Yersinia pestis is a gram-negative, rod-shaped coccobacillus bacteria, with no spores. It is a facultative anaerobic organism, it causes the disease plague, which takes three main forms: pneumonic and bubonic plagues. All three forms were responsible for a number of high-mortality epidemics throughout human history, including: the sixth century's Plague of Justinian; these plagues originated in China and were transmitted west via trade routes. Recent research indicates that the pathogen may have been the cause of what is described as the Neolithic Decline, when European populations declined significantly; this would push the date to much earlier and might be indicative of an origin in Europe rather than Eurasia. Y. pestis was discovered in 1894 by Alexandre Yersin, a Swiss/French physician and bacteriologist from the Pasteur Institute, during an epidemic of the plague in Hong Kong. Yersin was a member of the Pasteur school of thought. Kitasato Shibasaburō, a German-trained Japanese bacteriologist who practised Koch's methodology, was engaged at the time in finding the causative agent of the plague.
However, Yersin linked plague with Y. pestis. Named Pasteurella pestis in the past, the organism was renamed Yersinia pestis in 1944; every year, thousands of cases of the plague are still reported to the World Health Organization, although with proper treatment, the prognosis for victims is now much better. A five- to six-fold increase in cases occurred in Asia during the time of the Vietnam War due to the disruption of ecosystems and closer proximity between people and animals; the plague is now found in sub-Saharan Africa and Madagascar, areas which now account for over 95% of reported cases. The plague has a detrimental effect on nonhuman mammals. In the United States, mammals such as the black-tailed prairie dog and the endangered black-footed ferret are under threat. Y. pestis is a nonmotile, stick-shaped, facultative anaerobic bacterium with bipolar staining that produces an antiphagocytic slime layer. Similar to other Yersinia species, it tests negative for urease, lactose fermentation, indole.
The closest relative is the gastrointestinal pathogen Yersinia pseudotuberculosis, more distantly Yersinia enterocolitica. The complete genomic sequence is available for two of the three subspecies of Y. pestis: strain KIM, strain CO92. As of 2006, the genomic sequence of a strain of biovar Antiqua has been completed. Similar to the other pathogenic strains, signs exist of loss of function mutations; the chromosome of strain KIM is 4,600,755 base pairs long. Like Y. pseudotuberculosis and Y. enterocolitica, Y. pestis is host to the plasmid pCD1. It hosts two other plasmids, pPCP1 and pMT1 that are not carried by the other Yersinia species. PFra codes for a phospholipase D, important for the ability of Y. pestis to be transmitted by fleas. PPla codes for a protease, that activates plasmin in human hosts and is a important virulence factor for pneumonic plague. Together, these plasmids, a pathogenicity island called HPI, encode several proteins that cause the pathogenesis, for which Y. pestis is famous.
Among other things, these virulence factors are required for bacterial adhesion and injection of proteins into the host cell, invasion of bacteria in the host cell, acquisition and binding of iron harvested from red blood cells. Y. pestis is thought to be descended from Y. pseudotuberculosis, differing only in the presence of specific virulence plasmids. A comprehensive and comparative proteomics analysis of Y. pestis strain KIM was performed in 2006. The analysis focused on the transition to a growth condition mimicking growth in host cells. Numerous bacterial small noncoding RNAs have been identified to play regulatory functions; some can regulate the virulence genes. Some 63 novel putative sRNAs were identified through deep sequencing of the Y. pestis sRNA-ome. Among them was Yersinia-specific Ysr141. Ysr141 sRNA was shown to regulate the synthesis of the type III secretion system effector protein YopJ; the Yop-Ysc T3SS is a critical component of virulence for Yersinia species. Many novel sRNAs were identified from Y. pestis grown in vitro and in the infected lungs of mice suggesting they play role in bacterial physiology or pathogenesis.
