42-472: RF3 can refer to: Red Faction: Guerrilla , the third installment of the Red Faction franchise RF3, a candidate phylum of bacteria [REDACTED] Topics referred to by the same term This disambiguation page lists articles associated with the same title formed as a letter–number combination. If an internal link led you here, you may wish to change
84-410: A bacterial phylum are lacking or due to a lack of sequence diversity in databases when the phylum was first established. For example, it is suggested that candidate phylum Parcubacteria is actually a superphylum that encompasses 28 subordinate phyla and that phylum Elusimicrobia is actually a superphylum that encompasses 7 subordinate phyla. Given the rich history of the field of bacterial taxonomy and
126-415: A correlation of microbial composition in children with and without nonalcoholic fatty liver disease (NAFLD), wherein patients with NAFLD have a higher abundance of Gammaproteobacteria than patients without the disease. Classes Betaproteobacteria and Gammaproteobacteria are prevalent within the human oral cavity, and are markers for good oral health. The oral microbiome consists of 11 habitats, including
168-503: A diverse group. Though some species may stain Gram-positive or Gram-variable in the laboratory, they are nominally Gram-negative . Their unique outer membrane is mainly composed of lipopolysaccharides , which helps differentiate them from the Gram-positive species. Most Pseudomonadota are motile and move using flagella. Many move about using flagella , but some are nonmotile, or rely on bacterial gliding . Pseudomonadota have
210-553: A greater diversity of 16S rRNA sequences from uncultured organisms now available, it is estimated it may consist of up to 28 bacterial phyla. In line with this, over 14 phyla have now been described within the Parcubacteria group, including Kaiserbacteria, Adlerbacteria, Campbellbacteria, Nomurabacteria, Giovannonibacteria, Wolfebacteria, Jorgensenbacteria, Yanofskybacteria, Azambacteria, Moranbacteria, Uhrbacteria, and Magasanikbacteria. It has been proposed that some classes of
252-690: A proposal for its reclassification into distinct phyla: Desulfobacterota (encompassing Thermodesulfobacteria ), Myxococcota , and Bdellovibrionota (comprising Oligoflexia ). The class Epsilonproteobacteria was additionally identified within the Pseudomonadota phylum. This class is characterized by its significance as chemolithotrophic primary producers and its metabolic prowess in deep-sea hydrothermal vent ecosystems. Noteworthy pathogenic genera within this class include Campylobacter , Helicobacter , and Arcobacter . Analysis of phylogenetic tree topology and genetic markers revealed
294-426: A relevant signature of disease in the human gastrointestinal (GI) tract, by operating as a marker for microbiota instability. The human gut microbiome consists mainly of four phyla: Firmicutes , Bacteroidetes , Actinobacteria , and Pseudomonadota. Microorganism gut colonization is dynamic from birth to death, with stabilization at the first few years of life, to higher diversity in adults, to reduced diversity in
336-427: A variety of compounds. Bioleaching , done by various Thiobacillus species, are a primary example of this. Any iron and sulfur oxidizing species has the potential to uncover metals and low-grade ores that conventional mining techniques were unable to extract. At present, they are most often used for recovering copper and uranium, but researchers are looking to expand this field in the future. The downside of this method
378-475: A well-known pathogenic genus, Pseudomonas is also capable of biodegradation of certain materials, like cellulose. The Hydrogenophilalia are thermophilic chemoheterotrophs and autotrophs. The bacteria typically use hydrogen gas as an electron donor, but can also use reduced sulfuric compounds. Because of this ability, scientists have begun to use certain species of Hydrogenophilalia to remove sulfides that contaminate industrial wastewater systems. The type order
420-431: A wide variety of metabolism types. Most are facultative or obligate anaerobes , chemolithoautotrophs , and heterotrophs , though numerous exceptions exist. A variety of distantly related genera within the Pseudomonadota obtain their energy from light through conventional photosynthesis or anoxygenic photosynthesis . The Acidithiobacillia contain only sulfur, iron, and uranium-oxidizing autotrophs . The type order
462-498: Is present in the atmosphere, they are able to compete with the abiotic iron(II) oxidation that is already occurring in the environment. The only confirmed type order for this class is the Mariprofundaceae , which does not contain any known pathogenic species. Transformation , a process in which genetic material passes from one bacterium to another, has been reported in at least 30 species of Pseudomonadota distributed in
