Streptomyces | |
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Slide culture | |
Scientific classification ![]() | |
Domain: | Bacteria |
Phylum: | Actinomycetota |
Class: | Actinomycetia |
Order: | Streptomycetales |
Family: | Streptomycetaceae |
Genus: | Streptomyces Waksman and Henrici 1943 (Approved Lists 1980) |
Type species | |
Streptomyces albus (Rossi Doria 1891) Waksman and Henrici 1943 | |
Diversity | |
About 550 species | |
Synonyms [1] | |
List
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Streptomyces is the largest genus of Actinomycetota, and the type genus of the family Streptomycetaceae. [3] Over 700 species of Streptomyces bacteria have been described. [4] [5] [6] As with the other Actinomycetota, streptomycetes are gram-positive, and have very large genomes with high GC content. [5] [7] Found predominantly in soil and decaying vegetation, most streptomycetes produce spores, and are noted for their distinct "earthy" odor that results from production of a volatile metabolite, geosmin. [8] Different strains of the same species may colonize very diverse environments. [5]
Streptomycetes are characterised by a complex secondary metabolism. [7] Between 5-23% (average: 12%) of the protein-coding genes of each Streptomyces species are implicated in secondary metabolism. [5] Streptomycetes produce over two-thirds of the clinically useful antibiotics of natural origin (e.g., neomycin, streptomycin, cypemycin, grisemycin, bottromycins and chloramphenicol). [9] [10] The antibiotic streptomycin takes its name directly from Streptomyces. Streptomycetes are infrequent pathogens, though infections in humans, such as mycetoma, can be caused by S. somaliensis and S. sudanensis , and in plants can be caused by S. caviscabies , S. acidiscabies , S. turgidiscabies and S. scabies .
Streptomyces is the type genus of the family Streptomycetaceae [11] and currently covers more than 700 species with the number increasing every year. [12] [6] It is estimated that the total number of Streptomyces species is close to 1600. [5] Acidophilic and acid-tolerant strains that were initially classified under this genus have later been moved to Kitasatospora (1997) [13] and Streptacidiphilus (2003). [14] Species nomenclature are usually based on their color of hyphae and spores.
Saccharopolyspora erythraea was formerly placed in this genus (as Streptomyces erythraeus).
The genus Streptomyces includes aerobic, Gram-positive, multicellular, filamentous bacteria that produce well-developed vegetative hyphae (between 0.5-2.0 µm in diameter) with branches. They form a complex substrate mycelium that aids in scavenging organic compounds from their substrates. [15] Although the mycelia and the aerial hyphae that arise from them are amotile, mobility is achieved by dispersion of spores. [15] Spore surfaces may be hairy, rugose, smooth, spiny or warty. [16] In some species, aerial hyphae consist of long, straight filaments, which bear 50 or more spores at more or less regular intervals, arranged in whorls (verticils). Each branch of a verticil produces, at its apex, an umbel, which carries from two to several chains of spherical to ellipsoidal, smooth or rugose spores. [15] Some strains form short chains of spores on substrate hyphae. Sclerotia-, pycnidia-, sporangia-, and synnemata-like structures are produced by some strains.
