Chloroflexota

The Chloroflexota are a phylum of bacteria containing isolates with a diversity of phenotypes, including members that are aerobic thermophiles, which use oxygen and grow well in high temperatures; anoxygenic phototrophs, which use light for photosynthesis (green non-sulfur bacteria); and anaerobic halorespirers, which uses halogenated organics (such as the toxic chlorinated ethenes and polychlorinated biphenyls) as electron acceptors.

The members of the phylum Chloroflexota are monoderms (that is, have one cell membrane with no outer membrane), but they stain mostly gram-negative. Many well-studied phyla of bacteria are diderms and stain gram-negative, whereas well-known monoderms that stain Gram-positive include Firmicutes (or Bacillota) (low G+C gram-positives), Actinomycetota (high-G+C gram-positives) and Deinococcota (gram-positive diderms with thick peptidoglycan).

History
The taxon name was created in the 2001 edition of Volume 1 of Bergey's Manual of Systematic Bacteriology and is the Latin plural of the name Chloroflexus, the name of the type genus of the phylum, a common practice.

In 1987, Carl Woese, regarded as one of the forerunner of the molecular phylogeny revolution, divided Eubacteria into 11 divisions based on 16S ribosomal RNA (SSU) sequences and grouped the genera Chloroflexus, Herpetosiphon and Thermomicrobium into the "green non-sulfur bacteria and relatives", which was temporarily renamed as "Chloroflexi" in Volume One of Bergey's Manual of Systematic Bacteriology.

Chloroflexota being a deep branching phylum (see Bacterial phyla), it was considered in Volume One of Bergey's Manual of Systematic Bacteriology to include a single class with the same name. Since 2001, however, new classes have been created thanks to newly discovered species, and the phylum Chloroflexi is now divided into several classes.

"Dehalococcoidetes" is a placeholder name given by Hugenholtz & Stackebrandt, 2004, after "Dehalococcoides ethenogenes" a species partially described in 1997. The first species fully described was Dehalogenimonas lykanthroporepellens, by Moe et al. 2009, but in the description of that species the class was not made official nor were families or orders laid out as the two species share only 90% 16S ribosomal RNA identity, meaning that they could fall in different families or even orders.

Recent phylogenetic analysis of the Chloroflexota has found very weak support for the grouping together of the different classes currently part of the phylum. The six classes that make up the phylum did not consistently form a well-supported clade in phylogenetic trees based on concatenated sequences for large datasets of proteins, and no conserved signature indels were identified that were uniquely shared by the entire phylum. However, the classes Chloroflexi and Thermomicrobia were found to group together consistently by both the usual phylogenetic means and the identification of shared conserved signature indels in the 50S ribosomal protein L19 and the enzyme UDP-glucose 4-epimerase. It has been suggested that the phylum Chloroflexi sensu stricto should comprise only the classes Chloroflexi and Thermomicrobia, and the other four classes ("Dehalococcoidetes," Anaerolineae, Caldilineae and Ktedonobacteria) may represent one or more independent phyla branching in the neighborhood of the Chloroflexi.

Phylogeny
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN) and National Center for Biotechnology Information (NCBI).

Taxonomy
Genus "Candidatus Caldibacter" corrig. Spieck et al. 2020

Genus "Candidatus Chlorotrichoides" corrig. Oren et al. 2020 ["Candidatus Chlorothrix" Klappenbach & Pierson 2004 non Dyar 1921 non Berger-Perrot 1982 ]

