam antibiotic that is active against gram-negative aerobic bacteria including Pseudomonas aeruginosa. Violacein is active against amoebae and trypanosomes, Aerocyanidine is active against Gram-positive organisms and it has been described as a cause of infection in gibbons. Infection caused by C. violaceum is rare, therefore there are no clinical trials evaluating different treatments, antibiotics that have been used to successfully treat C. violaceum include pefloxacin, ciprofloxacin, amikacin, and co-trimoxazole. Other antibiotics that appear to be effective in vitro include chloramphenicol, for theoretical reasons, infection would not be expected to respond to penicillins, cephalosporins, or aztreonam, although carbapenems like meropenem or imipenem may possibly work. Though the bacteria is reported to be resistant to first generation cephalosporins, the complete genome was sequenced and the results were published in 2003. C. violaceum type strain ATCC12472 was found to have 4,751,080 base pairs with a G + C content of 64. 83% and 4,431 ORFs, type strain of Chromobacterium violaceum at BacDive - the Bacterial Diversity Metadatabase
Chromobacterium violaceum
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Chromobacterium violaceum
31.
Burkholderiales
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The Burkholderiales are an order of Proteobacteria. Like all Proteobacteria, they are Gram-negative and they include several pathogenic bacteria, including species of Burkholderia, Bordetella, and Ralstonia. They also include Oxalobacter and related genera, which are unusual in using oxalic acid as their source of carbon, Burkholderiales J. P. Euzéby, List of Prokaryotic names with Standing in Nomenclature
Burkholderiales
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Burkholderiales
32.
Burkholderia pseudomallei
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Burkholderia pseudomallei is a Gram-negative, bipolar, aerobic, motile rod-shaped bacterium. It is a soil-dwelling bacterium endemic in tropical and subtropical regions worldwide, particularly in Thailand and it infects humans and animals and causes the disease melioidosis. It is also capable of infecting plants, B. pseudomallei measures 2–5 μm in length and 0. 4–0.8 μm in diameter and is capable of self-propulsion using flagella. The bacteria can grow in a number of artificial nutrient environments, especially betaine-, in vitro, optimal proliferation temperature is reported around 40 °C in neutral or slightly acidic environments. The majority of strains are capable of fermentation of sugars without gas formation, bacteria produce both exo- and endotoxins. The role of the toxins identified in the process of melioidosis symptom development has not been fully elucidated, B. pseudomallei is not fastidious and grows on a large variety of culture media. Ashdowns medium may be used for selective isolation, cultures typically become positive in 24 to 48 hours. Colonies are wrinkled, have an appearance, and possess an earthy odour. On Gram staining, the organism is a Gram-negative rod with a safety pin appearance. On sensitivity testing, the organism appears highly resistant and that again differentiates it from B. mallei, for environmental specimens only, differentiation from the nonpathogenic B. thailandensis using an arabinose test is necessary. The laboratory identification of B. pseudomallei has been described in the literature, some suggest the Wayson stain is useful for this purpose, but this has been shown not to be the case. Laboratory identification of B. pseudomallei can be difficult, especially in Western countries where it is rarely seen, the large, wrinkled colonies look like environmental contaminants, so are often discarded as being of no clinical significance. Colony morphology is variable and a single strain may display multiple colony types. The organism grows more slowly than other bacteria that may be present in clinical specimens, nonsterile specimens should, therefore, be cultured in selective media. For heavily contaminated samples, such as faeces, a version of Ashdowns that includes norfloxacin, amoxicillin. In blood culture, the BacT/ALERT MB system by bioMérieux has been shown to have superior yields compared to conventional blood culture media. Again, because the disease is seen in Western countries. The pattern of resistance to antimicrobials is distinctive, and helps to differentiate the organism from P. aeruginosa, molecular methods of diagnosis are possible, but not routinely available for clinical diagnosis
Burkholderia pseudomallei
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Burkholderia pseudomallei
33.
