1.
Gut flora
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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
2.
Taxonomy (biology)
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Taxonomy is the science of defining groups of biological organisms on the basis of shared characteristics and giving names to those groups. The exact definition of taxonomy varies from source to source, but the core of the remains, the conception, naming. There is some disagreement as to whether biological nomenclature is considered a part of taxonomy, the broadest meaning of taxonomy is used here. The word taxonomy was introduced in 1813 by Candolle, in his Théorie élémentaire de la botanique, the term alpha taxonomy is primarily used today to refer to the discipline of finding, describing, and naming taxa, particularly species. In earlier literature, the term had a different meaning, referring to morphological taxonomy, ideals can, it may be said, never be completely realized. They have, however, a value of acting as permanent stimulants. Some of us please ourselves by thinking we are now groping in a beta taxonomy, turrill thus explicitly excludes from alpha taxonomy various areas of study that he includes within taxonomy as a whole, such as ecology, physiology, genetics, and cytology. He further excludes phylogenetic reconstruction from alpha taxonomy, thus, Ernst Mayr in 1968 defined beta taxonomy as the classification of ranks higher than species. This activity is what the term denotes, it is also referred to as beta taxonomy. How species should be defined in a group of organisms gives rise to practical and theoretical problems that are referred to as the species problem. The scientific work of deciding how to define species has been called microtaxonomy, by extension, macrotaxonomy is the study of groups at higher taxonomic ranks, from subgenus and above only, than species. While some descriptions of taxonomic history attempt to date taxonomy to ancient civilizations, earlier works were primarily descriptive, and focused on plants that were useful in agriculture or medicine. There are a number of stages in scientific thinking. Early taxonomy was based on criteria, the so-called artificial systems. Later came systems based on a complete consideration of the characteristics of taxa, referred to as natural systems, such as those of de Jussieu, de Candolle and Bentham. The publication of Charles Darwins Origin of Species led to new ways of thinking about classification based on evolutionary relationships and this was the concept of phyletic systems, from 1883 onwards. This approach was typified by those of Eichler and Engler, the advent of molecular genetics and statistical methodology allowed the creation of the modern era of phylogenetic systems based on cladistics, rather than morphology alone. Taxonomy has been called the worlds oldest profession, and naming and classifying our surroundings has likely been taking place as long as mankind has been able to communicate
3.
Bacteria
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Bacteria constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods, Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only half of the bacterial phyla have species that can be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology, There are typically 40 million bacterial cells in a gram of soil and a million bacterial cells in a millilitre of fresh water. There are approximately 5×1030 bacteria on Earth, forming a biomass which exceeds that of all plants, Bacteria are vital in many stages of the nutrient cycle by recycling nutrients such as the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of bodies and bacteria are responsible for the putrefaction stage in this process. In March 2013, data reported by researchers in October 2012, was published and it was suggested that bacteria thrive in the Mariana Trench, which with a depth of up to 11 kilometres is the deepest known part of the oceans. Other researchers reported related studies that microbes thrive inside rocks up to 580 metres below the sea floor under 2.6 kilometres of ocean off the coast of the northwestern United States. According to one of the researchers, You can find microbes everywhere—theyre extremely adaptable to conditions, the vast majority of the bacteria in the body are rendered harmless by the protective effects of the immune system, though many are beneficial particularly in the gut flora. However several species of bacteria are pathogenic and cause diseases, including cholera, syphilis, anthrax, leprosy. The most common fatal diseases are respiratory infections, with tuberculosis alone killing about 2 million people per year. In developed countries, antibiotics are used to treat infections and are also used in farming, making antibiotic resistance a growing problem. Once regarded as constituting the class Schizomycetes, bacteria are now classified as prokaryotes. Unlike cells of animals and other eukaryotes, bacterial cells do not contain a nucleus and these evolutionary domains are called Bacteria and Archaea. The ancestors of modern bacteria were unicellular microorganisms that were the first forms of life to appear on Earth, for about 3 billion years, most organisms were microscopic, and bacteria and archaea were the dominant forms of life. In 2008, fossils of macroorganisms were discovered and named as the Francevillian biota, however, gene sequences can be used to reconstruct the bacterial phylogeny, and these studies indicate that bacteria diverged first from the archaeal/eukaryotic lineage. Bacteria were also involved in the second great evolutionary divergence, that of the archaea, here, eukaryotes resulted from the entering of ancient bacteria into endosymbiotic associations with the ancestors of eukaryotic cells, which were themselves possibly related to the Archaea
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Proteobacteria