Genus "Candidatus Nitrocaldera" Spieck et al. 2020

Genus "Candidatus Nitrotheca" Spieck et al. 2020

Genus "Candidatus Poriflexus" Kogawa et al. 2022

Class "Limnocylindria" Mehrshad et al. 2018 Class Ktedonobacteria Cavaletti et al. 2007 emend. Yabe et al. 2010 Class "Umbricyclopia" Mehrshad et al. 2018 Class "Bathosphaeria" Mehrshad et al. 2018 Class Tepidiformia Kochetkova et al. 2020 Class Dehalococcoidia Löffler et al. 2013 Class "Thermofontia" corrig. Ward et al. 2018 Class Ardenticatenia Kawaichi et al. 2013 Class "Caldilineia" Oren, Parte & Garrity 2016 ex Cavalier-Smith 2020 Class Thermoflexia Dodsworth et al. 2014 Class "Anaerolineia" Oren, Parte & Garrity 2016 Class Thermomicrobiia Oren, Parte & Garrity 2016 Class "Spiritibacteria" Williams et al. 2024 Class "Martimicrobia" Williams et al. 2024 Class "Tarhunnaeia" Williams et al. 2024 Class "Uliximicrobia" Williams et al. 2024 Class Chloroflexia Gupta et al. 2013
 * Order "Limnocylindrales" Mehrshad et al. 2018
 * Family "Limnocylindraceae" Mehrshad et al. 2018 (SL56)
 * Genus "Candidatus Aquidulcis" corrig. Rodriguez-R et al. 2020
 * Genus "Candidatus Limnocylindrus" Mehrshad et al. 2018
 * Order Thermogemmatisporales Yabe et al. 2011
 * Family Thermogemmatisporaceae Yabe et al. 2011
 * Genus Thermogemmatispora Yabe et al. 2011
 * Order Ktedonobacterales Cavaletti et al. 2007
 * Family Dictyobacteraceae Wang et al. 2019
 * Genus Dictyobacter Yabe et al. 2017
 * Genus Tengunoibacter Wang et al. 2019
 * Family Ktedonobacteriaceae Cavaletti et al. 2007
 * Genus Ktedonobacter corrig. Cavaletti et al. 2007
 * Genus Ktedonospora Yabe et al. 2021
 * Family Ktedonosporobacteraceae Yan et al. 2020
 * Genus Ktedonosporobacter Yan et al. 2020
 * Family Reticulibacteraceae Yabe et al. 2021
 * Genus Reticulibacter Yabe et al. 2021
 * Family Thermosporotrichaceae Yabe et al. 2010
 * Genus Thermosporothrix Yabe et al. 2010
 * Order "Umbricyclopales" Mehrshad et al. 2018
 * Family "Umbricyclopaceae" Mehrshad et al. 2018
 * Genus "Candidatus Umbricyclops" Mehrshad et al. 2018 (TK10)
 * Order "Bathosphaerales" Mehrshad et al. 2018
 * Family "Bathosphaeraceae" Mehrshad et al. 2018
 * Genus "Candidatus Bathosphaera" Mehrshad et al. 2018 (JG30-KF-CM66)
 * Order Tepidiformales Kochetkova et al. 2020
 * Family Tepidiformaceae Kochetkova et al. 2020
 * Genus "Tepidiforma Kochetkova et al. 2020
 * Order Dehalococcoidales Löffler et al. 2013
 * Family Dehalococcoidaceae Löffler et al. 2013
 * Genus Dehalococcoides Löffler et al. 2013
 * Genus Dehalogenimonas Moe et al. 2009
 * Order "Phototrophicales" Zheng et al. 2022
 * Family "Phototrophicaceae" Zheng et al. 2022
 * Genus "Phototrophicus" Zheng et al. 2022
 * Order Ardenticatenales Kawaichi et al. 2013
 * Family Ardenticatenaceae Kawaichi et al. 2013
 * Genus Ardenticatena Kawaichi et al. 2013
 * Order Caldilineales Yamada et al. 2006
 * Genus "Candidatus Defluviifilum" Nierychlo et al. 2019
 * Family "Amarolineaceae" Andersen et al. 2019
 * Genus "Candidatus Amarolinea" Andersen et al. 2019
 * Family Caldilineaceae Yamada et al. 2006
 * Genus Caldilinea Sekiguchi et al. 2003
 * Genus Litorilinea Kale et al. 2013
 * Order Thermoflexales Dodsworth et al. 2014
 * Family Thermoflexaceae Dodsworth et al. 2014
 * Genus "Candidatus Roseilinea" Thiel et al. 2016
 * Genus Thermoflexus Dodsworth et al. 2014
 * Family "Profundisolitariaceae" Mehrshad et al. 2018
 * Genus "Candidatus Profundisolitarius" Mehrshad et al. 2018 (CL500-11)
 * Order "Promineifilales"
 * Family "Promineifilaceae"
 * Genus "Candidatus Promineifilum" corrig. McIlroy et al. 2016
 * Order Aggregatilineales Nakahara et al. 2019
 * Family Aggregatilineaceae Nakahara et al. 2019
 * Genus Aggregatilinea Nakahara et al. 2019
 * Order Anaerolineales Yamada et al. 2006
 * Family Anaerolineaceae Yamada et al. 2006
 * Genus Anaerolinea Sekiguchi et al. 2003 emend. Yamada et al. 2006
 * Genus Bellilinea Yamada et al. 2007
 * Genus "Brevefilum" McIlroy et al. 2017