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#1732791475422504-730: Is that the bacteria produce acidic byproducts that end up in acid mine drainage . Bioleaching has significant economic promise if it can be controlled and not cause any further harm to the environment. Pseudomonadota are microbes commonly found within soil systems. Microbes play a crucial role in the surrounding ecosystem by performing functions such as nutrient cycling , carbon dioxide fixation, decomposition , and nitrogen fixation. Pseudomonadota can be described as phototrophs , heterotrophs , and lithotrophs . As heterotrophs (examples Pseudomonas and Xanthomonas ) these bacteria are effective in breaking down organic matter, contributing to nutrient cycling. Additionally, photolithotrophs within
546-714: Is the Acidithiobacillaceae , which includes five different Acidithiobacillus species used in the mining industry. In particular, these microbes assist with the process of bioleaching , which involves microbes assisting in metal extraction from mining waste that typically extraction methods cannot remove. Some Alphaproteobacteria can grow at very low levels of nutrients and have unusual morphology within their life cycles. Some form stalks to help with colonization, and form buds during cell division. Others include agriculturally important bacteria capable of inducing nitrogen fixation in symbiosis with plants. The type order
588-647: Is the Caulobacterales , comprising stalk-forming bacteria such as Caulobacter . The mitochondria of eukaryotes are thought to be descendants of an alphaproteobacterium. The Betaproteobacteria are highly metabolically diverse and contain chemolithoautotrophs , photoautotrophs , and generalist heterotrophs . The type order is the Burkholderiales , comprising an enormous range of metabolic diversity, including opportunistic pathogens . These pathogens are primary for both humans and animals, such as
630-550: Is the Hydrogenophilaceae which contains the genera Thiobacillus, Petrobacter, Sulfuricella, Hydrogenophilus and Tepidiphilus . Currently, no members of this class have been identified as pathogenic. The Zetaproteobacteria are the iron-oxidizing neutrophilic chemolithoautotrophs , distributed worldwide in estuaries and marine habitats. This group is so successful in its environment due to their microaerophilic nature. Because they require less oxygen than what
672-682: Is unclear what to call the group. For example, the Candidate Phyla Radiation includes the Patescibacteria group which includes Microgenomates group which includes over 11 bacterial phyla. The CPR is a descriptive term referring to a massive monophyletic radiation of candidate phyla that exists within the Bacterial domain. It includes two main clades, the Microgenomates and Parcubacteria groups, each containing
714-501: The Bacteriological Code , the term phylum is preferred. In 1987, Carl Woese , regarded as the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences, listed below. Traditionally, phylogeny was inferred and taxonomy established based on studies of morphology. The advent of molecular phylogenetics has allowed for improved elucidation of
756-570: The LPSN , 89 bacterial phyla are recognized on the Silva database , dozens more have been proposed, and hundreds likely remain to be discovered. As of 2017, approximately 72% of widely recognized bacterial phyla were candidate phyla (i.e. have no cultured representatives). The rank of phylum has been included in the rules of the International Code of Nomenclature of Prokaryotes , using
798-420: The bacteria responsible for nitrogen fixation . Previously, the Pseudomonadota phylum included two additional classes, namely Deltaproteobacteria and Oligoflexia . However, further investigation into the phylogeny of these taxa through genomic marker analysis demonstrated their separation from the Pseudomonadota phylum. Deltaproteobacteria has been identified as a diverse taxonomic unit, leading to
840-603: The "purple bacteria and their relatives". The group was later formally named the 'Proteobacteria' after the Greek god Proteus, who was known to assume many forms. In 2021 the International Committee on Systematics of Prokaryotes designated the synonym Pseudomonadota, and renamed many other prokaryotic phyla as well. This renaming of several prokaryote phyla in 2021, including Pseudomonadota, remains controversial among microbiologists, many of whom continue to use
882-410: The classes alpha, beta, and gamma. The best-studied Pseudomonadota with respect to natural genetic transformation are the medically important human pathogens Neisseria gonorrhoeae (class beta), and Haemophilus influenzae (class gamma). Natural genetic transformation is a sexual process involving DNA transfer from one bacterial cell to another through the intervening medium and the integration of
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#1732791475422924-478: The direct divergence of Epsilonproteobacteria from the Pseudomonadota phylum. Limited outgroup data and low bootstrap values support these discoveries. Despite further investigations, consensus has not been reached regarding the monophyletic nature of Epsilonproteobacteria within Proteobacteria, prompting researchers to propose its taxonomic separation from the phylum. The proposed reclassification of