The complete genome of " S. coelicolor strain A3(2)" was published in 2002. [17] At the time, the "S. coelicolor" genome was thought to contain the largest number of genes of any bacterium. [17] The chromosome is 8,667,507 bp long with a GC-content of 72.1%, and is predicted to contain 7,825 protein-encoding genes. [17] In terms of taxonomy, "S. coelicolor A3(2)" belongs to the species S. violaceoruber , and is not a validly described separate species; "S. coelicolor A3(2)" is not to be mistaken for the actual S. coelicolor (Müller), although it is often referred to as S. coelicolor for convenience. [18] The transcriptome and translatome analyses of the strain A3(2) were published in 2016. [19]
The first complete genome sequence of S. avermitilis was completed in 2003. [20] Each of these genomes forms a chromosome with a linear structure, unlike most bacterial genomes, which exist in the form of circular chromosomes. [21] The genome sequence of S. scabiei , a member of the genus with the ability to cause potato scab disease, has been determined at the Wellcome Trust Sanger Institute. At 10.1 Mbp long and encoding 9,107 provisional genes, it is the largest known Streptomyces genome sequenced, probably due to the large pathogenicity island. [21] [22]
The genomes of the various Streptomyces species demonstrate remarkable plasticity, via ancient single gene duplications, block duplications (mainly at the chromosomal arms) and horizontal gene transfer. [5] [23] The size of their chromosome varies from 5.7-12.1 Mbps (average: 8.5 Mbps), the number of chromosomally encoded proteins varies from 4983-10,112 (average: 7130), whereas their high GC content varies from 68.8-74.7% (average: 71.7%). [5] The 95% soft-core proteome of the genus consists of approximately 2000-2400 proteins. [5] The pangenome is open. [24] [25] In addition, significant genomic plasticity is observed even between strains of the same species, where the number of accessory proteins (at the species level) ranges from 250 to more than 3000. [5] Intriguingly, a correlation has been observed between the number of carbohydrate-active enzymes and secondary metabolite biosynthetic gene clusters (siderophores, e-Polylysin and type III lanthipeptides) that are related to competition among bacteria, in Streptomyces species. [5] Streptomycetes are major biomass degraders, mainly via their carbohydrate-active enzymes. [26] Thus, they also need to evolve an arsenal of siderophores and antimicrobial agents to suppress competition by other bacteria in these nutrient-rich environments that they create. [5] Several evolutionary analyses have revealed that the majority of evolutionarily stable genomic elements are localized mainly at the central region of the chromosome, whereas the evolutionarily unstable elements tend to localize at the chromosomal arms. [5] [27] [28] [29] [30] Thus, the chromosomal arms emerge as the part of the genome that is mainly responsible for rapid adaptation at both the species and strain level. [5]
Biotechnology researchers have used Streptomyces species for heterologous expression of proteins. Traditionally, Escherichia coli was the species of choice to express eukaryotic genes, since it was well understood and easy to work with. [31] [32] Expression of eukaryotic proteins in E. coli may be problematic. Sometimes, proteins do not fold properly, which may lead to insolubility, deposition in inclusion bodies, and loss of bioactivity of the product. [33] Though E. coli strains have secretion mechanisms, these are of low efficiency and result in secretion into the periplasmic space, whereas secretion by a Gram-positive bacterium such as a Streptomyces species results in secretion directly into the extracellular medium. In addition, Streptomyces species have more efficient secretion mechanisms than E.coli. The properties of the secretion system is an advantage for industrial production of heterologously expressed protein because it simplifies subsequent purification steps and may increase yield. These properties among others make Streptomyces spp. an attractive alternative to other bacteria such as E. coli and Bacillus subtilis . [33] In addition, the inherently high genomic instability suggests that the various Streptomycetes genomes may be amenable to extensive genome reduction for the construction of synthetic minimal genomes with industrial applications. [5]
Several species belonging to this genus have been found to be pathogenic to plants: [12]
Streptomyces is the largest antibiotic-producing genus, producing antibacterial, antifungal, and antiparasitic drugs, and also a wide range of other bioactive compounds, such as immunosuppressants. [36] Almost all of the bioactive compounds produced by Streptomyces are initiated during the time coinciding with the aerial hyphal formation from the substrate mycelium. [15]
Streptomycetes produce numerous antifungal compounds of medicinal importance, including nystatin (from S. noursei ), amphotericin B (from S. nodosus ), [37] and natamycin (from S. natalensis ).
Members of the genus Streptomyces are the source for numerous antibacterial pharmaceutical agents; among the most important of these are:
Clavulanic acid (from S. clavuligerus ) is a drug used in combination with some antibiotics (like amoxicillin) to block and/or weaken some bacterial-resistance mechanisms by irreversible beta-lactamase inhibition. Novel antiinfectives currently being developed include Guadinomine (from Streptomyces sp. K01-0509), [54] a compound that blocks the Type III secretion system of Gram-negative bacteria.
S. avermitilis is responsible for the production of one of the most widely employed drugs against nematode and arthropod infestations, avermectin, [55] and thus its derivatives including ivermectin.
