Actinomycetota

{{Short description|Phylum of bacteria}} {{Automatic taxobox | image = Actinomyces_israelii.jpg | image_caption = Scanning electron micrograph of ''Actinomyces israelii''. | taxon = Actinomycetota | authority = Goodfellow 2021<ref>{{cite journal | vauthors = Oren A, Garrity GM | title = Valid publication of the names of forty-two phyla of prokaryotes | journal = Int J Syst Evol Microbiol | year = 2021 | volume = 71 | issue = 10 | page = 5056 | doi = 10.1099/ijsem.0.005056 | pmid = 34694987 | s2cid = 239887308 | doi-access = free }}</ref><ref name=LPSN/> | type_genus = ''Actinomyces'' | type_genus_authority = Harz 1877 (Approved Lists 1980) | subdivision_ranks = Classes | subdivision_ref = <ref name=NCBI/> | subdivision = * Acidimicrobiia * Actinomycetes * "Aquicultoria" * Coriobacteriia * "Geothermincolia" * "Humimicrobiia" * Nitriliruptoria * Rubrobacteria * "Syntrophaliphaticia" * Thermoleophilia | synonyms = * "Actinobacteraeota" Oren ''et al''. 2015 * "Actinobacteria" Goodfellow 2012<ref>{{cite book |vauthors=Goodfellow M | chapter = Phylum XXVI. ''Actinobacteria'' phyl. nov. |veditors=Goodfellow M, Kämpfer P, Trujillo ME, Suzuki K, Ludwig W, Whitman WB | title = Bergey's Manual of Systematic Bacteriology | edition = 2nd | volume =5 | publisher = Springer | location = New York, NY | year = 2012 | pages = 33–34}}</ref> * "Actinobacteria" Margulis 1974 ''ex'' Cavalier-Smith 2020 * "Actinobacteria" Stackebrandt, Rainey & Ward-Rainey 1997 * "Actinobacteriota" Whitman ''et al''. 2018 * "Actinomycetes" Krasil'nikov 1949 }}

The '''Actinomycetota''' (previously known as '''"Actinobacteria"''') are a diverse phylum of Gram-positive bacteria with high guanine-cytosine content (GC content or G+C content).<ref>{{cite journal | vauthors = Gao B, Gupta RS | title = Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria | journal = Microbiology and Molecular Biology Reviews | volume = 76 | issue = 1 | pages = 66–112 | date = March 2012 | pmid = 22390973 | pmc = 3294427 | doi = 10.1128/MMBR.05011-11 | bibcode = 2012MMBR...76...66G }}</ref> They can be terrestrial or aquatic.<ref name="pmid18003601">{{cite journal |vauthors=Servin JA, Herbold CW, Skophammer RG, Lake JA |title=Evidence excluding the root of the tree of life from the actinobacteria |journal=Mol. Biol. Evol. |volume=25 |issue=1 |pages=1–4 |date=January 2008 |pmid=18003601 |doi=10.1093/molbev/msm249 |doi-access=free }}</ref> They are of great importance to land flora because of their contributions to soil systems. In soil, they help decompose organic matter of dead organisms so the molecules can be taken up anew by plants. While this role is also played by fungi, actinomycetota are much smaller and likely do not occupy the same ecological niche. In this role, the colonies often grow extensive mycelia, as fungi do, and the name of an important order of the phylum, Actinomycetales (the actinomycetes), reflects that they were long believed to be fungi. Some soil actinomycetota (such as ''Frankia'') live symbiotically with the plants whose roots pervade the soil, fixing nitrogen for the plants in exchange for access to some of the plant's saccharides. Other species, such as many members of the genus ''Mycobacterium'', are important pathogens.

