1.
Enteric bacteria
–
Gut flora is the complex community of microorganisms that live in the digestive tracts of humans and other animals, including insects. The gut metagenome is the aggregate of all the genomes of gut microbiota, the gut is one niche that human microbiota inhabit. In humans, the gut microbiota has the largest numbers of bacteria, the relationship between some gut flora and humans is not merely commensal, but rather a mutualistic relationship. Some human gut microorganisms benefit the host by fermenting dietary fiber into short-chain fatty acids, such as acid and butyric acid. Intestinal bacteria also play a role in synthesizing vitamin B and vitamin K as well as metabolizing bile acids, sterols, the composition of human gut flora changes over time, when the diet changes, and as overall health changes. The microbial composition of the gut flora varies across the digestive tract, in the stomach and small intestine, relatively few species of bacteria are generally present. The colon, in contrast, contains a densely-populated microbial ecosystem with up to 1012 cells per gram of intestinal content and these bacteria represent between 300 and 1000 different species. However, 99% of the come from about 30 or 40 species. As a consequence of their abundance in the intestine, bacteria also make up to 60% of the dry mass of feces, fungi, archaea, and viruses are also present in the gut flora, but less is known about their activities. Over 99% of the bacteria in the gut are anaerobes, but in the cecum and it is estimated that these gut flora have around a hundred times as many genes in total as there are in the human genome. Many species in the gut have not been studied outside of their hosts because most cannot be cultured, while there are a small number of core species of microbes shared by most individuals, populations of microbes can vary widely among different individuals. Within an individual, microbe populations stay fairly constant over time, even though some alterations may occur with changes in lifestyle, diet, the Human Microbiome Project has set out to better describe the microflora of the human gut and other body locations. The four dominant bacterial phyla in the gut are Firmicutes, Bacteroidetes, Actinobacteria. Most bacteria belong to the genera Bacteroides, Clostridium, Faecalibacterium, Eubacterium, Ruminococcus, Peptococcus, Peptostreptococcus, other genera, such as Escherichia and Lactobacillus, are present to a lesser extent. Species from the genus Bacteroides alone constitute about 30% of all bacteria in the gut, fungal genera that have been detected in the gut include Candida, Saccharomyces, Aspergillus, Penicillium, Rhodotorula, Trametes, Pleospora, Sclerotinia, Bullera, and Galactomyces, among others. Rhodotorula is most frequently found in individuals with inflammatory bowel disease while Candida is most frequently found in individuals with hepatitis B cirrhosis, archaea constitute another large class of gut flora which are important in the metabolism of the bacterial products of fermentation. An enterotype is a classification of living based on its bacteriological ecosystem in the human gut microbiome not dictated by age, gender, body weight. There are indications that long-term diet influences enterotype, three human enterotypes have been proposed, but these claims remain highly controversial
Enteric bacteria
–
Escherichia coli, one of the many species of
bacteria present in the human gut
Enteric bacteria
–
Candida albicans, a dimorphic fungus that grows as a yeast in the gut
2.
Taxonomy (biology)
–
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)
–
Title page of
Systema Naturae, Leiden, 1735
Taxonomy (biology)
–
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)
–
Type specimen for
Nepenthes smilesii, a tropical
pitcher plant.
3.
Bacteria
–
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
Bacteria
–
Had'n
Bacteria
Bacteria
–
A
biofilm of thermophilic bacteria in the outflow of
Mickey Hot Springs,
Oregon, approximately 20 mm thick.
Bacteria
–
Helicobacter pylori electron micrograph, showing multiple flagella on the cell surface
4.
Proteobacteria
–
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
5.
Gammaproteobacteria
–
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
–
Gammaproteobacteria
6.
Family (biology)
–
In biological classification, family is one of the eight major taxonomic ranks, it is classified between order and genus. A family may be divided into subfamilies, which are intermediate ranks above the rank of genus. In vernacular usage, a family may be named one of its common members, for example, walnuts and hickory trees belong to the family Juglandaceae. What does or does not belong to a family—or whether a family should be recognized at all—are proposed and determined by practicing taxonomists. There are no rules for describing or recognizing a family. Taxonomists often take different positions about descriptions of taxa, and there may be no broad consensus across the community for some time. Some described taxa are accepted broadly and quickly, but others only rarely, if at all, the naming of families is codified by various international codes. In zoological nomenclature, the names of animals end with the suffix -idae. The concept of rank at time was not yet settled, and in the preface to the Prodromus Magnol spoke of uniting his families into larger genera. Carolus Linnaeus used the word familia in his Philosophia botanica to denote groups of plants, trees, herbs, ferns, palms. He used this term only in the section of the book. In zoology, the family as an intermediate between order and genus was introduced by Pierre André Latreille in his Précis des caractères génériques des insectes. He used families in some but not in all his orders of insects, families can be used for evolutionary, palaeontological and generic studies because they are more stable than lower taxonomic levels such as genera and species
Family (biology)
–
The hierarchy of
biological classification 's eight major
taxonomic ranks. An
order contains one or more families. Intermediate minor rankings are not shown.
7.
Gram-negative bacteria
–
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 bacteria
–
Microscopic image of gram-negative
Pseudomonas aeruginosa bacteria (pink-red rods)
8.