Among them sR035 predicted to pair with SD region and transcription initiation site of a thermo-sensitive regulator ymoA, sR084 predicted to pair with fur, ferric uptake regulator. Intergenic RNA thermometer In the urban and sylvatic cycles of Y. pestis, most of the spreading occurs between rodents and fleas. In the sylvatic cycle, the rodent is wild, but in the urban cycle, the rodent is the brown rat. In addition, Y. pestis can spread from the urban environment and back. Transmission to humans is through the bite of infected fleas. If the disease has progressed to the pneumonic form, humans can spread the bacterium to others by coughing and sneezing. Several species of rodents serve as the main reservoir for Y. pes
Rickettsia rickettsii is a gram-negative, coccobacillus bacterium, around 0.8 to 2.0 micrometers long. R. rickettsi is the causative agent of Rocky Mountain spotted fever. R. rickettsii is one of the most pathogenic Rickettsia strains. It affects small portions of the Eastern 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. At this time, the trademark rash now began to emerge in the western Montana area, with an 80-90% mortality rate, his research entailed interviewing victims of the disease and collecting and studying infected animals. He was known to inject himself with pathogens to measure their effects, his research was cut short after his death from an insect bite. S. Burt Wolbach is credited for the first detailed description of the pathogenic agent that causes R. rickettsii in 1919.
He recognized it as an intracellular bacterium, seen most 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 known as "hard bodied" ticks. Ticks are vectors and amplifiers of this disease. There are three known tick specifics that carry R. rickettsii. American dog tick Rocky Mountain Wood Tick Brown dog tick. Ticks can contract R. rickettsii by many means. First, an uninfected tick can become infected when feeding on the blood of an infected vertebrate host. Once a tick becomes infected with this pathogen, they are infected for life. Both the American dog tick and the Rocky Mountain wood tick serve as long-term reservoirs for Rickettsia rickettsii, in which the organism resides in the tick posterior diverticulae of the midgut, the small intestine and the ovaries. In addition, an infected male tick can transmit the organism to an uninfected female during mating. Once infected, the female tick can transmit the infection to her offspring, in a process known as transovarian passage.
Due to its confinement in the midgut and small intestine, Rickettsia rickettsii can be transmitted to mammals, including humans. 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. After getting bitten by an infected tick, R. rickettsiae is transmitted to the bloodstream by tick salivary secretions. R. Rickettsii has been found to distort the sex ratio of their hosts; this is done by eradicating males and undergoing pathogenesis, this is done via horizontal gene transfer. By eradicating male hosts, female host can pass the R. rickettsii gene to her offspring giving R. rickettsii bacteria yet another way to infect hosts.
By having multiple modes of transmission this ensures the persistence of R. rickettsii in a population. By having multiple modes of transmission this helps the disease adapt better to new environments and prevents it from becoming eradicated. R. rickettsii has evolved a number of strategical mechanisms or virulence factors that allow them to invade the host immune system and infect the host. Since R. rickettsii needs a moving vector to contract the disease to a viable host it is more that this pathogen has moderately low virulence levels. This idea is supported by the tradeoff hypothesis which suggests that virulence of a pathogen will evolve until the level of virulence balances out with the level of transmission to maximize the spread of the pathogen. R. rickettsii invades the endothelial cells. Endothelial cells are not phagocytic in nature. Since the bacteria can now induce phagocytosis the R. rickettsii gene can be replicated and further invade other cells in the hosts body. R. rickettsii is found on every continent excluding Antarctica.