Beyond the great interest in Actinomycetota for their soil role, much is yet to be learned about them. Although currently understood primarily as soil bacteria, they might be more abundant in fresh waters.<ref name="amazonMetagenome">{{cite journal | vauthors = Ghai R, Rodriguez-Valera F, McMahon KD, Toyama D, Rinke R, Cristina Souza de Oliveira T, Wagner Garcia J, Pellon de Miranda F, Henrique-Silva F | display-authors = 6 | title = Metagenomics of the water column in the pristine upper course of the Amazon river | journal = PLOS ONE | volume = 6 | issue = 8 | article-number = e23785 | year = 2011 | pmid = 21915244 | pmc = 3158796 | doi = 10.1371/journal.pone.0023785 | veditors = Lopez-Garcia P | doi-access = free | bibcode = 2011PLoSO...623785G }}</ref> Actinomycetota is one of the dominant bacterial phyla and contains one of the largest of bacterial genera: ''Streptomyces''.<ref>{{cite book | vauthors = Hogan CM | date = 2010 | chapter-url = http://www.eoearth.org/article/Bacteria?topic=49480 | chapter = Bacteria | title = Encyclopedia of Earth | veditors = Draggan S, Cleveland CJ | publisher = National Council for Science and the Environment | location = Washington DC | archive-url = https://web.archive.org/web/20110511132823/http://www.eoearth.org/article/Bacteria?topic=49480 | archive-date = 2011-05-11 }}</ref> ''Streptomyces'' and other actinomycetota are major contributors to biological buffering of soils.<ref>{{cite journal | vauthors = Ningthoujam DS, Sanasam S, Tamreihao K, Nimaichand S | date = November 2009 | title = Antagonistic activities of local actinomycete isolates against rice fungal pathogens | journal = African Journal of Microbiology Research | volume = 3 | issue = 11| pages = 737–742 }}</ref> They are also the source of many antibiotics.<ref>{{Cite journal |last1=Donald |first1=Lavinia |last2=Pipite |first2=Atanas |last3=Subramani |first3=Ramesh |last4=Owen |first4=Jeremy |last5=Keyzers |first5=Robert A. |last6=Taufa |first6=Taitusi |date=2022 |title=Streptomyces: Still the Biggest Producer of New Natural Secondary Metabolites, a Current Perspective |journal=Microbiology Research |language=en |volume=13 |issue=3 |pages=418–465 |doi=10.3390/microbiolres13030031 |doi-access=free |issn=2036-7481}}</ref><ref name=j.bjid.2012.08.014>{{Cite journal |last1=Procópio |first1=Rudi Emerson de Lima |last2=Silva |first2=Ingrid Reis da |last3=Martins |first3=Mayra Kassawara |last4=Azevedo |first4=João Lúcio de |last5=Araújo |first5=Janete Magali de |date=2012 |title=Antibiotics produced by Streptomyces |journal=The Brazilian Journal of Infectious Diseases|volume=16 |issue=5 |pages=466–471 |doi=10.1016/j.bjid.2012.08.014 |issn=1678-4391 |pmid=22975171|doi-access=free }}</ref>

Bacteria of the Actinomycetota genus ''Bifidobacterium'' are the most common in the microbiome of human infants.<ref>{{cite journal | vauthors = Turroni F, Peano C, Pass DA, Foroni E, Severgnini M, Claesson MJ, Kerr C, Hourihane J, Murray D, Fuligni F, Gueimonde M, Margolles A, De Bellis G, O'Toole PW, van Sinderen D, Marchesi JR, Ventura M | title = Diversity of bifidobacteria within the infant gut microbiota | journal = PLOS ONE | volume = 7 | issue = 5 | article-number = e36957 | date = 2012-05-11 | pmid = 22606315 | pmc = 3350489 | doi = 10.1371/journal.pone.0036957 | bibcode = 2012PLoSO...736957T | doi-access = free }}</ref> Although adults have fewer bifidobacteria, intestinal bifidobacteria help maintain the mucosal barrier and reduce lipopolysaccharides in the intestine.<ref name="Pinzone-2012">{{cite journal | vauthors = Pinzone MR, Celesia BM, Di Rosa M, Cacopardo B, Nunnari G | title = Microbial translocation in chronic liver diseases | journal = International Journal of Microbiology | volume = 2012 | article-number = 694629 | year = 2012 | pmid = 22848224 | pmc = 3405644 | doi = 10.1155/2012/694629 | doi-access = free }}</ref>