Burkholderia mallei
–
It is closely related to B. pseudomallei, and by multilocus sequence typing it is a subspecies of B. pseudomallei. B. mallei evolved from B. pseudomallei by selective reduction, wilhelm Schütz and Friedrich Löffler first isolated B. mallei in 1882. It was isolated from a liver and spleen of a horse. He further refined his observations with the pathogen in 1886, most organisms within the Burkholderiaceae live in soil, however, B. mallei does not. Because B. mallei is an obligate mammalian pathogen, it must infect a host mammal to live, B. mallei is very closely related to B. pseudomallei, being 99% identical in conserved genes when compared to B. pseudomallei. B. malllei has about 1.4 Mb less DNA than B. pseudomallei, B. mallei may have actually evolved from a strain of B. pseudomallei after the latter had infected an animal. The bacterium would have lost the genes that were not necessary for living in an animal host and this suggestion has found support from studies that compare strains of B. mallei to B. pseudomallei and indicate that their two respective genomes are very similar. The genes that allowed the bacterium to survive in an environment, like genes that gave B. mallei the capacity to protect against bactericidals, antibiotics. Thus, the reason that B. mallei is not found outside of a host is because it lacks the necessary for survival in the soil. Genome comparisons also seem to indicate that the B. mallei is still evolving and adapting to an intracellular lifestyle, the genome of B. mallei was sequenced in the United States by The Institute of Genomic Research. The size of the genome is smaller than that of B. pseudomallei, the B. mallei sequence revealed a chromosome of 3.5 mega base pairs and a 2.3 Mb megaplasmid”. Many insertion sequences and phase-variable genes were also found, the genome for B. mallei is made up of two circular chromosomes. Chromosome 1 is where genes relating to metabolism, capsule formation, B. mallei has a polysaccharide capsule which indicates its potential as a pathogen. Chromosome 2 is where most of the information regarding secretion systems, multilocus sequence typing has revealed that B. mallei most likely evolved from a B. pseudomallei clone reduction. About 1000 B. pseudomellei genes are absent or varying in the B. mallei genome, B. mallei’s genome also has a large amount of insertion sequences. B. mallei was first called Bacillus mallei and was in the genus Pseudomonas until the early 1990s and it has also been referred to as farcy. It is now part of the genus Burkholderia, no standardized system exists for differentiating between B. mallei and B. pseudomallei. Comparing the DNA of B. mallei and B. pseudomallei must be done at the 23S rDNA level, however, both B. mallei and B. pseudomallei can be cultured in a laboratory, nutrient agar can be used to grow the bacteria
Burkholderia mallei
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Burkholderia mallei
34.
Burkholderia cepacia complex
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B. cepacia is an opportunistic human pathogen that most often causes pneumonia in immunocompromised individuals with underlying lung disease. Patients with sickle-cell haemoglobinopathies are also at risk, the species also attacks young onion and tobacco plants, as well as displaying a remarkable ability to digest oil. BCC organisms are found in water and soil and can survive for prolonged periods in moist environments. They show a relatively poor virulence, virulence factors include adherence to plastic surfaces and production of several enzymes such as elastase and gelatinase. Also relevant might be the ability to survive to nonoxidative killing by neutrophils, person-to-person spread has been documented, as a result, many hospitals, clinics, and camps have enacted strict isolation precautions for those infected with BCC. Infected individuals are treated in a separate area from uninfected patients to limit spread, since BCC infection can lead to a rapid decline in lung function. Diagnosis of BCC involves culturing the bacteria from clinical specimens, such as sputum or blood, BCC organisms are naturally resistant to many common antibiotics, including aminoglycosides and polymyxin B. and this fact is exploited in the identification of the organism. It also contains phenol red pH indicator which turns pink when it reacts with alkaline byproducts generated by the bacteria when it grows, alternatively, oxidation-fermentation polymyxin-bacitracin-lactose agar can be used. Treatment typically includes multiple antibiotics and may include ceftazidime, doxycycline, piperacillin, meropenem, chloramphenicol, B. cepacia has a large genome, containing twice the amount of genetic material as E. coli. Contamination control Barlasov J, Sutton S, Jakober R. Recovery of Stressed Burkholderia cepacia Complex Organisms, UMR, Burkholderia cepacia CFF, Research Pathema-Burkholderia Resource Loutet SA, Valvano MA. A decade of Burkholderia cenocepacia virulence determinant research, type strain of Burkholderia cepacia complex at BacDive - the Bacterial Diversity Metadatabase
Burkholderia cepacia complex
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Burkholderia cepacia complex
35.