966-436: The donor sequence into the recipient genome. In pathogenic Pseudomonadota, 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 . Due to the distinctive nature of each of the six classes of Pseudomonadota, this phylum occupies a multitude of habitats. These include: Studies have suggested Pseudomonadota as
1008-463: The earlier name Proteobacteria, of long standing in the literature. The phylum Pseudomonadota encompasses classes Acidithiobacillia, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Hydrogenophilia , and Zetaproteobacteria. The phylum includes a wide variety of pathogenic genera, such as Escherichia , Salmonella , Vibrio , Yersinia , Legionella , and many others. Others are free-living (non- parasitic ) and include many of
1050-535: The elderly. The gut microbiome conducts processes like nutrient synthesis, chemical metabolism , and the formation of the gut barrier. Additionally, the gut microbiome facilitates host interactions with its surrounding environment through regulation of nutrient absorption and bacterial intake. In 16s rRNA and metagenome sequencing studies, Proteobacteria have been identified as bacteria that prompts endotoxemia (an inflammatory gut response) and metabolic disorders in human GI tracts. Another study by Michail et al. showed
1092-449: The ending –ota for phylum names that must be based on the name of a genus as its nomenclatural type. The following is a list of bacterial phyla that have been validly published (not current). Despite the unclear branching order for most bacterial phyla, several groups of phyla consistently cluster together and are referred to as supergroups or superphyla. In some instances, bacterial clades clearly consistently cluster together but it
1134-629: The eponymous superphyla and a few other phyla. The superphylum Patescibacteria was originally proposed to encompass the phyla Microgenomates (OP11), Parcubacteria (OD1), and Gracilibacteria (GNO2 / BD1-5). More recent phylogenetic analyses show that the last common ancestor of these taxa is the same node as that of CPR. The Sphingobacteria (FCB group) includes Bacteroidota, Calditrichota, Chlorobiota, candidate phylum "Cloacimonetes", Fibrobacterota, Gemmatimonadota, Ignavibacteriota, candidate phylum "Latescibacteria", candidate phylum "Marinimicrobia", and candidate phylum "Zixibacteria". Microgenomates
1176-617: The evolutionary relationship of species by analyzing their DNA and protein sequences, for example their ribosomal DNA . The lack of easily accessible morphological features, such as those present in animals and plants , hampered early efforts of classification and resulted in erroneous, distorted and confused classification, an example of which, noted Carl Woese , is Pseudomonas whose etymology ironically matched its taxonomy, namely "false unit". Many bacterial taxa were re-classified or re-defined using molecular phylogenetics. The advent of molecular sequencing technologies has allowed for
1218-502: The horse pathogen Burkholderia mallei , and Burkholderia cepacia which causes respiratory tract infections in people with cystic fibrosis. The Gammaproteobacteria are one of the largest classes in terms of genera, containing approximately 250 validly published names. The type order is the Pseudomonadales , which include the genera Pseudomonas and the nitrogen-fixing Azotobacter , along with many others. Besides being
1260-450: The link to point directly to the intended article. Retrieved from " https://en.wikipedia.org/w/index.php?title=RF3&oldid=898582819 " Category : Letter–number combination disambiguation pages Hidden categories: Short description is different from Wikidata All article disambiguation pages All disambiguation pages Bacterial phyla#Uncultivated Phyla and metagenomics Bacterial phyla constitute
1302-500: The major lineages of the domain Bacteria . While the exact definition of a bacterial phylum is debated, a popular definition is that a bacterial phylum is a monophyletic lineage of bacteria whose 16S rRNA genes share a pairwise sequence identity of ~75% or less with those of the members of other bacterial phyla. It has been estimated that ~1,300 bacterial phyla exist. As of May 2020, 41 bacterial phyla are formally accepted by
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1344-682: The name Epsilonproteobacteria is Epsilonbacteraeota , later revised to Campylobacterota in 2018. The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LSPN) and the National Center for Biotechnology Information (NCBI). The group Pseudomonadota is defined based on ribosomal RNA (rRNA) sequencing, and are divided into several subclasses. These subclasses were regarded as such for many years, but are now treated as various classes of
1386-704: The oral cavity. Pseudomonadota bacteria have a symbiotic or mutualistic association with plant roots, an example being in the rhizomes of potato plants. Because of this symbiotic relationship, farmers have the ability to increase their crop yields. Healthier root systems can lead to better nutrient uptake, improved water retention, increased resistance to diseases and pests, and ultimately higher crop yields per acre. Increased agricultural output can spark economic growth, contribute to food security, and lead to job creation in rural areas. As briefly mentioned in previous sections, members of Pseudomonadota have vast metabolic abilities that allow them to utilize and produce