Although some of the largest and most complex bacterial cells belong to the Actinomycetota, the group of marine Actinomarinales has been described as possessing the smallest free-living prokaryotic cells.<ref name="Actinomarina">{{cite journal |vauthors=Ghai R, Mizuno CM, Picazo A, Camacho A, Rodriguez-Valera F |title=Metagenomics uncovers a new group of low GC and ultra-small marine Actinobacteria |journal=Scientific Reports |volume=3 |year=2013 |doi=10.1038/srep02471 |pmid= 23959135 |pmc=3747508 |article-number=2471|bibcode=2013NatSR...3.2471G}}</ref>

Some Siberian or Antarctic actinomycetota are said to be the oldest living organisms on Earth, frozen in permafrost at around half a million years ago.<ref>{{cite web | vauthors = Sample I | date = 2 May 2010 | url = https://www.theguardian.com/theobserver/2010/may/02/rachel-sussman-oldest-plants | title = The oldest living organisms: ancient survivors with a fragile future | archive-url = https://web.archive.org/web/20130302140701/http://www.guardian.co.uk/theobserver/2010/may/02/rachel-sussman-oldest-plants | archive-date=2013-03-02 | url-status = live | work = The Guardian }}</ref><ref>{{Cite web | vauthors = Hanson J | url=https://www.itsokaytobesmart.com/post/91481365622/siberian-actinobacteria-oldest-living-thing | work = It's Okay to be Smart | title = The oldest living thing in the world | access-date=2018-07-13 | archive-url=https://web.archive.org/web/20180713074804/https://www.itsokaytobesmart.com/post/91481365622/siberian-actinobacteria-oldest-living-thing | archive-date=2018-07-13 }}</ref> The symptoms of life were detected by {{co2}} release from permafrost samples 640 kya or younger.<ref>{{cite journal | vauthors = Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, Brand T, Gilbert MT, Zuber MT, Bunce M, Rønn R, Gilichinsky D, Froese D, Willerslev E | display-authors = 6 | title = Ancient bacteria show evidence of DNA repair | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 36 | pages = 14401–14405 | date = September 2007 | pmid = 17728401 | pmc = 1958816 | doi = 10.1073/pnas.0706787104 | doi-access = free | bibcode = 2007PNAS..10414401J }}</ref>

==General== Most actinomycetota of medical or economic significance are in class Actinomycetia, and belong to the order Actinomycetales. While many of these cause disease in humans, ''Streptomyces'' is notable as a source of antibiotics.<ref name=j.bjid.2012.08.014/>

Of those actinomycetota not in the Actinomycetales, ''Gardnerella'' is one of the most researched. Classification of ''Gardnerella'' is controversial, and MeSH catalogues it as both a Gram-positive and Gram-negative organism.<ref>{{MeshName|Gardnerella}}</ref>

Actinomycetota, especially ''Streptomyces'' spp., are recognized as the producers of many bioactive metabolites that are useful to humans in medicine, such as antibacterials,<ref>{{cite journal | vauthors = Mahajan GB | year = 2012 | title = Antibacterial agents from actinomycetes - a review | journal = Frontiers in Bioscience | volume = 4 | pages = 240–53 | article-number = 373 | doi = 10.2741/e373 }}</ref> antifungals,<ref>{{cite journal | vauthors = Gupte M, Kulkarni P, Ganguli BN | title = Antifungal antibiotics | journal = Applied Microbiology and Biotechnology | volume = 58 | issue = 1 | pages = 46–57 | date = January 2002 | pmid = 11831475 | doi = 10.1007/s002530100822 | s2cid = 8015426 }}</ref> antivirals, antithrombotics, immunomodifiers, antitumor drugs, and enzyme inhibitors; and in agriculture, including insecticides, herbicides, fungicides, and growth-promoting substances for plants and animals.<ref>{{cite journal | vauthors = Bressan W | year = 2003 | title =Biological control of maize seed pathogenic fungi by use of actinomycetes | journal = Biocontrol | volume = 48 | issue =2 | pages = 233–240 | doi=10.1023/a:1022673226324| bibcode = 2003BioCo..48..233B | s2cid = 29320215 }}</ref> Actinomycetota-derived antibiotics that are important in medicine include aminoglycosides, anthracyclines, chloramphenicol, macrolides, tetracyclines, etc.{{citation needed|date=January 2023}}