Symbiosis
–
Symbiosis is any type of a close and long-term biological interaction between two different species, be it mutualistic, commensalistic, or parasitic. In 1879, Heinrich Anton de Bary defined it as the living together of unlike organisms, Symbiosis can be obligatory, which means that one or both of the symbionts entirely depend on each other for survival, or facultative when they can generally live independently. When one organism lives on another such as mistletoe, it is called ectosymbiosis, or endosymbiosis when one partner lives inside the tissues of another, as in Symbiodinium in corals. In 1877, Albert Bernhard Frank used the term symbiosis which previously had used to depict people living together in community to describe the mutualistic relationship in lichens. In 1879, the German mycologist Heinrich Anton de Bary defined it as the living together of unlike organisms, symbiotic relationships can be obligate, meaning that one or both of the symbionts entirely depend on each other for survival. For example, in lichens, which consist of fungal and photosynthetic symbionts, the algal or cyanobacterial symbionts in lichens, such as Trentepohlia, can generally live independently, and their symbiosis is, therefore, facultative. Endosymbiosis is any relationship in which one symbiont lives within the tissues of the other, either within the cells or extracellularly. Mutualism or interspecies reciprocal altruism is a relationship between individuals of different species where both individuals benefit, in general, only lifelong interactions involving close physical and biochemical contact can properly be considered symbiotic. Mutualistic relationships may be either obligate for both species, obligate for one but facultative for the other, or facultative for both, a large percentage of herbivores have mutualistic gut flora to help them digest plant matter, which is more difficult to digest than animal prey. This gut flora is made up of cellulose-digesting protozoans or bacteria living in the herbivores intestines, coral reefs are the result of mutualisms between coral organisms and various types of algae which live inside them. Most land plants and land ecosystems rely on mutualisms between the plants, which fix carbon from the air, and mycorrhyzal fungi, which help in extracting water, an example of mutual symbiosis is the relationship between the ocellaris clownfish that dwell among the tentacles of Ritteri sea anemones. The territorial fish protects the anemone from anemone-eating fish, and in turn the stinging tentacles of the anemone protect the clownfish from its predators, a special mucus on the clownfish protects it from the stinging tentacles. A further example is the fish, which sometimes lives together with a shrimp. The shrimp digs and cleans up a burrow in the sand in which both the shrimp and the fish live. The shrimp is almost blind, leaving it vulnerable to predators when outside its burrow, in case of danger the goby fish touches the shrimp with its tail to warn it. When that happens both the shrimp and goby fish quickly retreat into the burrow, different species of gobies also exhibit mutualistic behavior through cleaning up ectoparasites in other fish. Another non-obligate symbiosis is known from encrusting bryozoans and hermit crabs, the bryozoan colony develops a cirumrotatory growth and offers the crab a helicospiral-tubular extension of its living chamber that initially was situated within a gastropod shell. A spectacular examples of mutualism is between the siboglinid tube worms and symbiotic bacteria that live at hydrothermal vents and cold seeps
Symbiosis
Symbiosis
–
Alder tree root nodule
Symbiosis
–
Hermit crab, Calcinus laevimanus, with sea anemone.
Symbiosis
–
Bryoliths document a mutualistic symbiosis between a
hermit crab and encrusting
bryozoans;
Banc d'Arguin,
Mauritania
9.
Salmonella
–
Salmonella /ˌsælməˈnɛlə/ is a genus of rod-shaped gram-negative bacteria of the Enterobacteriaceae family. The two species of Salmonella are Salmonella enterica and Salmonella bongori, Salmonella enterica is the type species and is further divided into six subspecies that include over 2,500 serotypes. S. enterica subspecies are found worldwide in all warm-blooded animals, S. bongori is restricted to cold-blooded animals, particularly reptiles. Strains of Salmonella cause illnesses such as fever, paratyphoid fever. Salmonella species are nonspore-forming, predominantly motile enterobacteria with cell diameters between about 0.7 and 1.5 µm, lengths from 2 to 5 µm and they are chemotrophs, obtaining their energy from oxidation and reduction reactions using organic sources. They are also facultative anaerobes, capable of surviving with or without oxygen, the genus Salmonella is part of the family of Enterobacteriaceae. Its taxonomy has been revised and has the potential to confuse, the taxonomic group contains more than 2500 serovars, defined on the basis of the somatic O and flagellar H antigens. The full name of a serovar is given as, for example, enterica serovar Typhimurium, but can be abbreviated to Salmonella Typhimurium. Historically, salmonellae have been categorized as invasive or noninvasive based on host preference. Salmonella was first visualized in 1880 by Karl Eberth in the Peyers patches, four years later in 1884 Georg Theodor Gaffky was able to successfully grow the pathogen in pure culture. A year after that, medical research scientist Theobald Smith discovered what would be known as Salmonella enterica. At the time, Smith was working as a laboratory assistant in the Veterinary Division of the United States Department of Agriculture. The department was under the administration of Daniel Elmer Salmon, a veterinary pathologist, initially, Salmonella Choleraesuis was thought to be the causative agent of hog cholera, so Salmon and Smith named it Hog-cholerabacillus. The name Salmonella was not used until 1900, when Joseph Leon Lignières proposed that the discovered by Daniel Salmons group be called Salmonella in his honor. Most subspecies of Salmonella produce hydrogen sulfide, which can readily be detected by growing them on media containing ferrous sulfate, most isolates exist in two phases, a motile phase I and a nonmotile phase II. Cultures that are nonmotile upon primary culture may be switched to the motile phase using a Craigie tube or ditch plate, Salmonella can also be detected and subtyped using multiplex or real-time polymerase chain reactions from extracted Salmonella DNA. Mathematical models of Salmonella growth kinetics have been developed for chicken, pork, tomatoes, Salmonella reproduce asexually with a cell division interval of 40 minutes. The bacteria are not destroyed by freezing, but UV light and they perish after being heated to 55 °C for 90 min, or to 60 °C for 12 min
Salmonella
–
Salmonella
10.