The disease was first discovered in North America and since has been identified in every corner of the earth. The spread of R. rickettsii is due to the migration of humans and animals around the globe. However, R. rickettsii tends to thrive in warm damp places and this can be seen by contraction rates around the world. Environments are changing so the fluctuation of the disease is never constant in a population and this correlates to the evolution of R. rickettsii. The Centers for Disease Control and Prevention states that the diagnosis of Rocky Mountain Spotted Fever must be made based on the clinical signs and symptoms of the patient and later confirmed using specialized laboratory tests. However, the diagnosis of Rocky Mountain Spotted Fever is misdiagnosed due to its non-specific onset. If not treated properly the illness may become serious, leading to hospital
Proteobacteria is a major phylum of gram-negative bacteria. They include a wide variety of pathogens, such as Escherichia, Vibrio, Yersinia and many other notable genera. Others include many of the bacteria responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the "purple bacteria and their relatives"; because of the great diversity of forms found in this group, it was named after Proteus, a Greek god of the sea capable of assuming many different shapes and is not named after the Proteobacteria genus Proteus. Some Alphaproteobacteria can grow at low levels of nutrients and have unusual morphology such as stalks and buds. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants; the type order is the Caulobacterales. The Betaproteobacteria are metabolically diverse and contain chemolithoautotrophs and generalist heterotrophs; the type order is the Burkholderiales, comprising an enormous range of metabolic diversity, including opportunistic pathogens.
The Hydrogenophilalia are obligate include heterotrophs and autotrophs. The type order is the Hydrogenophilales; 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 Acidithiobacillia contain only sulfur and uranium-oxidising autotrophs. The type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp; the Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the anaerobic 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 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 Oligoflexia are filamentous aerobes. The type order is the Oligoflexales. All "Proteobacteria" are Gram-negative, with an outer membrane composed of lipopolysaccharides. Many move about using flagella; the latter include the myxobacteria, an order of bacteria that can aggregate to form multicellular fruiting bodies. A wide variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, chemolithoautotrophic, heterotrophic, but numerous exceptions occur. A variety of genera, which are not related to each other, convert energy from light through photosynthesis. "Proteobacteria" are associated with the imbalance of microbiota of the lower reproductive tract of women. These species are associated with inflammation. "Proteobacteria" are part of a healthy placental microbiome. The group is defined in terms of ribosomal RNA sequences; the "Proteobacteria" are divided into six classes with validly published names, referred to by the Greek letters alpha through epsilon and the Acidithiobacillia and Oligoflexia.
These were regarded as subclasses of the phylum, but they are now treated as classes. These classes are monophyletic; the genus Acidithiobacillus, part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013, was regarded as paraphyletic to the Betaproteobacteria according to multigenome alignment studies. In 2017, the Betaproteobacteria was subject to major revisions and the class Hydrogenophilalia was created to contain the order HydrogenophilalesProteobacterial classes with validly published names include some prominent genera: e.g.: Alphaproteobacteria: Brucella, Agrobacterium, Rickettsia, etc. Betaproteobacteria: Bordetella, Neisseria, etc. Gammaproteobacteria: Escherichia, Salmonella, Buchnera, Vibrio, etc. Deltaproteobacteria: Desulfovibrio, Bdellovibrio, etc. Epsilonproteobacteria: Helicobacter, Wolinella, etc. Oligoflexia: Oligoflexus. Acidithiobacillia: Acidithiobacillus thiooxidans, Thermithiobacillus tepidarius Hydrogenophilalia: Hydrogenophilus thermoluteolus, Tepidiphilus margaritifer Transformation, a process in which genetic material passes from bacterium to another, has been reported in at least 30 species of "Proteobacteria" distributed in the classes alpha, beta and epsilon.
The best-studied "Proteobacteria" with respect to natural genetic transformation are the medically important human pathogens Neisseria gonorrhoeae, Haemophilus influenzae and Helicobacter pylori. Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium and the integration of the donor sequence into the recipient genome. In pathogenic "Proteobacteria", transformation appears to serve as a DNA repair process that protects the pathogen's DNA from attack by their host's phagocytic defenses that employ oxidative free radicals. Proteobacteria information from Palaeos. Proteobacteria. – J. P. Euzéby: List of Prokaryotic names with Standing in Nomenclature
Yersinia enterocolitica is a Gram-negative bacillus-shaped bacterium, belonging to the family Enterobacteriaceae. It becomes nonmotile at normal human body temperature. Y. enterocolitica infection causes the disease yersiniosis, an animal-borne disease occurring in humans, as well as in a wide array of animals such as cattle, deer and birds. Many of these animals become carriers; the bacterium infects the host by sticking to its cells using trimeric autotransporter adhesins. The genus Yersinia includes 11 species: Y. pestis, Y. pseudotuberculosis, Y. enterocolitica, Y. frederiksenii, Y. intermedia, Y. kristensenii, Y. bercovieri, Y. mollaretii, Y. rohdei, Y. aldovae, Y. ruckeri. Among them, only Y. pestis, Y. pseudotuberculosis, certain strains of Y. enterocolitica are of pathogenic importance for humans and certain warm-blooded animals, whereas the other species are of environmental origin and may, at best, act as opportunists. However, Yersinia strains can be isolated from clinical materials, so they have to be identified at the species level.