Actinomycetota have high guanine and cytosine content in their DNA.<ref name="pmid17804669">{{cite journal | vauthors = Ventura M, Canchaya C, Tauch A, Chandra G, Fitzgerald GF, Chater KF, van Sinderen D | title = Genomics of Actinobacteria: tracing the evolutionary history of an ancient phylum | journal = Microbiology and Molecular Biology Reviews | volume = 71 | issue = 3 | pages = 495–548 | date = September 2007 | pmid = 17804669 | pmc = 2168647 | doi = 10.1128/MMBR.00005-07 | bibcode = 2007MMBR...71..495V | hdl = 11381/1721088 }}</ref> The GC content of actinomycetota can be as high as 70%, though some may have a low GC content.<ref name="lowGCActinoacteria">{{cite journal | vauthors = Ghai R, McMahon KD, Rodriguez-Valera F | title = Breaking a paradigm: cosmopolitan and abundant freshwater actinobacteria are low GC | journal = Environmental Microbiology Reports | volume = 4 | issue = 1 | pages = 29–35 | date = February 2012 | pmid = 23757226 | doi = 10.1111/j.1758-2229.2011.00274.x | bibcode = 2012EnvMR...4...29G }}</ref>

Analysis of glutamine synthetase sequence has been suggested for phylogenetic analysis of the Actinomycetota.<ref name="pmid19245690">{{cite journal |vauthors=Hayward D, van Helden PD, Wiid IJ |title=Glutamine synthetase sequence evolution in the mycobacteria and their use as molecular markers for Actinomycetota speciation |journal=BMC Evol. Biol. |volume=9|page=48 |year=2009 |pmid=19245690 |pmc=2667176 |doi=10.1186/1471-2148-9-48 |doi-access=free }}</ref>

==Phylogeny== The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)<ref name=LPSN>{{lpsn3|phylum/actinomycetota|Actinomycetota}}</ref> and National Center for Biotechnology Information (NCBI).<ref name=NCBI>{{cite web |author=C.L. Schoch |url=https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?command=show&mode=tree&id=201174&lvl=3 |title=Actinomycetota |access-date=2025-02-28 |publisher=National Center for Biotechnology Information (NCBI) taxonomy database |display-authors=et al.}}</ref>