Escherichia coli
–
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
–
Escherichia coli
11.
Yersinia pestis
–
Yersinia pestis is a Gram-negative, rod-shaped coccobacillus, a facultative anaerobic organism that can infect humans via the oriental rat flea. It causes the disease called bubonic plague. Human Y. pestis infection takes three forms, pneumonic, septicemic, and bubonic plagues. These plagues probably originated in China and were transmitted west via trade routes, 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 Kochs methodology, was also engaged at the time in finding the causative agent of the plague. However, Yersin actually 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, possibly due to the disruption of ecosystems, the plague also has a detrimental effect on non-human mammals. In the United States, mammals such as the prairie dog. Y. pestis is a non-motile, stick-shaped, facultative anaerobic bacterium with bipolar staining that produces an anti-phagocytic slime layer, similar to other Yersinia species, it tests negative for urease, lactose fermentation, and indole. The closest relative is the gastrointestinal pathogen Yersinia pseudotuberculosis, and more distantly Yersinia enterocolitica, the complete genomic sequence is available for two of the three subspecies of Y. pestis, strain KIM, and strain CO92. As of 2006, the sequence of a strain of biovar Antiqua has been recently completed. Similar to the pathogenic strains, there are signs 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. In addition, it hosts two other plasmids, pPCP1 and pMT1 that are not carried by the other Yersinia species. PFra codes for a phospholipase D that is important for the ability of Y. pestis to be transmitted by fleas, pPla codes for a protease, Pla, that activates plasmin in human hosts and is a very important virulence factor for pneumonic plague. Together, these plasmids, and a pathogenicity island called HPI, encode proteins that cause the pathogenesis. Y. pestis is thought to be descendant from Y. pseudotuberculosis, a comprehensive and comparative proteomics analysis of Y. pestis strain KIM was performed in 2006
Yersinia pestis
–
Yersinia pestis
Yersinia pestis
–
Oriental rat flea (Xenopsylla cheopis) infected with the Y. pestis
bacterium which appears as a dark mass in the gut: The foregut (proventriculus) of this flea is blocked by a Y. pestis biofilm; when the flea attempts to feed on an uninfected
host, Y. pestis is regurgitated into the wound, causing infection.
12.
Shigella
–
Shigella is a genus of Gram-negative, facultative anaerobic, nonspore-forming, nonmotile, rod-shaped bacteria genetically closely related to E. coli. The genus is named after Kiyoshi Shiga, who first discovered it in 1897, the causative agent of human shigellosis, Shigella causes disease in primates, but not in other mammals. It is only found in humans and gorillas. During infection, it typically causes dysentery, Shigella is one of the leading bacterial causes of diarrhea worldwide, causing an estimated 80-165 million cases. The number of deaths it causes each year is estimated at between 74,000 and 600,000 deaths and it is in the top four pathogens that cause moderate-to-severe diarrhea in African and South Asian children. Each of the Shigella genomes includes a virulence plasmid that encodes conserved primary virulence determinants, the Shigella chromosomes share most of their genes with those of E. coli K12 strain MG1655. Shigella infection is typically by ingestion, depending on the health of the host, fewer than 100 bacterial cells can be enough to cause an infection. Shigella species generally invade the epithelial lining of the colon, causing severe inflammation and this inflammation results in the diarrhea and even dysentery that are the hallmarks of Shigella infection. Some strains of Shigella produce toxins which contribute to disease during infection, S. flexneri strains produce ShET1 and ShET2, which may contribute to diarrhea. S. dysenteriae strains produce the enterotoxin Shiga toxin, which is similar to the produced by enterohemorrhagic E. coli. Both Shiga toxin and verotoxin are associated with causing potentially fatal hemolytic uremic syndrome, Shigella uses a type-III secretion system, which acts as a biological syringe to translocate toxic effector proteins to the target human cell. For instance, the IcsA effector protein triggers actin reorganization by N-WASP recruitment of Arp2/3 complexes, after invasion, Shigella cells multiply intracellularly and spread to neighboring epithelial cells, resulting in tissue destruction and characteristic pathology of shigellosis. The most common symptoms are diarrhea, fever, nausea, vomiting, stomach cramps and it is also commonly known to cause large and painful bowel movements. The stool may contain blood, mucus, or pus, hence, Shigella cells may cause dysentery. In rare cases, young children may have seizures, symptoms can take as long as a week to appear, but most often begin two to four days after ingestion. Symptoms usually last for days, but can last for weeks. Shigella is implicated as one of the causes of reactive arthritis worldwide. The diagnosis of shigellosis is made by isolating the organism from diarrheal fecal sample cultures, Shigella species are negative for motility and are generally not lactose fermenters, but S. sonnei can ferment lactose
Shigella
–
Shigella
13.