Bordetella pertussis
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Bordetella pertussis is a Gram-negative, aerobic, pathogenic, encapsulated coccobacillus of the genus Bordetella, and the causative agent of pertussis or whooping cough. Unlike B. bronchiseptica, B. pertussis is not motile and its virulence factors include pertussis toxin, filamentous hæmagglutinin, pertactin, fimbria, and tracheal cytotoxin. The bacterium is spread by airborne droplets, its period is to human whooping cough in average 9–10 days. Humans are the only known reservoir for B. pertussis, the complete B. pertussis genome of 4,086,186 base pairs was published in 2003. Pertussis is an infection of the respiratory system characterized by a sound when the person breathes in. In the US, it killed between 10,000 and 20,000 people per year before a vaccine was available, vaccination has transformed this, between 1985 and 1988, fewer than 100 children died from pertussis. Worldwide in 2000, according to the WHO, around 39 million people were infected annually, a graph is available showing the dramatic effect of introducing vaccination in England. B. pertussis infects its host by colonizing lung epithelial cells, the bacterium contains a surface protein, filamentous haemagglutinin adhesin, which binds to the sulfatides found on cilia of epithelial cells. Once anchored, the bacterium produces tracheal cytotoxin, which stops the cilia from beating and this prevents the cilia from clearing debris from the lungs, so the body responds by sending the host into a coughing fit. These coughs expel some bacteria into the air, which are free to infect other hosts, B. pertussis has the ability to inhibit the function of the hosts immune system. The toxin, known as pertussis toxin, inhibits G protein coupling that regulates an adenylate cyclase-mediated conversion of ATP to cyclic AMP. The end result is phagocytes convert too much ATP to cyclic AMP, which can cause disturbances in cellular signaling mechanisms and this is unique in that many bacterial infections illustrate neutrophil-predominance instead. The infection occurs mostly in children under the age of one when they are unimmunized, or children with faded immunity, the signs and symptoms are similar to a common cold, runny nose, sneezing, mild cough, and low-grade fever. The patient becomes most contagious during the stage of infection. It may become airborne when the person coughs, sneezes, or laughs, pertussis vaccine is part of the diphtheria, tetanus, and acellular pertussis immunization. The paroxysmal cough precedes a crowing inspiratory sound characteristic of pertussis, after a spell, the patient might make a “whooping” sound when breathing in, or may vomit. Adults have milder symptoms, such as prolonged coughing without the “whoop”, infants less than six months also may not have the typical whoop. A coughing spell may last a minute or more, producing cyanosis, apnoea, however, when not in a coughing fit, the patient does not experience trouble breathing
Bordetella pertussis
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Bordetella pertussis
36.
Gammaproteobacteria
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Gammaproteobacteria are a class of several medically, ecologically, and scientifically important groups of bacteria. An exceeding number of important pathogens belong to this class, like all Proteobacteria, the Gammaproteobacteria are Gram-negative. The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae, a number of important pathogens belong to this class, e. g. Salmonella spp. Yersinia pestis, Vibrio cholerae, Pseudomonas aeruginosa, and Escherichia coli, important plant pathogens such as Xanthomonas axonopodis pv. citri and Pseudomonas syringae pv. actinidiae are also Gammaproteobacteria. Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, some Gammaproteobacteria are methane oxidizers, and many are symbiotic with geothermic ocean vent-dwelling animals. Due to a genus, Acidithiobacillus, the Gammaproteobacteria class is paraphyletic to Betaproteobacteria. A number of bacteria have been described as members of Gammaproteobacteria, Betaproteobacteria Proteobacteria Gammaproteobacteria at the US National Library of Medicine Medical Subject Headings
Gammaproteobacteria
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Gammaproteobacteria
37.