{| class="wikitable" |- ! colspan=1 | Whole-genome based phylogeny<ref name="Nouioui">{{cite journal |vauthors=Nouioui I, Carro L, García-López M, Meier-Kolthoff JP, Woyke T, Kyrpides NC, Pukall R, Klenk HP, Goodfellow M, Markus Göker M | year = 2018 | title = Genome-Based Taxonomic Classification of the Phylum ''Actinobacteria'' | journal = Front. Microbiol. | volume = 9 | article-number = 2007 | pmid = 30186281 | pmc = 6113628 | doi = 10.3389/fmicb.2018.02007 | doi-access = free }}</ref> ! colspan=1 | 16S rRNA based LTP_10_2024<ref>{{cite web |title=The LTP |url=https://imedea.uib-csic.es/mmg/ltp/#LTP| access-date=10 December 2024}}</ref><ref>{{cite web |title=LTP_all tree in newick format |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_all_10_2024.ntree |access-date=10 December 2024}}</ref><ref>{{cite web |title=LTP_10_2024 Release Notes |url=https://imedea.uib-csic.es/mmg/ltp/wp-content/uploads/ltp/LTP_10_2024_release_notes.pdf |access-date=10 December 2024}}</ref> ! colspan=1 | 120 marker proteins based GTDB 10-RS226<ref name="about">{{cite web |title=GTDB release 10-RS226 |url=https://gtdb.ecogenomic.org/about#4%7C |website=Genome Taxonomy Database|access-date=1 May 2025}}</ref><ref name="tree_bac">{{cite web |title=bac120_r226.sp_label |url=https://data.gtdb.ecogenomic.org/releases/release226/226.0/auxillary_files/bac120_r226.sp_labels.tree |website=Genome Taxonomy Database|access-date=1 May 2025}}</ref><ref name="taxon_history">{{cite web |title=Taxon History |url=https://gtdb.ecogenomic.org/taxon_history/ |website=Genome Taxonomy Database|access-date=1 May 2025}}</ref> |- | style="vertical-align:top| {{Clade | style=font-size:90%;line-height:80% |label1=Actinomycetota |1={{clade |1=Rubrobacteria |2={{clade |1=Thermoleophilia |2={{clade |1=Coriobacteriia |2={{clade |1=Acidimicrobiia |2={{clade |1=Nitriliruptoria |2=Actinomycetia }} }} }} }} }} }} | {{Clade | style=font-size:90%;line-height:80% |label1=Actinomycetota |1={{clade |1=Bifidobacteriales |2={{clade |1={{clade |1={{clade |1=Acidimicrobiia |2=Nitriliruptoria }} |2={{clade |1={{clade |1=Rubrobacteria |2=Thermoleophilia }} |2=Coriobacteriia }} }} |2=Actinomycetia }} }} }} | {{clade|style=font-size:90%;line-height:80% |label1=Actinomycetota |1={{Clade |1={{Clade |1={{Clade |1="Geothermincolia" Jiao et al. 2021 |2={{Clade |1="Humimicrobiia" Jiao et al. 2021 |2={{Clade |1="Geothermocultorales" Jiao et al. 2021 {CALKMS01} |2="Aquicultoria" Jiao et al. 2021 }} }} }} |2=Coriobacteriia König 2013 }} |2={{Clade |1={{Clade |1=Rubrobacteria Suzuki 2013 |2=Thermoleophilia Suzuki and Whitman 2013 }} |2={{Clade |1=Acidimicrobiia Norris 2013 |2={{Clade |1=Nitriliruptoria Ludwig et al. 2013 |2=Actinomycetia Salam et al. 2020 }} }} }} }} }} |}

== References == {{Reflist|2}}

== Further reading == {{Refbegin}} * {{cite journal | vauthors = Baltz RH |title=Antibiotic discovery from Actinomycetes: Will a renaissance follow the decline and fall? |year=2005 |journal=SIM News |volume=55 |pages=186–196}} * {{cite journal | vauthors = Baltz RH |year=2007 |journal=Microbe |volume=2 |issue=3 |pages=125–131 |title=Antimicrobials from Actinomycetes: Back to the Future |url=http://www.microbemagazine.org/index.php?option=com_content&view=article&id=2221:antimicrobials-from-actinomycetes-back-to-the-future&catid=546&Itemid=731 |archive-url=https://web.archive.org/web/20131231184650/http://www.microbemagazine.org/index.php?option=com_content&view=article&id=2221%3Aantimicrobials-from-actinomycetes-back-to-the-future&catid=546&Itemid=731 |archive-date=2013-12-31 }} * {{cite conference| vauthors = Pandey B, Ghimire P, Agrawal VP |date=January 12–15, 2004 |conference=International Conference on the Great Himalayas: Climate, Health, Ecology, Management and Conservation |location=Kathmandu |title=Studies on the antibacterial activity of the Actinomycetes isolated from the Khumbu Region of Nepal |url=http://www.aehms.org/pdf/Panday%20F.pdf |archive-url=https://web.archive.org/web/20130810065528/http://www.aehms.org/pdf/panday%20f.pdf |archive-date=2013-08-10 }} {{Refend}}

==External links== * [http://www.broad.mit.edu/annotation/genome/streptomyces_group/MultiHome.html Actinomycetes genome database]

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