Proteus (bacterium)
–
Proteus is a genus of Gram-negative Proteobacteria. Proteus bacilli are widely distributed in nature as saprophytes, being found in decomposing animal matter, sewage, manure soil, the mamallian intestine and they are opportunistic pathogens, commonly responsible for urinary and septic infections, often nosocomial. Vulgaris, P. mirabilis, and P. penneri—are opportunistic human pathogens, Proteus includes pathogens responsible for many human urinary tract infections. P. mirabilis causes wound and urinary tract infections, most strains of P. mirabilis are sensitive to ampicillin and cephalosporins. P. vulgaris is not sensitive to these antibiotics, however, this organism is isolated less often in the laboratory and usually only targets immunosuppressed individuals. P. vulgaris occurs naturally in the intestines of humans and a variety of animals, and in manure, soil. P. mirabilis, once attached to the tract, infects the kidney more commonly than E. coli. P. mirabilis is found as a free-living organism in soil. About 10–15% of kidney stones are stones, caused by alkalinization of the urine by the action of the urease enzyme of Proteus bacterial species. Proteus species do not usually ferment lactose, but have shown to be capable lactose fermenters depending on the species in a triple sugar iron test, since it belongs to the family Enterobacteriaceae, general characters are applied on this genus. It is oxidase-negative but catalase- and nitrate-positive, specific tests include positive urease and phenylalanine deaminase tests. On the species level, indole is considered reliable, as it is positive for P. vulgaris, most strains produce a powerful urease enzyme, which rapidly hydrolyzes urea to ammonia and carbon monoxide, exceptions are some Providencia strains. Species can be motile, and have characteristic swarming patterns, underlying these behaviors are the somatic O and flagellar H antigens, so named based on Kauffman–White classification. Flagellated variants were therefore designated H forms, nonflagellated variants growing as isolated colonies, the cell wall O-antigen of certain strains of Proteus, such as OX-2, OX-19, OX-k, crossreact with several species of Rickettsiae. These Proteus antigens can be used in laboratory to detect the presence of antibodies against certain Rickettsiae members in patients serum and this test is called Weil-Felix reaction after its originators
Proteus (bacterium)
–
Proteus
14.
Enterobacter
–
Enterobacter is a genus of common Gram-negative, facultatively anaerobic, rod-shaped, non-spore-forming bacteria of the family Enterobacteriaceae. Several strains of bacteria are pathogenic and cause opportunistic infections in immunocompromised hosts. The urinary and respiratory tracts are the most common sites of infection, the genus Enterobacter is a member of the coliform group of bacteria. It does not belong to the fecal coliforms group of bacteria, unlike Escherichia coli, some of them showed quorum sensing properties as reported before Two clinically important species from this genus are E. aerogenes and E. cloacae. The genus Enterobacter ferments lactose with gas production during a 48-hour incubation at 35-37 °C in the presence of salts and detergents. It is oxidase-negative, indole-negative, and urease-variable, note, Treatment is dependent on local trends of antibiotic resistance. Cefepime, a fourth-generation cephalosporin from the β-Lactam antibiotic class, imipenem is often the antibiotic of choice. Aminoglycosides such as amikacin have been found to be very effective, quinolones can be an effective alternative. A recent study has shown that the presence of Enterobacter cloacae B29 in the gut of a morbidly obese individual may have contributed to the patient’s obesity. Furthermore, the bacterial strain, isolated from the patient, induced obesity. The study concludes that E. cloacae B29 may contribute to obesity in its hosts through an endotoxin-induced, inflammation-mediated mechanism. Enterobacter at BacDive - the Bacterial Diversity Metadatabase
Enterobacter
–
Enterobacter
15.
Serratia
–
Serratia is a genus of Gram-negative, facultatively anaerobic, endosporeforming, rod-shaped bacteria of the Enterobacteriaceae family. The most common and pathogenic of the species in the genus, S. marcescens, is normally the only pathogen, however, rare strains of S. plymuthica, S. liquefaciens, S. rubidaea, and S. odoriferae have caused diseases through infection. S. marcescens is typically found in showers, toilet bowls, a pan-genome analysis of the genus Serratia revealed that it does not depict exceptional genetic conservation or diversity as compared to other bacterial genera. The bacterium is a human pathogen, capitalizing on its ability to form tight-knit surface communities called biofilms wherever it can. S. marcescens is thought to be transmitted through hand-to-hand transmission by hospital personnel, in the hospital, Serratia species tend to colonize the respiratory and urinary tracts, rather than the gastrointestinal tract, in adults. Serratia infection is responsible for about 2% of nosocomial infections of the bloodstream, lower respiratory tract, urinary tract, surgical wounds, outbreaks of S. marcescens meningitis, wound infections, and arthritis have occurred in pediatric wards. Cases of Serratia arthritis have been reported in outpatients receiving intra-articular injections, several methods can be used to study the epidemiology of Serratia marcescens. Serological typing and different types of Polymerase Chain Reactions can be used to identify the bacteria, marcescensand S. liquefaciens can be easily confused in the lab when using the API system. The bacterium was named in honour of Italian physicist Serafino Serrati and marcescens because of the pigments rapid discolouration
Serratia
–
Serratia
16.
Citrobacter
–
Citrobacter is a genus of Gram-negative coliform bacteria in the Enterobacteriaceae family. The species C. amalonaticus, C. koseri, and C. freundii can use citrate as a carbon source. Citrobacter species are differentiated by their ability to convert tryptophan to indole, ferment lactose, Citrobacter shows the ability to accumulate uranium by building phosphate complexes. These bacteria can be found almost everywhere in soil, water, wastewater and they can also be found in the human intestine. They are rarely the source of illnesses, except for infections of the urinary tract, C. freundii strains have inducible ampC genes encoding resistance to ampicillin and first-generation cephalosporins. In addition, isolates of Citrobacter may be resistant to other antibiotics as a result of plasmid-encoded resistance genes. Citrobacter at DSMZ - German Collection of Microorganisms and Cell Cultures Canada Public Health Data Sheet
Citrobacter
–
Citrobacter
17.