Enterobacteriaceae
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Other disease-causing bacteria in this family include Proteus, Enterobacter, Serratia, and Citrobacter. This family is the representative in the order Enterobacteriales of the class Gammaproteobacteria in the phylum Proteobacteria. Members of the Enterobacteriaceae can be referred to as enterobacteria or enteric bacteria. In fact, the etymology of the family is enterobacterium with the suffix to designate a family —not after the genus Enterobacter —and the type genus is Escherichia, members of the Enterobacteriaceae are rod-shaped, and are typically 1–5 μm in length. They appear as small colonies on blood agar. Like other proteobacteria, enterobacteria have Gram-negative stains, and they are anaerobes, fermenting sugars to produce lactic acid. Most also reduce nitrate to nitrite, although exceptions exist, unlike most similar bacteria, enterobacteria generally lack cytochrome C oxidase, although there are exceptions. Most have many flagella used to move about, but a few genera are nonmotile, Escherichia coli is one of the most important model organisms, and its genetics and biochemistry have been closely studied. Most members of Enterobacteriaceae have peritrichous, type I fimbriae involved in the adhesion of the cells to their hosts. Endotoxins reside in the wall and are released when the cell dies. Some members of the Enterobacteriaceae produce endotoxins that, when released into the following cell lysis. The most severe form of this is known as endotoxic shock, to identify different genera of Enterobacteriaceae, a microbiologist may run a series of tests in the lab. The methyl red tests for acid endproducts, the Voges Proskauer tests for the production of acetylmethylcarbinol. Catalase test on nutrient agar tests for the production of catalase enzyme, oxidase test on nutrient agar tests for the production of the enzyme oxidase, which reacts with an aromatic amine to produce a purple color. Nutrient gelatin tests to detect activity of the enzyme gelatinase, in a clinical setting, three species make up 80 to 95% of all isolates identified. These are Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis, for instance, some Klebsiella pneumoniae strains are carbapenem resistant. E. Bensons microbiological applications, laboratory manual in general microbiology
Enterobacteriaceae
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Enterobacteriaceae
38.
Oxidase test
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The oxidase test is a test used in microbiology to determine if a bacterium produces certain cytochrome c oxidases. It uses disks impregnated with a reagent such as N, N, N′, N′-tetramethyl-p-phenylenediamine or N, N-dimethyl-p-phenylenediamine, the reagent is a dark-blue to maroon color when oxidized, and colorless when reduced. Oxidase-positive bacteria possess cytochrome oxidase or indophenol oxidase and these both catalyze the transport of electrons from donor compounds to electron acceptors. The test reagent, TMPD dihydrochloride acts as an electron donor for the enzyme oxidase. The oxidized reagent forms the colored compound indophenol blue, the cytochrome system is usually only present in aerobic organisms that are capable of using oxygen as the terminal electron acceptor. The end-product of this metabolism is either water or hydrogen peroxide, strains may be either oxidase-positive or oxidase-negative. OX+ normally means the bacterium contains cytochrome c oxidase and can use oxygen for energy production by converting O2 to H2O2 or H2O with an electron transfer chain. The Pseudomonadaceae are typically OX+ The Gram-negative diplococci Neisseria and Moraxella are oxidase-positive, many Gram-negative, spiral curved rods are also oxidase-positive, which includes Helicobacter pylori, Vibrio cholerae, and Campylobacter jejuni. Wet each disk with about four inoculating loops of deionized water, use a loop to aseptically transfer a large mass of pure bacteria to the disk. Observe the disk for up to three minutes, if the area of inoculation turns dark-blue to maroon to almost black, then the result is positive. If a color change does not occur within three minutes, the result is negative, in alternative manner, live bacteria cultivated on trypticase soy agar plates may be prepared using sterile technique with a single-line streak inoculation. The inoculated plates are incubated at 37 °C for 24–48 hours to establish colonies, fresh bacterial preparations should be used. After colonies have grown on the medium, 2-3 drops of the reagent DMPD are added to the surface of each organism to be tested, a positive test will result in a color change violet to purple, within 10–30 seconds. A negative test will result in a light-pink or absence of coloration, Oxidase test video Oxidase Test Procedure
Oxidase test
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DMPD
39.