Less commonly, streptomycetes produce compounds used in other medical treatments: migrastatin (from S. platensis) and bleomycin (from S. verticillus) are antineoplastic (anticancer) drugs; boromycin (from S. antibioticus ) exhibits antiviral activity against the HIV-1 strain of HIV, as well as antibacterial activity. Staurosporine (from S. staurosporeus ) also has a range of activities from antifungal to antineoplastic (via the inhibition of protein kinases).
S. hygroscopicus and S. viridochromogenes produce the natural herbicide bialaphos.
Saptomycins are chemical compounds isolated from Streptomyces. [56]
Sirex wasps cannot perform all of their own cellulolytic functions and so some Streptomyces do so in symbiosis with the wasps. [57] Book et al. have investigated several of these symbioses. [57] Book et al., 2014 and Book et al., 2016 identify several lytic isolates. [57] The 2016 study isolates Streptomyces sp. Amel2xE9 and Streptomyces sp. LamerLS-31b and finds that they are equal in activity to the previously identified Streptomyces sp. SirexAA-E. [57]
Bacillus is a genus of Gram-positive, rod-shaped bacteria, a member of the phylum Bacillota, with 266 named species. The term is also used to describe the shape (rod) of other so-shaped bacteria; and the plural Bacilli is the name of the class of bacteria to which this genus belongs. Bacillus species can be either obligate aerobes which are dependent on oxygen, or facultative anaerobes which can survive in the absence of oxygen. Cultured Bacillus species test positive for the enzyme catalase if oxygen has been used or is present.
Pseudomonas fluorescens is a common Gram-negative, rod-shaped bacterium. It belongs to the Pseudomonas genus; 16S rRNA analysis as well as phylogenomic analysis has placed P. fluorescens in the P. fluorescens group within the genus, to which it lends its name.
Agrobacterium tumefaciens is the causal agent of crown gall disease in over 140 species of eudicots. It is a rod-shaped, Gram-negative soil bacterium. Symptoms are caused by the insertion of a small segment of DNA, from a plasmid into the plant cell, which is incorporated at a semi-random location into the plant genome. Plant genomes can be engineered by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors.
Mycobacterium smegmatis is an acid-fast bacterial species in the phylum Actinomycetota and the genus Mycobacterium. It is 3.0 to 5.0 µm long with a bacillus shape and can be stained by Ziehl–Neelsen method and the auramine-rhodamine fluorescent method. It was first reported in November 1884 by Lustgarten, who found a bacillus with the staining appearance of tubercle bacilli in syphilitic chancres. Subsequent to this, Alvarez and Tavel found organisms similar to that described by Lustgarten also in normal genital secretions (smegma). This organism was later named M. smegmatis.
Lacticaseibacillus casei is an organism that belongs to the largest genus in the family Lactobacillaceae, a lactic acid bacteria (LAB), that was previously classified as Lactobacillus casei. This bacteria has been identified as facultatively anaerobic or microaerophilic, acid-tolerant, non-spore-forming bacteria.
The avermectins are a series of drugs and pesticides used to treat parasitic worm infestations and to reduce insect pests. They are a group of 16-membered macrocyclic lactone derivatives with potent anthelmintic and insecticidal properties. These naturally occurring compounds are generated as fermentation products by Streptomyces avermitilis, a soil actinomycete. Eight different avermectins were isolated in four pairs of homologue compounds, with a major (a-component) and minor (b-component) component usually in ratios of 80:20 to 90:10. Avermectin B1, a mixture of B1a and B1b, is the drug and pesticide abamectin. Other anthelmintics derived from the avermectins include ivermectin, selamectin, doramectin, eprinomectin.
Pseudomonas stutzeri is a Gram-negative soil bacterium that is motile, has a single polar flagellum, and is classified as bacillus, or rod-shaped. While this bacterium was first isolated from human spinal fluid, it has since been found in many different environments due to its various characteristics and metabolic capabilities. P. stutzeri is an opportunistic pathogen in clinical settings, although infections are rare. Based on 16S rRNA analysis, this bacterium has been placed in the P. stutzeri group, to which it lends its name.
Streptomyces griseus is a species of bacteria in the genus Streptomyces commonly found in soil. A few strains have been also reported from deep-sea sediments. It is a Gram-positive bacterium with high GC content. Along with most other streptomycetes, S. griseus strains are well known producers of antibiotics and other such commercially significant secondary metabolites. These strains are known to be producers of 32 different structural types of bioactive compounds. Streptomycin, the first antibiotic ever reported from a bacterium, comes from strains of S. griseus. Recently, the whole genome sequence of one of its strains had been completed.