Peptidoglycan
–
Peptidoglycan, also known as murein, is a polymer consisting of sugars and amino acids that forms a mesh-like layer outside the plasma membrane of most bacteria, forming the cell wall. The sugar component consists of alternating residues of β- linked N-acetylglucosamine, attached to the N-acetylmuramic acid is a peptide chain of three to five amino acids. The peptide chain can be cross-linked to the chain of another strand forming the 3D mesh-like layer. Peptidoglycan serves a role in the bacterial cell wall, giving structural strength. Peptidoglycan is also involved in binary fission during bacterial cell reproduction, the peptidoglycan layer is substantially thicker in gram-positive bacteria than in gram-negative bacteria, with the attachment of the S-layer. Peptidoglycan forms around 90% of the dry weight of gram-positive bacteria, thus, presence of high levels of peptidoglycan is the primary determinant of the characterisation of bacteria as gram-positive. In gram-positive strains, it is important in attachment roles and serotyping purposes, for both gram-positive and gram-negative bacteria, particles of approximately 2 nm can pass through the peptidoglycan. The peptidoglycan layer in the cell wall is a crystal lattice structure formed from linear chains of two alternating amino sugars, namely N-acetylglucosamine and N-acetylmuramic acid. The alternating sugars are connected by a β--glycosidic bond, peptidoglycan is one of the most important sources of D-amino acids in nature. Cross-linking between amino acids in different linear amino sugar chains occurs with the help of the enzyme DD-transpeptidase and results in a 3-dimensional structure that is strong, the specific amino acid sequence and molecular structure vary with the bacterial species. The peptidoglycan monomers are synthesized in the cytosol and are attached to a membrane carrier bactoprenol. Bactoprenol transports peptidoglycan monomers across the membrane where they are inserted into the existing peptidoglycan. In the first step of peptidoglycan synthesis, the glutamine, which is an acid, donates an amino group to a sugar. This turns fructose 6-phosphate into glucosamine-6-phosphate, in step two, an acetyl group is transferred from acetyl CoA to the amino group on the glucosamine-6-phosphate creating N-acetyl-glucosamine-6-phosphate. In step three of the process, the N-acetyl-glucosamine-6-phosphate is isomerized, which will change N-acetyl-glucosamine-6-phosphate to N-acetyl-glucosamine-1-phosphate. In step 4, the N-acetyl-glucosamine-1-phosphate, which is now a monophosphate, uridine triphosphate, which is a pyrimidine nucleotide, has the ability to act as an energy source. In this particular reaction, after the monophosphate has attacked the UTP and this initial stage, is used to create the precursor for the NAG in peptidoglycan. In step 5, some of the UDP-N-acetylglucosamine is converted to UDP-MurNAc by the addition of a group to the glucosamine
Peptidoglycan
–
Peptidoglycan.
18.
Buchnera (proteobacteria)
–
Buchnera aphidicola, a member of the Proteobacteria, is the primary endosymbiont of aphids, and has been studied in the pea aphid, Acyrthosiphon pisum. Buchnera is believed to have had a free-living, Gram-negative ancestor similar to a modern Enterobacteriaceae, Buchnera is 3 µm in diameter and has some of the key characteristics of their Enterobacteriaceae relatives, such as a Gram-negative cell wall. However, unlike most other Gram-negative bacteria, Buchnera lacks the genes to produce lipopolysaccharides for its outer membrane and this has resulted not only in one of the smallest known genomes of any living organism, but also one of the most genetically stable. The symbiotic relationship with aphids began between 160 million and 280 million years ago, and has persisted through maternal transmission and cospeciation, aphids have developed bacteriocyte cells to house Buchnera. A mature aphid may carry an estimated 5.6 ×106 Buchnera cells, Buchnera has lost regulatory factors, allowing continuous overproduction of tryptophan and other amino acids. Each bacteriocyte contains multiple vesicles, symbiosomes derived from the plasma membrane, the genomes of various Buchnera genomes are in the range of 600 to 650 kb and encode on the order of 500 to 560 proteins. Many contain also one or two plasmids, Buchnera also increases the transmission of plant viruses by producing symbionin, a protein that binds to the viral coat and protects it inside the aphid. This makes it likely that the virion will survive and be able to infect another plant when the aphid next feeds. Buchnera was named after Paul Buchner by Paul Baumann and his student. Buchnera Genome Projects Comparative Analysis of Buchnera Genomes
Buchnera (proteobacteria)
–
Buchnera aphidicola
19.
Blochmannia
–
Blochmannia is a genus of symbiotic bacteria found in carpenter ant. There are over 1000 species of ants and, as of 2014, of the over 30 species of carpenter ant that have been investigated. The bacteria filled cells currently known as members of the genus Blochmannia were first discovered by zoologist F. Blochmann in the ovaries, in 2000 Candidatus Blochmannia was proposed as its own genus. Endosymbiosis, or when the Blochmannia bacteria and the ant hosts became bonded, occurred around 30-40 million years ago, the high amounts of genetic conservation suggest that the Blochmannia genes lack some recombination mechanisms. Blochmannia bacteria are found in the midguts of carpenter ants, as well as the ovaries of the carpenter ants. Blochmannia is important in synthesizing essential and non essential amino acids, including tyrosine, the Blochmannia bacteria improves the ants’ nutrition and, in doing this, it is also important to the overall health of the ant colony. According to the study by Zientz et al, Blochmannia improves the health of the colony of ants as a whole because worker ants use a trophallaxis and regurgitation system to provide the colony with food. Blochmannia bacteria are sensitive to heat, in one experiment, when exposed to an increased heat of 99.87 °F for 4 weeks, over 99% of Blochmannia disappeared. However, even after 16 weeks exposure of heat exposure. According to researchers Fan and Wernegreen, this experiment suggests that the Blochmannia in ants could be vulnerable to the effects of global warming
Blochmannia
–
Like other species of the ant genus Camponotus (
carpenter ants), the wood-nesting
C. pennsylvanicus (shown here) possesses the obligate bacterial endosymbiont Blochmannia.
20.