MacConkey agar
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MacConkey agar is a selective and differential culture medium for bacteria designed to selectively isolate Gram-negative and enteric bacilli and differentiate them based on lactose fermentation. The crystal violet and bile salts inhibit the growth of organisms which allows for the selection and isolation of gram-negative bacteria. Enteric bacteria that have the ability to ferment lactose can be detected using the carbohydrate lactose, and it contains bile salts, crystal violet dye, neutral red dye. If the spreading or swarming of Proteus species is not required, crystal violet at a concentration of 0. 0001% is included when needing to check if Gram-positive bacteria are inhibited. MacConkey with sorbitol is used to isolate E. coli O157, the medium was developed by Alfred Theodore MacConkey while working as a bacteriologist for the Royal Commission on Sewage Disposal. Using neutral red pH indicator, the agar distinguishes those Gram-negative bacteria that can ferment the sugar lactose from those that cannot fermentation and this medium is also known as an indicator medium and a low selective medium. Presence of bile salts inhibits swarming by Proteus species, the bile salts precipitate in the immediate neighbourhood of the colony, causing the medium surrounding the colony to become hazy. Non-Lactose fermenting bacteria such as Salmonella, Proteus species, Yersinia, Pseudomonas aeruginosa and Shigella cannot utilize lactose and this forms ammonia, which raises the pH of the agar, and leads to the formation of white/colorless colonies on the petri plate. Some organisms ferment lactose slowly or weakly, and are put in their own category. Some organisms, especially Klebsiella and Enterobacter, produce mucoid colonies which appear very moist and this phenomenon happens because the organism is producing a capsule, which is predominantly made from the lactose sugar in the agar
MacConkey agar
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A MacConkey agar plate with an active bacterial culture.
MacConkey agar
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MacConkey agar with LF and non-LF colonies
40.
Klebsiella pneumoniae
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Klebsiella pneumoniae is a Gram-negative, nonmotile, encapsulated, lactose-fermenting, facultative anaerobic, rod-shaped bacterium. It appears as a mucoid lactose fermenter on MacConkey agar, although found in the normal flora of the mouth, skin, and intestines, it can cause destructive changes to human and animal lungs if aspirated, specifically to the alveoli resulting in bloody sputum. In the clinical setting, it is the most significant member of the Klebsiella genus of the Enterobacteriaceae, K. oxytoca and K. rhinoscleromatis have also been demonstrated in human clinical specimens. In recent years, Klebsiella species have become important pathogens in nosocomial infections and it naturally occurs in the soil, and about 30% of strains can fix nitrogen in anaerobic conditions. Members of the Klebsiella genus typically express two types of antigens on their cell surfaces, the first, O antigen, is a component of the lipopolysaccharide, of which 9 varieties exist. The second is K antigen, a polysaccharide with more than 80 varieties. Both contribute to pathogenicity and form the basis for serogrouping and it is closely related to K. oxytoca from which it is distinguished by being indole-negative and by its ability to grow on melezitose but not 3-hydroxybutyrate. The genus Klebsiella was named after the German bacteriologist Edwin Klebs, as a general rule, Klebsiella infections are seen mostly in people with a weakened immune system. Most often, illness affects middle-aged and older men with debilitating diseases, many of these infections are obtained when a person is in the hospital for some other reason. Feces are the most significant source of patient infection, followed by contact with contaminated instruments, the most common condition caused by Klebsiella bacteria outside the hospital is pneumonia, typically in the form of bronchopneumonia and also bronchitis. These patients have an tendency to develop lung abscess, cavitation, empyema. It has a rate around 50%, even with antimicrobial therapy. The mortality rate can be nearly 100% for people with alcoholism, in addition to pneumonia, Klebsiella can also cause infections in the urinary tract, lower biliary tract, and surgical wound sites. Also, the use of antibiotics can be a factor that increases the risk of infection with Klebsiella bacteria. Sepsis and septic shock can follow entry of the bacteria into the blood, research conducted at Kings College, London has implicated molecular mimicry between HLA-B27 and two Klebsiella surface molecules as the cause of ankylosing spondylitis. Klebsiella ranks second to E. coli for urinary infections in older people. It is also an opportunistic pathogen for patients with pulmonary disease, enteric pathogenicity, nasal mucosa atrophy. New antibiotic-resistant strains of K. pneumoniae are appearing, Klebsiella organisms are often resistant to multiple antibiotics
Klebsiella pneumoniae
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Klebsiella pneumoniae
41.