Y. enterocolitica is a heterogeneous group of strains, which are traditionally classified by biotyping into six biogroups on the basis of phenotypic characteristics, by serotyping into more than 57 O serogroups, on the basis of their O surface antigen. Five of the six biogroups are regarded as pathogens. However, only a few of these serogroups have been associated with disease in either humans or animals. Strains that belong to serogroups O:3, O:5,27, O:8, O:9 are most isolated worldwide from human samples. However, the most important Y. enterocolitica serogroup in many European countries is serogroup O:3 followed by O:9, whereas the serogroup O:8 is detected in the United States. Y. enterocolitica is widespread in nature, occurring in reservoirs ranging from the intestinal tracts of numerous mammals, avian species, cold-blooded species, from terrestrial and aquatic niches. Most environmental isolates are avirulent. In addition, sheep, wild rodents, environmental water may be a reservoir of pathogenic Y. enterocolitica strains.
Human pathogenic strains are confined to the intestinal tract and lead to enteritis/diarrhea. The portal of entry is the gastrointestinal tract; the organism is acquired by insufficiently cooked pork or contaminated water, meat, or milk. Acute Y. enterocolitica infections lead to mild self-limiting enterocolitis or terminal ileitis and adenitis in humans. Symptoms may include watery or bloody diarrhea and fever, resembling appendicitis or salmonellosis or shigellosis. After oral uptake, Yersinia species invade Peyer's patches. From here they can disseminate further to mesenteric lymph nodes causing lymphadenopathy; this condition can be confused with appendicitis. In immunosuppressed individuals, they can disseminate from the gut to the liver and spleen and form abscesses; because Yersinia species are siderophilic bacteria, people with hereditary hemochromatosis are more susceptible to infection with Yersinia. In fact, the most common contaminant of stored blood is Y. enterocolitica. See yersiniosis for further details.
Yersiniosis is self-limiting and does not require treatment. For sepsis or severe focal infections if associated with immunosuppression, the recommended regimen includes doxycycline in combination with an aminoglycoside. Other antibiotics active against Y. enterocolitica include trimethoprim-sulfamethoxasole, fluoroquinolones and chloramphenicol. Y. enterocolitica is resistant to penicillin G, cefalotin due to beta-lactamase production. Y. enterocolitica infections are sometimes followed by chronic inflammatory diseases such as arthritis, erythema nodosum, reactive arthritis. This is most because of some immune-mediated mechanism. Y. Enterocolitica seems to be associated with autoimmune Graves-Basedow thyroiditis. Whilst indirect evidence exists, direct causative evidence is limited. Y. Enterocolitica is not a major cause of this disease but may contribute to the development of thyroid autoimmunity arising for other reasons in genetically susceptible individuals. Y. Enterocolitica infection has been suggested to be not the cause of autoimmune thyroid disease but rather an associated condition, with both sharing a common inherited susceptibility.