Rickettsias
–
Rickettsia is a genus of nonmotile, gram-negative, nonspore-forming, highly pleomorphic bacteria that can be present as cocci, rods, or thread-like. The term rickettsia, named after Howard Taylor Ricketts, is used interchangeably for any member of the Rickettsiales. Being obligate intracellular parasites, the Rickettsia survival depends on entry, growth, Rickettsia species are transmitted by numerous types of arthropod, including chigger, ticks, fleas, and lice, and are associated with both human and plant disease. Despite the similar name, Rickettsia bacteria do not cause rickets, the majority of Rickettsia bacteria are susceptible to antibiotics of the tetracycline group. The classification of Rickettsia into three groups was based on serology. This grouping has since confirmed by DNA sequencing. All three of these contain human pathogens, the scrub typhus group has been reclassified as a related new genus – Orientia – but many medical textbooks still list this group under the rickettsial diseases. Rickettsia are more widespread than previously believed and are known to be associated with arthropods, leeches, divisions have also been identified in the spotted fever group and this group likely should be divided into two clades. Tsutsugamushi has been reclassified into the genus Orientia, peach phony RLO Papaya Bunchy Top Disease Infection occurs in nonhuman mammals, for example, species of Rickettsia have been found to afflict the South American guanaco, Lama guanacoe. Certain segments of rickettsial genomes resemble those of mitochondria, the deciphered genome of R. prowazekii is 1,111,523 bp long and contains 834 genes. Unlike free-living bacteria, it contains no genes for anaerobic glycolysis or genes involved in the biosynthesis and regulation of amino acids, in this regard, it is similar to mitochondrial genomes, in both cases, nuclear resources are used. ATP production in Rickettsia is the same as that in mitochondria, in fact, of all the microbes known, the Rickettsia is probably the closest relative to the mitochondria. Unlike the latter, the genome of R. prowazekii, however, contains a set of genes encoding for the tricarboxylic acid cycle. Still, the genomes of the Rickettsia, as well as the mitochondria, are said to be small. The recent discovery of another parallel between Rickettsia and viruses may become a basis for fighting HIV infection. A probable reason for this actively studied phenomenon is a degree of homology between the rickettsiae and the virus – namely, common epitope due to common genome fragment in both pathogens. Surprisingly, the other reported to be likely to provide the same effect is the virus-caused illness dengue fever. Comparative analysis of sequences have also identified five conserved signature indels in important proteins which are uniquely found in members of the genus Rickettsia
Rickettsias
–
Rickettsia
21.
Bacterial taxonomy
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Bacterial taxonomy is the taxonomy, i. e. the rank-based classification, of bacteria. In the scientific classification established by Carl von Linné, each species has to be assigned to a genus, Prokaryotes share many common features, such as lack of nuclear membrane, unicellularity, division by binary-fission and generally small size. The various species differ amongst each other based on several characteristics and he called them animalcules and published his observations in a series of letters to the Royal Society. O. F. Müller described eight species of the genus Vibrio, the term Bacterium was introduced much later, by Christian Gottfried Ehrenberg in 1838. Bacteria were first classified as plants constituting the class Schizomycetes, which along with the Schizophyceae formed the phylum Schizophyta. Haeckel in 1866 placed the group in the phylum Moneres in the kingdom Protista and defines them as completely structureless and homogeneous organisms, die Lepomoneren Protomonas—now classed as a eukaryote and not a bacterium. The name was reused in 1984 for a genus of Bacteria Vampyrella—now classed as a eukaryote. The classification of Cyanobacteria has been fought between being algae or bacteria, in 1905 Erwin F. Ferdinand Cohn recognized 4 tribes, Spherobacteria, Microbacteria, Desmobacteria, and Spirobacteria. Stanier and van Neil recognized the Kingdom Monera with 2 phyla, Myxophyta and Schizomycetae, the latter comprising classes Eubacteriae, Myxobacteriae, bisset distinguished 1 class and 4 orders, Eubacteriales, Actinomycetales, Streptomycetales, and Flexibacteriales. However, a few argue that the Archaea and Eukaryota arose from a group of bacteria. In any case, it is thought that viruses and archaea began relationships approximately two years ago, and that co-evolution may have been occurring between members of these groups. Since the Archaea and Bacteria are no more related to other than they are to eukaryotes. These lineages were formalised into the rank Domain which divided Life into 3 domains, the Eukaryota, the Archaea and this scheme is still followed today. In 1987 Carl Woese divided the Eubacteria into 11 divisions based on 16S ribosomal RNA sequences, while the three domain system is widely accepted, some authors have opposed it for various reasons. Hori and Osawas molecular analysis indicated a link between Metabacteria and eukaryotes, the only cladistic analyses for bacteria based on classical evidence largely corroborate Guptas results. He has also discovered evidence that Gram-negative bacteria arose from a symbiosis between 2 Gram-positive bacteria, classification is the grouping of organisms into progressively more inclusive groups based on phylogeny and phenotype, while nomenclature is the application of formal rules for naming organisms. The taxa which have been described are reviewed in Bergeys manual of Systematic Bacteriology. An online version of the outline of bacteria and archaea is available
Bacterial taxonomy
22.