Escherichia coli
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Escherichia coli is a gram-negative, facultatively anaerobic, rod-shaped, coliform bacterium of the genus Escherichia that is commonly found in the lower intestine of warm-blooded organisms. Most E. coli strains are harmless, but some serotypes can cause food poisoning in their hosts. The harmless strains are part of the flora of the gut, and can benefit their hosts by producing vitamin K2. E. coli is expelled into the environment within fecal matter, the bacterium grows massively in fresh fecal matter under aerobic conditions for 3 days, but its numbers decline slowly afterwards. E. coli and other facultative anaerobes constitute about 0. 1% of gut flora, cells are able to survive outside the body for a limited amount of time, which makes them potential indicator organisms to test environmental samples for fecal contamination. A growing body of research, though, has examined environmentally persistent E. coli which can survive for extended periods outside of a host, the bacterium can be grown and cultured easily and inexpensively in a laboratory setting, and has been intensively investigated for over 60 years. E. coli is a chemoheterotroph whose chemically defined medium must include a source of carbon, under favorable conditions, it takes only 20 minutes to reproduce. E. coli is a Gram-negative, facultative anaerobic and nonsporulating bacterium, cells are typically rod-shaped, and are about 2.0 μm long and 0. 25–1.0 μm in diameter, with a cell volume of 0. 6–0.7 μm3. E. coli stains Gram-negative because its cell wall is composed of a peptidoglycan layer. During the staining process, E. coli picks up the color of the counterstain safranin, the outer membrane surrounding the cell wall provides a barrier to certain antibiotics such that E. coli is not damaged by penicillin. Strains that possess flagella are motile, the flagella have a peritrichous arrangement. E. coli can live on a variety of substrates and uses mixed-acid fermentation in anaerobic conditions, producing lactate, succinate, ethanol, acetate. Optimum growth of E. coli occurs at 37 °C, and it uses oxygen when it is present and available. It can, however, continue to grow in the absence of oxygen using fermentation or anaerobic respiration, the ability to continue growing in the absence of oxygen is an advantage to bacteria because their survival is increased in environments where water predominates. The bacterial cell cycle is divided into three stages, the B period occurs between the completion of cell division and the beginning of DNA replication. The C period encompasses the time it takes to replicate the chromosomal DNA, the D period refers to the stage between the conclusion of DNA replication and the end of cell division. The doubling rate of E. coli is higher when more nutrients are available, However, the length of the C and D periods do not change, even when the doubling time becomes less than the sum of the C and D periods. At the fastest growth rates, replication begins before the round of replication has completed, resulting in multiple replication forks along the DNA
Escherichia coli
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Escherichia coli
42.