1428-857: The order Hydrogenophilales Pseudomonadota classes with validly published names include some prominent genera: e.g.: Alphaproteobacteria Zetaproteobacteria Gammaproteobacteria Betaproteobacteria Hydrogenophilalia Alphaproteobacteria " Mariprofundia " ( Zetaproteobacteria ) " Thiohalorhabdales " Methylothermaceae 2 Algiphilaceae Methylothermaceae Acidithiobacillia Gammaproteobacteria (nested Betaproteobacteria & Hydrogenophilalia ) " Caulobacteria " ( Alphaproteobacteria ) " Mariprofundia " ( Zetaproteobacteria ) " Magnetococcia " clade 1 "Foliamicales" clade 3 Immundisolibacterales clade 5 "Acidithiobacillidae" ( Acidithiobacillia ) "Neisseriidae" ( Betaproteobacteria & nested Hydrogenophilalia ) "Pseudomonadidae" ( Gammaproteobacteria ) Pseudomonadota are
1470-1001: The phylum Proteobacteria may be phyla in their own right, which would make Proteobacteria a superphylum. For example, the Deltaproteobacteria group does not consistently form a monophyletic lineage with the other Proteobacteria classes. The Planctobacteria (PVC group) includes Chlamydiota , Lentisphaerota , candidate phylum " Omnitrophica ", Planctomycetota , candidate phylum " Poribacteria ", and Verrucomicrobiota . The proposed superphylum, Terrabacteria , includes Actinomycetota , " Cyanobacteria "/" Melainabacteria "- group , Deinococcota , Chloroflexota , Bacillota , and candidate phylum OP10. Several candidate phyla ( Microgenomates , Omnitrophica, Parcubacteria, and Saccharibacteria ) and several accepted phyla ( Elusimicrobiota , Caldisericota , and Armatimonadota ) have been suggested to actually be superphyla that were incorrectly described as phyla because rules for defining
1512-640: The phylum are able to perform photosynthesis using sulfide or elemental sulfur as electron donors , which enables them to participate in carbon fixation and oxygen production even in anaerobic conditions. These Pseudomonadota bacteria are also considered copiotrophic organisms, meaning they can be found in environments with high nutrient availability. These environments have ample sources of carbon and other nutrients, environments like fertile soils, compost, and sewage. These copiotrophic bacteria are able to enhance soil health by performing nutrient cycling and waste decomposition. Because this phylum are able to form
1554-553: The phylum. These classes are monophyletic . The genus Acidithiobacillus , part of the Gammaproteobacteria until it was transferred to class Acidithiobacillia in 2013, was previously 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
1596-551: The predominant phylum within the realm of bacteria. They are naturally found as pathogenic and free-living (non- parasitic ) genera. The phylum comprises six classes Acidithiobacillia , Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Hydrogenophilia , and Zetaproteobacteria . The Pseudomonadota are widely diverse, with differences in morphology , metabolic processes, relevance to humans, and ecological influence. American microbiologist Carl Woese established this grouping in 1987, calling it informally
1638-467: The rapidity of changes therein in modern times, it is often useful to have a historical perspective on how the field has progressed in order to understand references to antiquated definitions or concepts. When bacterial nomenclature was controlled under the Botanical Code , the term division was used, but now that bacterial nomenclature (with the exception of cyanobacteria ) is controlled under
1680-399: The recovery of genomes directly from environmental samples (i.e. bypassing culturing), leading to rapid expansion of our knowledge of the diversity of bacterial phyla. These techniques are genome-resolved metagenomics and single-cell genomics . Proteobacteria Pseudomonadota (synonym Proteobacteria ) is a major phylum of Gram-negative bacteria . Currently, they are considered
1722-407: The tongue dorsum, hard palate , tonsils, throat, saliva, and more. Changes in the oral microbiome are due to endogenous and exogenous factors like host lifestyle, genotype , environment, immune system, and socioeconomic status. Considering diet as a factor, high saturated fatty acid (SAF) content, achieved through poor diet, has been correlated to increased abundance of Betaproteobacteria in
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1764-415: Was originally thought to be a single phylum although evidence suggests it actually encompasses over 11 bacterial phyla, including Curtisbacteria, Daviesbacteria, Levybacteria, Gottesmanbacteria, Woesebacteria, Amesbacteria, Shapirobacteria, Roizmanbacteria, Beckwithbacteria, Collierbacteria, Pacebacteria. Parcubacteria was originally described as a single phylum using fewer than 100 16S rRNA sequences. With
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