Genus
–
A genus is a taxonomic rank used in the biological classification of living and fossil organisms in biology. In the hierarchy of classification, genus comes above species. In binomial nomenclature, the name forms the first part of the binomial species name for each species within the genus. Felis catus and Felis silvestris are two species within the genus Felis, Felis is a genus within the family Felidae. The composition of a genus is determined by a taxonomist, the standards for genus classification are not strictly codified, so different authorities often produce different classifications for genera. Moreover, genera should be composed of units of the same kind as other genera. The term comes from the Latin genus, a noun form cognate with gignere, linnaeus popularized its use in his 1753 Species Plantarum, but the French botanist Joseph Pitton de Tournefort is considered the founder of the modern concept of genera. The scientific name of a genus may be called the name or generic epithet. It plays a role in binomial nomenclature, the system of naming organisms. The rules for the names of organisms are laid down in the Nomenclature Codes. The standard way of scientifically describing species and other lower-ranked taxa is by binomial nomenclature, the generic name forms its first half. For example, the gray wolfs binomial name is Canis lupus, with Canis being the name shared by the wolfs close relatives. The specific name is written in lower-case and may be followed by names in zoology or a variety of infraspecific names in botany. Especially with these names, when the generic name is known from context. Because animals are typically only grouped within subspecies, it is written as a trinomen with a third name. Dog breeds, meanwhile, are not scientifically distinguished, there are several divisions of plant species and therefore their infraspecific names generally include contractions explaining the relation. For example, the genus Hibiscus includes hundreds of other species apart from the Rose of Sharon or common garden hibiscus, Rose of Sharon doesnt have subspecies but has cultivars that carry desired traits, such as the bright white H. syriaca Diana. Hawaiian hibiscus, meanwhile, includes several separate species, since not all botanists agree on the divisions or names between species, it is common to specify the source of the name using author abbreviations
Genus
–
Number of reptile genera with a given number of species. Most genera have only one or a few species but a few may have hundreds. Based on data from the
Reptile Database (as of May 2015).
23.
Escherichia
–
Escherichia /ˌɛʃəˈrɪkiə/ is a genus of Gram-negative, nonspore forming, facultatively anaerobic, rod-shaped bacteria from the family Enterobacteriaceae. In those species which are inhabitants of the tracts of warm-blooded animals. A number of the species of Escherichia are pathogenic, the genus is named after Theodor Escherich, the discoverer of Escherichia coli. While E. coli is responsible for the vast majority of Escherichia-related pathogenesis, Escherichia are associated with the imbalance of microbiota of the lower reproductive tract of women. These species are associated with inflammation, E. coli O157, H7 List of bacterial genera named after personal names Escherichia genomes and related information at PATRIC, a Bioinformatics Resource Center funded by NIAID
Escherichia
–
Escherichia
24.
Bacillus
–
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
25.
Fermentation (biochemistry)
–
Fermentation is a metabolic process that converts sugar to acids, gases, or alcohol. It occurs in yeast and bacteria, and also in oxygen-starved muscle cells, Fermentation is also used more broadly to refer to the bulk growth of microorganisms on a growth medium, often with the goal of producing a specific chemical product. French microbiologist Louis Pasteur is often remembered for his insights into fermentation, the science of fermentation is known as zymology. Fermentation takes place when the transport chain is unusable. In this case it becomes the primary means of ATP production. Fermentation turns NADH and pyruvate produced in glycolysis into NAD+. In the presence of O2, NADH and pyruvate are used to generate ATP in respiration and this is called oxidative phosphorylation, and it generates much more ATP than glycolysis alone. For that reason, cells generally benefit from avoiding fermentation when oxygen is available, the exception being obligate anaerobes which cannot tolerate oxygen. The first step, glycolysis, is common to all fermentation pathways, two ADP molecules and two Pi are converted to two ATP and two water molecules via substrate-level phosphorylation. Two molecules of NAD+ are also reduced to NADH, in oxidative phosphorylation the energy for ATP formation is derived from an electrochemical proton gradient generated across the inner mitochondrial membrane via the electron transport chain. Humans have used fermentation to produce drinks and beverages since the Neolithic age, Fermentation can even occur within the stomachs of animals, such as humans. To many people, fermentation simply means the production of alcohol, grains and fruits are fermented to produce beer, if a food soured, one might say it was off or fermented. Here are some definitions of fermentation and they range from informal, general usage to more scientific definitions. Preservation methods for food via microorganisms, any process that produces alcoholic beverages or acidic dairy products. Any large-scale microbial process occurring with or without air, any energy-releasing metabolic process that takes place only under anaerobic conditions. Fermentation does not necessarily have to be carried out in an anaerobic environment, for example, even in the presence of abundant oxygen, yeast cells greatly prefer fermentation to aerobic respiration, as long as sugars are readily available for consumption. The antibiotic activity of hops also inhibits aerobic metabolism in yeast, Fermentation reacts NADH with an endogenous, organic electron acceptor. Usually this is formed from the sugar during the glycolysis step. Sugars are the most common substrate of fermentation, and typical examples of products are ethanol, lactic acid, carbon dioxide
Fermentation (biochemistry)
–
Fermentation in progress: Bubbles of
CO2 form a froth on top of the fermentation mixture.
Fermentation (biochemistry)
–
Louis Pasteur in his laboratory
26.