Enterobacter cloacae
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Enterobacter cloacae is a clinically significant Gram-negative, facultatively-anaerobic, rod-shaped bacterium. In microbiology labs, E. cloacae is frequently grown at 30 °C on nutrient agar or broth or at 35 °C in tryptic soy broth and it is a rod-shaped, Gram-negative bacterium, is facultatively anaerobic, and bears peritrichous flagella. Enterobacter cloacae has been used in a method for the biodegradation of explosives. E. cloacae is considered a biosafety level 1 organism in the United States, a draft genome sequence of Enterobacter cloacae subsp. The bacteria used in the study were isolated from giant panda feces, Enterobacter cloacae is a member of the normal gut flora of many humans and is not usually a primary pathogen. It is sometimes associated with urinary tract and respiratory tract infections, treatment with cefepime and gentamicin has been reported. E. cloacae in 1960, by which it is known today. E. cloacae is ubiquitous in terrestrial and aquatic environments and these strains occur as commensal microflora in the intestinal tracts of humans and animals and play an important role as pathogens in plants and insects. This diversity of habitats is mirrored by the variety of the nomenspecies E. cloacae. The skin and the GI tract are the most common sites through which E. cloacae can be contracted, E. cloacae tends to contaminate various medical, intravenous and other hospital devices. Nosocomial outbreaks have also associated with colonization of certain surgical equipment. Another potential reservoir for nosocomial bacteremia is the solution used to irrigate certain intravascular devices continually. This fluid had been implicated as a reservoir for outbreaks of device-associated bacteremia in several instances, in recent years, E. cloacae has emerged as one of the most commonly found nosocomial pathogen in neonatal units, with several outbreaks of infection being reported. This microorganism may be transmitted to neonates through contaminated intravenous fluids, total parenteral nutrition solutions, many single-clone outbreaks, probably caused by cross-transmission via healthcare workers, have been described, suggesting that inpatients can also act as a reservoir. The type strains of the species are E. cloacae ATCC49162 and 13047 and this latter strain is the first complete genome sequence of the E. cloacae species and the type strain is E. cloacae subsp. Cloacae ATCC13047 genome contains a circular chromosome of 5,314,588 bp. The other genomes of E. cloacae that have been sequenced are deposited in GenBank under accession numbers CP002272, CP002886, FP929040, E. E. asburiae sp. nov. was described in 1986 based on the enteric group 17. This group was defined in 1978 as a group of biochemically similar strains isolated from different human specimens, before the designation of enteric group 17, these strains had been reported as unidentified or atypical Citrobacter or Enterobacter strains
Enterobacter cloacae
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Enterobacter cloacae
43.
Serratia marcescens
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Serratia marcescens is a species of rod-shaped gram-negative bacteria in the family Enterobacteriaceae. It is commonly found in the respiratory and urinary tracts of hospitalized adults, due to its abundant presence in the environment, and its preference for damp conditions, S. Once established, complete eradication of the organism is often difficult, rinsing and drying surfaces after use can also prevent the establishment of the bacterium by removing its food source and making the environment less hospitable. S. marcescens may also be found in such as dirt, supposedly sterile places. Due to this, and because S. marcescens produces a reddish-orange tripyrrole pigment called prodigiosin, the biochemical pathway for the production of prodigiosin by S. marcescens is unknown except for the final two steps. In these steps, a monopyrrole and a bipyrrole undergo a reaction by way of an enzyme to form prodigiosin. S. marcescens is an organism and can grow in temperatures ranging from 5–40 °C. S. marcescens also exhibits tryptophan and citrate degradation, one of the end products of tryptophan degradation is pyruvic acid, which is then incorporated into different metabolic processes of S. marcescens. A final product of citrate degradation is carbon, thus, S. marcescens can rely on citrate as a carbon source. In identifying the organism, one may perform a methyl red test. S. marcescens results in a negative test, another determination of S. marcescens is its capability to produce lactic acid by oxidative and fermentative metabolism. Therefore, it is said that S. marcescens is lactic acid O/F+ and it is also a rare cause of endocarditis and osteomyelitis, pneumonia, and meningitis. In elkhorn coral, S. marcescens is the cause of the known as white pox disease. In silkworms, S. marcescens can also cause a lethal disease, in research laboratories employing Drosophila fruit flies, infection of them with S. marcescens is common. It manifests as a pink discoloration or plaque in or on larvae, pupae, or the usually starch, a rare clinical form of gastroenteritis occurring in early infancy caused by infection with S. marcescens. The red color of the diaper can be mistaken for hematuria which may cause unnecessary investigations by the physicians, S. marcescens causes cucurbit yellow vine disease, leading to sometimes serious losses in melon fields. Professor Jim Burritt and his students at the University of Wisconsin-Stout have discovered a new strain of S. marcescens in bee blood from hives decimated by winterkill and his research findings have been published and the new strain was named sicaria, which means assassin in Latin. The professor states that S. marcescens sicaria may contribute to the failure of honey bee colonies
Serratia marcescens
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Serratia marcescens
Serratia marcescens
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The antibiogram of S. marcescens on
Mueller-Hinton agar.