Penicillium chrysogenum is a species of fungus in the genus Penicillium. It is common in temperate and subtropical regions and can be found on salted food products, but it is mostly found in indoor environments, especially in damp or water-damaged buildings. It has been recognised as a species complex that includes P. notatum, P. meleagrinum, and P. cyaneofulvum. Molecular phylogeny has established that Alexander Fleming's first discovered penicillin producing strain is of a distinct species, P. rubens, and not of P. notatum. It has rarely been reported as a cause of human disease. It is the source of several β-lactam antibiotics, most significantly penicillin. Other secondary metabolites of P. chrysogenum include roquefortine C, meleagrin, chrysogine, 6-MSA YWA1/melanin, andrastatin A, fungisporin, secalonic acids, sorbicillin, and PR-toxin.
Streptomyces scabiei is a streptomycete bacterium species found in soils around the world. Unlike most of the 500 or so Streptomyces species it is a plant pathogen causing corky lesions to form on tuber and root crops as well as decreasing the growth of seedlings. Along with other closely related species it causes the potato disease common scab, which is an economically important disease in many potato growing areas. It was first described in 1892, being classified as a fungus, before being renamed in 1914 and again in 1948. Several other species of Streptomyces cause similar diseases to S. scabiei but other, more closely related species, do not.
Streptomyces avermitilis is a species of bacteria in the genus Streptomyces. This bacterium was discovered by Satoshi Ōmura in Shizuoka Prefecture, Japan.
Penicillium rubens is a species of fungus in the genus Penicillium and was the first species known to produce the antibiotic penicillin. It was first described by Philibert Melchior Joseph Ehi Biourge in 1923. For the discovery of penicillin from this species Alexander Fleming shared the Nobel Prize in Physiology or Medicine in 1945. The original penicillin-producing type has been variously identified as Penicillium rubrum, P. notatum, and P. chrysogenum among others, but genomic comparison and phylogenetic analysis in 2011 resolved that it is P. rubens. It is the best source of penicillins and produces benzylpenicillin (G), phenoxymethylpenicillin (V) and octanoylpenicillin (K). It also produces other important bioactive compounds such as andrastin, chrysogine, fungisporin, roquefortine, and sorbicillins.
Streptomyces isolates have yielded the majority of human, animal, and agricultural antibiotics, as well as a number of fundamental chemotherapy medicines. Streptomyces is the largest antibiotic-producing genus of Actinomycetota, producing chemotherapy, antibacterial, antifungal, antiparasitic drugs, and immunosuppressants. Streptomyces isolates are typically initiated with the aerial hyphal formation from the mycelium.
Mervyn James Bibb is an Emeritus Fellow at the John Innes Centre, Norwich, UK.
Streptomyces antibioticus is a gram-positive bacterium discovered in 1941 by Nobel-prize-winner Selman Waksman and H. Boyd Woodruff. Its name is derived from the Greek "strepto-" meaning "twisted", alluding to this genus' chain-like spore production, and "antibioticus", referring to this species' extensive antibiotic production. Upon its first characterization, it was noted that S. antibioticus produces a distinct soil odor.
Streptomyces albidoflavus is a bacterium species from the genus of Streptomyces which has been isolated from soil from Poland. Streptomyces albidoflavus produces dibutyl phthalate and streptothricins.
Streptomyces lavendulae is a species of bacteria from the genus Streptomyces. It is isolated from soils globally and is known for its production of medically useful biologically active metabolites. To see a photo of this organism click here.
Streptomyces glaucescens is a bacterium species from the genus of Streptomyces which has been isolated from soil. Streptomyces glaucescens produces tetracenomycin C, tetracenomycin D and tetracenomycin E.
Streptomyces sanglieri is a bacterium species from the genus of Streptomyces which has been isolated from soil from a hay meadow. Streptomyces sanglieri produces the antibiotic lactonamycin Z.
Streptomyces vietnamensis is a bacterium species from the genus of Streptomyces which has been isolated from forest soil in Vietnam.
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