Lactic acid
–
Lactic acid is an organic compound with the formula CH3CHCO2H. In its solid state, it is white and water-soluble, in its liquid state, it is clear. It is produced naturally and synthetically. With a hydroxyl group adjacent to the group, lactic acid is classified as an alpha-hydroxy acid. In the form of its base called lactate, it plays a role in several biochemical processes. In solution, it can ionize a proton from the carboxyl group, compared to acetic acid, its pKa is 1 unit less, meaning lactic acid deprotonates ten times more easily than acetic acid does. This higher acidity is the consequence of the hydrogen bonding between the α-hydroxyl and the carboxylate group. Lactic acid is chiral, consisting of two optical isomers, one is known as L--lactic acid or -lactic acid and the other, its mirror image, is D--lactic acid or -lactic acid. A mixture of the two in equal amounts is called DL-lactic acid, or racemic lactic acid, DL-lactic acid is miscible with water and with ethanol above its melting point which is around 17 or 18 °C. D-lactic acid and L-lactic acid have a melting point. In animals, L-lactate is constantly produced from pyruvate via the enzyme lactate dehydrogenase in a process of fermentation during normal metabolism and exercise. The concentration of lactate is usually 1–2 mmol/L at rest. In industry, lactic acid fermentation is performed by lactic acid bacteria and these bacteria can also grow in the mouth, the acid they produce is responsible for the tooth decay known as caries. In medicine, lactate is one of the components of lactated Ringers solution. These intravenous fluids consist of sodium and potassium cations along with lactate and chloride anions in solution with distilled water and it is most commonly used for fluid resuscitation after blood loss due to trauma, surgery, or burns. Lactic acid was isolated for the first time by the Swedish chemist Carl Wilhelm Scheele in 1780 from sour milk, the name reflects the lact- combining form derived from the Latin word for milk. In 1808, Jöns Jacob Berzelius discovered that lactic acid also is produced in muscles during exertion and its structure was established by Johannes Wislicenus in 1873. In 1856, Louis Pasteur discovered Lactobacillus and its role in the making of lactic acid, lactic acid started to be produced commercially by the German pharmacy Boehringer Ingelheim in 1895
Lactic acid
–
DL -Lactic acid
Lactic acid
27.
Nitrate
–
Nitrate is a polyatomic ion with the molecular formula NO−3 and a molecular mass of 62.0049 g/mol. Nitrates also describe the functional group RONO2. These nitrate esters are a class of explosives. The anion is the base of nitric acid, consisting of one central nitrogen atom surrounded by three identically bonded oxygen atoms in a trigonal planar arrangement. The nitrate ion carries a charge of −1. This arrangement is used as an example of resonance. Like the isoelectronic carbonate ion, the ion can be represented by resonance structures. A common example of a nitrate salt is potassium nitrate. A rich source of nitrate in the human body comes from diets rich in leafy green foods, such as spinach. NO3- is the active component within beetroot juice and other vegetables. Nitrite and water are converted in the body to nitric oxide, nitrate salts are found naturally on earth as large deposits, particularly of nitratine, a major source of sodium nitrate. Nitrates are found in man-made fertilizers, as a byproduct of lightning strikes in earths nitrogen-oxygen rich atmosphere, nitric acid is produced when nitrogen dioxide reacts with water vapor. Nitrates are mainly produced for use as fertilizers in agriculture because of their solubility and biodegradability. The main nitrate fertilizers are ammonium, sodium, potassium, several million kilograms are produced annually for this purpose. The second major application of nitrates is as oxidizing agents, most notably in explosives where the oxidation of carbon compounds liberates large volumes of gases. Sodium nitrate is used to air bubbles from molten glass. Mixtures of the salt are used to harden some metals. Explosives and table tennis balls are made from celluloid, although nitrites are the nitrogen compound chiefly used in meat curing, nitrates are used in certain specialty curing processes where a long release of nitrite from parent nitrate stores is needed
Nitrate
–
Table tennis balls are made from celluloid, an organic nitrate.
Nitrate
–
Nitrate
28.
Nitrite
–
The nitrite ion, which has the chemical formula NO−2, is a symmetric anion with equal N–O bond lengths. Upon protonation, the weak acid nitrous acid is produced. Nitrite can be oxidized or reduced, with the product somewhat dependent on the oxidizing/reducing agent, the nitrite ion is an ambidentate ligand, and is known to bond to metal centers in at least five different ways. Nitrite is also important in biochemistry as a source of the potent vasodilator nitric oxide, in organic chemistry the –NO2 group is present in nitrous acid esters and nitro compounds. Nitrites are also used in the production industry for curing meat. Sodium nitrite is made industrially by passing nitrous fumes into aqueous sodium hydroxide or sodium carbonate solution, alkali metal nitrites are thermally stable up to and beyond their melting point. Ammonium nitrite can be made from dinitrogen trioxide, N2O3, which is formally the anhydride of nitrous acid,2 NH3 + H2O + N2O3 →2 NH4NO2 This compound may decompose explosively on heating, in organic chemistry nitrites are used in diazotization reactions. The nitrite ion has a structure, with both N–O bonds having equal length. In valence bond theory, it is described as a hybrid with equal contributions from two canonical forms that are mirror images of each other. The negative charge of the ion is equally distributed on the two oxygen atoms, both nitrogen and oxygen atoms carry a lone pair of electrons. Therefore, the ion is a Lewis base. Moreover, it can act as an ambidentate ligand towards a metal ion, donating a pair of electrons from either nitrogen or oxygen atoms. In aqueous solution, nitrous acid is an acid, HNO2 ⇌ H+ + NO−2. In solution, it is unstable with respect to the disproportionation reaction, addition of acid to a solution of a nitrite in the presence of a reducing agent, such as iron, is a way to make nitric oxide in the laboratory. The formal oxidation state of the atom in a nitrite is +3. This means that it can be oxidized to oxidation states +4 and +5. Standard reduction potentials for reactions directly involving nitrous acid are shown in the table below, The data can be extended to include products in lower oxidation states. For example, H2N2O2 +2 H+ +2 e− ⇌ N2 +2 H2O, E0 = +2.65 V Oxidation reactions usually result in the formation of the nitrate ion, with nitrogen in oxidation state +5
Nitrite
–
Nitrite
. PMID 20207755. doi:10.1128/JB.01480-09.