 * Genus "Candidatus Denitrolinea" Okubo et al. 2021
 * Genus "Desulfolinea" Van Vliet et al. 2020
 * Genus Flexilinea Sun et al. 2015
 * Genus Levilinea Yamada et al. 2006
 * Genus Leptolinea Yamada et al. 2006
 * Genus Longilinea Yamada et al. 2007
 * Genus Ornatilinea Podosokorskaya et al. 2013
 * Genus Pelolinea Imachi et al. 2014
 * Genus Thermomarinilinea Nunoura et al. 2013
 * Genus "Thermanaerothrix" Gregoire et al. 2011
 * Genus "Candidatus" Villigracilis'' Nierychlo et al. 2019
 * Order Sphaerobacterales Stackebrandt, Rainey & Ward-Rainey 1997
 * Family Sphaerobacteraceae Stackebrandt, Rainey & Ward-Rainey 1997
 * Genus Nitrolancea Sorokin et al. 2014 ["Nitrolancetus" Sorokin et al. 2012 ]
 * Genus Sphaerobacter Demharter et al. 1989
 * Order Thermomicrobiales Garrity & Holt 2002
 * Family Thermomicrobiaceae Garrity & Holt 2002
 * Genus Thermalbibacter Zhao et al. 2023
 * Genus Thermomicrobium Jackson, Ramaley & Meinschein 1973
 * Genus Thermorudis King & King 2014
 * Order "Spiritibacterales" Williams et al. 2024
 * Family "Spiritibacteraceae" Williams et al. 2024
 * Genus "Candidatus Spiritibacter" Williams et al. 2024
 * Genus "Candidatus Aglaurobacter" Williams et al. 2024
 * Genus "Candidatus Otrerea" Williams et al. 2024
 * Order "Martimicrobiales" Williams et al. 2024
 * Family "Martimicrobiaceae" Williams et al. 2024
 * Genus "Candidatus Martimicrobium" Williams et al. 2024
 * Genus "Candidatus Laranimicrobium" Williams et al. 2024
 * Order "Tarhunnaeales" Williams et al. 2024
 * Family "Tarhunnaeaceae" Williams et al. 2024
 * Genus "Candidatus Tarhunnaea" Williams et al. 2024
 * Genus "Candidatus Sutekhia" Williams et al. 2024
 * Order "Uliximicrobiales" Williams et al. 2024
 * Family "Uliximicrobiaceae" Williams et al. 2024
 * Genus "Candidatus Uliximicrobium" Williams et al. 2024
 * Genus "Dehalobium" Wu et al. 2002
 * Genus "Candidatus Lithoflexus" Saghai et al. 2020
 * Genus "Candidatus Sarcinithrix" Nierychlo et al. 2019
 * Order "Thermobaculales"
 * Family "Thermobaculaceae"
 * Genus "Thermobaculum" Botero et al. 2004
 * Order Kallotenuales Cole et al. 2013
 * Family Kallotenuaceae Cole et al. 2013
 * Genus Kallotenue Cole et al. 2013
 * Order Herpetosiphonales Gupta et al. 2013
 * Family Herpetosiphonaceae Gupta et al. 2013
 * Genus "Candidatus Anthektikosiphon" Ward, Fischer & McGlynn 2020
 * Genus Herpetosiphon Holt & Lewin 1968 [Flavilitoribacter García-López et al. 2020 ]
 * Order Chloroflexales Gupta et al. 2013
 * Suborder Roseiflexineae Gupta et al. 2013
 * Family Roseiflexaceae Gupta et al. 2013 ["Kouleotrichaceae" Mehrshad et al. 2018 ]
 * Genus "Kouleothrix" Kohno et al. 2002
 * Genus Heliothrix Pierson et al. 1986
 * Genus Roseiflexus Hanada et al. 2002
 * Suborder Chloroflexineae Gupta et al. 2013
 * Family Chloroflexaceae Gupta et al. 2013
 * Genus Candidatus Chloranaerofilum Thiel et al. 2016
 * Genus Chloroflexus Pierson & Castenholz 1974 ["Chlorocrinis"]
 * Family Oscillochloridaceae Gupta et al. 2013
 * Genus Candidatus Chloroploca Gorlenko et al. 2014
 * Genus Chloronema ♪ Dubinina & Gorlenko 1975
 * Genus Oscillochloris Gorlenko & Pivovarova 1989
 * Genus Candidatus Viridilinea Grouzdev et al. 2018

Etymology
The name Chloroflexi is a Neolatin nominative case masculine plural of Chloroflexus, which is the name of the first genus described. The noun is a combination of the Greek adjective chloros, -a, on (χλωρός, -ά, -όν), meaning "greenish-yellow," and the Latin masculine passive perfect participle flexus (of flecto), meaning "bent." The etymology is unrelated to chlorine, an element that was discovered in 1810 by Sir Humphry Davy and named after its pale green colour. Another phylum with the same root is Chlorobiota, whereas "Cyanobacteria" has the root cyanos (κύανος), meaning "blue-green."

Unlike some other phyla, there is no theme root in the name of genera of Chloroflexota, and in fact many genera beginning with "Chloro-" or ending in "-chloris" are either cyanobacteria or chlorobi.