More the role for Y. enterocolitica has been disputed. Yersinia enterocolitica genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID "Yersinia enterocolitica". NCBI Taxonomy Browser. 630. Type strain of Yersinia enterocolitica subsp. Enterocolitica at BacDive - the Bacterial Diversity Metadatabase
Alphaproteobacteria is a class of bacteria in the phylum Proteobacteria. Its members are diverse and possess few commonalities, but share a common ancestor. Like all Proteobacteria, its members are gram-negative and some of its intracellular parasitic members lack peptidoglycan and are gram variable; the Alphaproteobacteria is a diverse taxon and comprises several phototrophic genera, several genera metabolising C1-compounds, symbionts of plants, endosymbionts of arthropods and intracellular pathogens. Moreover, the class includes the protomitochondrion, the bacterium, engulfed by the eukaryotic ancestor and gave rise to the mitochondria, which are organelles in eukaryotic cells. A species of technological interest is Rhizobium radiobacter: scientists use this species to transfer foreign DNA into plant genomes. Aerobic anoxygenic phototrophic bacteria, such as Pelagibacter ubique, are alphaproteobacteria that are a distributed and may constitute over 10% of the open ocean microbial community.
There is some disagreement on the phylogeny of the orders for the location of the Pelagibacterales, but overall there is some consensus. The discord stems from the large difference in gene content and the large difference in GC-richness between members of several orders. Pelagibacterales and Holosporales contain species with AT-rich genomes, it has been argued that it could be a case of convergent evolution that would result in an artefactual clustering. However, several studies disagree. Furthermore, it has been found that the GC-content of ribosomal RNA little reflects the GC-content of the genome. One example of this atypical decorrelation of ribosomal GC-content with phylogeny is that members of the Holosporales have a much higher ribosomal GC-content than members of the Pelagibacterales and Rickettsiales though they are more related to species with high genomic GC-contents than to members of the latter two orders; the Class Alphaproteobacteria is divided into three subclasses Magnetococcidae and Caulobacteridae.
The basal group is Magnetococcidae, composed by a large diversity of magnetotactic bacteria, but only one is described, Magnetococcus marinus. The Rickettsidae is composed of the intracellular Rickettsiales and the free-living Pelagibacterales; the Caulobacteridae is composed of the Holosporales, Sphingomonadales, Caulobacterales, Kordiimonadales and Sneathiellales. Comparative analyses of the sequenced genomes have led to discovery of many conserved insertion-deletions in distributed proteins and whole proteins that are distinctive characteristics of either all Alphaproteobacteria, or their different main orders and families; these molecular signatures provide novel means for the circumscription of these taxonomic groups and for identification/assignment of new species into these groups. Phylogenetic analyses and conserved indels in large numbers of other proteins provide evidence that Alphaproteobacteria have branched off than most other phyla and Classes of Bacteria except Betaproteobacteria and Gammaproteobacteria.
The accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature and National Center for Biotechnology Information and the phylogeny is based on 16S rRNA-based LTP release 106 by'The All-Species Living Tree' Project Notes:♠ Strains found at the National Center for Biotechnology Information but not listed in the List of Prokaryotic names with Standing in Nomenclature Although only a few studies have been reported on natural genetic transformation in the Alphaproteobacteria, this process has been described in Agrobacterium tumefaciens, Methylobacterium organophilum, Bradyrhizobium japonicum. Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium, the integration of the donor sequence into the recipient genome by homologous recombination. Alphaproteobacteria at the US National Library of Medicine Medical Subject Headings Bacterial Phylogeny Webpage: Alpha Proteobacteria
Chitterlings are a prepared food made from the small intestines of a pig, although the intestines of cattle and other animals are sometimes used. Chitterling is first documented in Middle English by the Oxford English Dictionary, in the form cheterling, c1400. Various other spellings and dialect forms were used; the primary form and derivation are uncertain. A 1743 English cookery book The Lady's Companion: or, An Infallible Guide to the Fair Sex contained a recipe for "Calf's Chitterlings", a bacon and offal sausage in a calf's intestine casing; the recipe explained the use of calf's, rather than the more usual pig's, intestines with the comment that " sort of... puddings must be made in summer, when hogs are killed". This recipe was repeated by the English cookery writer Hannah Glasse in her 1784 cookery book Art of Cookery. Linguist Paul Anthony Jones has written, "in the late 1500s a chitterling was an ornate type of neck ruff, so called because its frilled edge looked like the folds of a slaughtered animal's entrails".