Serratia marcescens
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"Bloody bread": S. marcescens growing on bread
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Salmonella enterica
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Salmonella enterica is a rod-shaped, flagellated, facultative anaerobic, Gram-negative bacterium and a member of the genus Salmonella. A number of its serovars are serious human pathogens, raw chicken eggs and goose eggs can harbor S. enterica, initially in the egg whites, although most eggs are not infected. As the egg ages at room temperature, the yolk membrane begins to break down, refrigeration and freezing do not kill all the bacteria, but substantially slow or halt their growth. Pasteurizing and food irradiation are used to kill Salmonella for commercially produced foodstuffs containing raw eggs such as ice cream, foods prepared in the home from raw eggs such as mayonnaise, cakes, and cookies can spread salmonella if not properly cooked before consumption. Secreted proteins are of importance for the pathogenesis of infectious diseases caused by Salmonella enterica. A remarkable large number of fimbrial and non-fimbrial adhesins are present in Salmonella, secreted proteins are also involved in host cell invasion and intracellular proliferation, two hallmarks of Salmonella pathogenesis. Small non-protein coding RNAs are able to perform specific functions without being translated into proteins,97 bacterial sRNAs from Salmonella Typhi were discovered by Chinni et al. Salmonella enterica has 7 subspecies, and each subspecies has associated serovars that differ by antigenic specificity, there are over 2500 serovars for S. enterica. Salmonella bongori was previously considered a subspecies of S. enterica, most of the human pathogenic Salmonella serovars belong to the S. enterica subsp. These serogroups include Salmonella Typhi, Salmonella Enteritidis, Salmonella Paratyphi, Salmonella Typhimurium, the serovars can be designated as written in the previous sentence, or as follows, S. enterica subsp. Type strain of Salmonella enterica at BacDive - the Bacterial Diversity Metadatabase
Salmonella enterica
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Salmonella enterica
45.
Shigella flexneri
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Shigella flexneri is a species of Gram-negative bacteria in the genus Shigella that can cause diarrhea in humans. Several different serogroups of Shigella are described, S. flexneri belongs to group B. S. flexneri infections can usually be treated with antibiotics, less severe cases are not usually treated because they become more resistant in the future. The species was named after the American physician Simon Flexner, the genus is named for Japanese physician Kiyoshi Shiga, S. flexneri contains a virulence plasmid that codes for three virulence factors, a type-3 secretion system, invasion plasmid antigen proteins, and IcsA. Upon infection, S. flexneri injects the host cell cytoplasm with ipa proteins using the T3SS—a needle-and-syringe-like apparatus common to many Gram-negative pathogens and these ipa proteins induce membrane ruffling by the host cell. Membrane ruffling creates membrane pockets which capture and engulf the bacteria and it dampens the inflammatory response during bacterial invasion by suppressing the TNF-α-receptor-associated factor 6 -mediated signalling pathway. Bacterial small RNAs play important roles in cellular processes. RnaG and RyhB sRNAs have been studied in S. flexneri. Ssr1 sRNA, which could play role in resistance to acidic stress, type strain of Shigella flexneri at BacDive - the Bacterial Diversity Metadatabase
Shigella flexneri
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Shigella flexneri
46.
Shigella boydii
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Shigella boydii is a Gram-negative bacterium of the genus Shigella. Like other members of the genus, S. boydii is a nonmotile, nonsporeforming, S. boydii is the most genetically divergent species of the Shigella genus. There are 19 known serotypes of Shigella boydii, S. boydii is restricted to the Indian subcontinent. The species is named after the American bacteriologist Mark Frederick Boyd, S. boydii strain BS512 has one chromosome and five plasmids. Shigella boydii Genome Project Page — by Entrez Shigella boydii, type strain of Shigella boydii at BacDive - the Bacterial Diversity Metadatabase
Shigella boydii
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Shigella boydii
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