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The Proteobacteria are a major phylum of Gram-negative bacteria. The name of the phylum has never been published as no type genus has been proposed. They include a variety of pathogens, such as Escherichia, Salmonella, Vibrio, Helicobacter, Yersinia. Others are free-living, and include many of the responsible for nitrogen fixation. Carl Woese established this grouping in 1987, calling it informally the purple bacteria, the Alphaproteobacteria grow at very low levels of nutrients and have unusual morphology such as stalks and buds. They include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants, the type order is the Caulobacterales, comprising stalk-forming bacteria such as Caulobacter. The Betaproteobacteria are highly diverse and contain chemolithoautotrophs, photoautotrophs. The type order is the Burkholderiales, comprising a range of metabolic diversity. The Gammaproteobacteria are the largest class in terms of species with validly published names, the type order is the Pseudomonadales, which include the genera Pseudomonas and the nitrogen-fixing Azotobacter. The Deltaproteobacteria include bacteria that are predators on other bacteria and are important contributors to the side of the sulfur cycle. The type order is the Myxococcales, which includes organisms with self-organising abilities such as Myxococcus spp, the Epsilonproteobacteria are often slender, Gram-negative rods that are helical or curved. The type order is the Campylobacterales, which includes important food pathogens such as Campylobacter spp, the type order is the Oligoflexales, which contains the genus Oligoflexus. The Acidithiobacillia contain only sulfur-oxidising autotrophs, the type order is the Acidithiobacillales, which includes economically important organisms used in the mining industry such as Acidithiobacillus spp. All Proteobacteria are Gram-negative, though some may stain Gram-positive or Gram-variable in practice, many move about using flagella, but some are nonmotile or rely on bacterial gliding. The last include the Myxobacteriales, an order of bacteria that can aggregate to form fruiting bodies. Also, a variety in the types of metabolism exists. Most members are facultatively or obligately anaerobic, Chemolithoautotrophic, and heterotrophic, a variety of genera, which are not closely related to each other, convert energy from light through photosynthesis. Proteobacteria are associated with the imbalance of microbiota of the reproductive tract of women
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Gammaproteobacteria
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Gammaproteobacteria are a class of several medically, ecologically, and scientifically important groups of bacteria. An exceeding number of important pathogens belong to this class, like all Proteobacteria, the Gammaproteobacteria are Gram-negative. The Gammaproteobacteria comprise several medically and scientifically important groups of bacteria, such as the Enterobacteriaceae, Vibrionaceae, a number of important pathogens belong to this class, e. g. Salmonella spp. Yersinia pestis, Vibrio cholerae, Pseudomonas aeruginosa, and Escherichia coli, important plant pathogens such as Xanthomonas axonopodis pv. citri and Pseudomonas syringae pv. actinidiae are also Gammaproteobacteria. Members of Chromatium are photosynthetic and oxidize hydrogen sulfide instead of water, some Gammaproteobacteria are methane oxidizers, and many are symbiotic with geothermic ocean vent-dwelling animals. Due to a genus, Acidithiobacillus, the Gammaproteobacteria class is paraphyletic to Betaproteobacteria. A number of bacteria have been described as members of Gammaproteobacteria, Betaproteobacteria Proteobacteria Gammaproteobacteria at the US National Library of Medicine Medical Subject Headings
6.
Family (biology)
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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
7.
Gram-negative bacteria
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Gram-negative bacteria are a group of bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a peptidoglycan cell wall sandwiched between an inner cytoplasmic cell membrane and a bacterial outer membrane. Gram-negative bacteria are spread worldwide, in all environments that support life. Several classes of antibiotics target gram-negative bacteria specifically, including aminoglycosides, historically, the kingdom Monera was divided into four divisions based on Gram staining, Firmacutes, Gracillicutes, Mollicutes and Mendocutes. Since 1987, the monophyly of the bacteria has been disproven with molecular studies. However some authors, such as Cavalier-Smith still treat them as a monophyletic taxon, bacteria are traditionally divided into the two groups, gram-positive and gram-negative, based on their Gram stain retention. These groups are thought of as lineages, with gram-negative bacteria more closely related to one another than to gram-positive bacteria. While this is true, the classification system breaks down in some cases. A given bacterias Gram stain result, bacterial membrane organization, as such, the Gram stain cannot be reliably used to assess familial relationships of bacteria. That said, Gram staining does often give information about the composition of the cell membrane. Of these two distinct groups of prokaryotic organisms, monoderm prokaryotes are indicated to be ancestral. In addition, a number of taxa that are either part of the phylum Firmicutes or branches in its proximity are also found to possess a diderm cell structure. Other notable groups of bacteria include the cyanobacteria, spirochaetes, green sulfur. Medically relevant gram-negative cocci include the four types that cause a sexually transmitted disease, a meningitis, medically relevant gram-negative bacilli include a multitude of species. Some of them cause primarily respiratory problems, primarily urinary problems, transformation is one of three processes for horizontal gene transfer, in which exogenous genetic material passes from bacterium to another, the other two being conjugation and transduction. In transformation, the material passes through the intervening medium. One of the unique characteristics of gram-negative bacteria is the structure of the bacterial outer membrane. The outer leaflet of this comprises a complex lipopolysaccharide whose lipid portion acts as an endotoxin
8.
Symbiosis
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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
. PMID 20207755.