As pigs are a common source of meat in many parts of the world, the dish known as chitterlings can be found in most pork-eating cultures. Chitterlings made from pig intestines are popular in many parts of Europe, are still eaten in the southern U. S. Chitterlings were common peasant food in medieval England, remained a staple of the diet of low-income families right up until the late 19th century and not uncommon into the mid 20th century. Thomas Hardy wrote of chitterlings in his novel Tess of the D'Urbervilles, when the father of a poor family, John Durbeyfield, talks of what he would like to eat: Tell'em at home that I should like for supper, – well, lamb's fry if they can get it, it illustrates. George Sturt, writing in 1919 details the food eaten by his farming family in Farnborough when he was a child: During the winter they had chance to weary of every form and kind of pig-meat: hog's puddings, chitterlings, salted spareribs -they knew all the varieties and welcomed any change. Mutton they never tasted: but sometimes they had a calf's head.
Chitterlings are the subject of a song by 1970s Scrumpy and Western comedy folk band, The Wurzels, who come from the southwest of England. Chitterlings, though much declined in popularity, are still enjoyed in the UK today. Kokoretsi, kukurec, or kokoreç, are prepared and stuffed grilled on a spit. In several countries such as Turkey, Albania, lamb intestines are used. In Turkish cuisine, the intestines are chopped and cooked with oregano and other spices. Gallinejas are a traditional dish in Madrid; the dish consists of sheep's small intestines and pancreas, fried in their own fat in such a manner that they form small spirals. The dish is served hot with French fries. Few establishments today serve gallinejas, as this is considered to be more of a speciality than a common dish, it is most served during festivals. Zarajo: A traditional dish from Cuenca is zarajo, braided sheep's intestines rolled on a vine branch and broiled, but sometimes fried, sometimes smoked served hot as an appetizer or tapa.
A similar dish from La Rioja is embuchados, from the province of Aragon, all made with sheep's intestines and served as tapas. Tricandilles are a traditional dish in Gironde, they are made of pig's small intestines, boiled in bouillon grilled on a fire of grapevine cane. This is considered an expensive delicacy. Andouillette is a type of sausage, found in Troyes, made predominantly of pig chitterlings. Andouille is another kind of French chitterlings sausage found in Brittany and Normandy. People in the Caribbean and Latin America eat chitterlings. Chinchulín or chunchule is the cow's small intestine used as a foodstuff. Other name variations from country to country are caldo avá, tripas or mondongo, chunchullo, chinchurria or chunchurria, tripa mishqui and tripa. In Mexico, tripas are considered a delicacy, they are popular served as a guisado in tacos. They are cleaned, boiled and fried until crispy, they are served with a spicy, tangy tomatillo-based salsa. In Guadalajara, along with the traditional preparation for tacos, they are prepared as a dish, served with a specialized sauce in a bowl and accompanied by a stack of tortillas, additional complementary sauces and salt.
Chunchullo Chitterlings are eaten as a dish in many East Asian cuisines. Both large and small intestine is eaten throughout China. Large intestine is called feichang "fat intestine" because it is fatty. Small intestine is called zhufenchang "pig powder intestine" because it contains a white, pasty or powdery substance; the character "zhu" or "pig" is added at the beginning to disambiguate. This is because, in Cantonese cuisine, there is a dish called chang fen which uses intestine-shaped noodles. Large intestine is chopped into rings and has a stronger odor than small intestine, it is added to stir-fry soups. It is slow-cooked or boiled and served as a standalone dish, it releases oil. Small intestine is chopped into tubes and may be boiled and served with a dipping sauce. Preparation techniques and ser
Rickettsia sibirica is a species of Rickettsia. This bacterium is the etiologic agent of North Asian tick typhus, known as Siberian tick typhus; the ticks that transmit it are various species of Dermacentor and Haemaphysalis