Phylum "Chloroflexi"

Name: "Chloroflexi" Garrity and Holt 2001

Category: Phylum

Proposed as: phyl. nov.

Etymology: N.L. masc. pl. n. Chloroflexi, the phylum of the genus Chloroflexus (nominative plural of Chloroflexus)

Gender: masculine

Type order: Chloroflexales Gupta et al. 2013

Original publication: Garrity GM, Holt JG. Phylum BVI. Chloroflexi phy. nov. In: Boone DR, Castenholz RW, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1 (The Archaea and the Deeply Branching and Phototrophic Bacteria), Springer, New York, 2001, p. 427-446.

IJSEM list: Anonymous. Validation list no. 85. List of new names and new combinations previously effectively, but not validly, published. Int J Syst Evol Microbiol 2002; 52:685-690.

Nomenclatural status: not validly published

Taxonomic status: synonym (and no standing)

Correct name: Chloroflexota Garrity and Holt 2021

Synonyms:

Name	Kind
"Chlorobacteria" Cavalier-Smith 2006	homotypic synonym, not validly published
"Chloroflexota" Whitman et al. 2018	homotypic synonym, not validly published
"Chloroflexaeota" Oren et al. 2015	homotypic synonym, not validly published
Chloroflexota Garrity and Holt 2021	homotypic synonym, validly published under the ICNP

Emendations:
- Hugenholtz and Stackebrandt 2004 Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 2004; 54:2049-2051.
  Notes:
  - 🧍 Cavalier-Smith and Chao (2020) cited the name as Chloroflexi Garrity and Holt 2002 (sic).

Notes:
- 🧕 Boone et al. (2001) assigned this phylum to the domain "Bacteria" Woese et al. 1990. Publication: Garrity GM, Holt JG. Phylum BVI. Chloroflexi phy. nov. In: Boone DR, Castenholz RW, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1 (The Archaea and the Deeply Branching and Phototrophic Bacteria), Springer, New York, 2001, p. 427-446.
- 🧕 Cavalier-Smith and Chao (2020) assigned this phylum to the subkingdom "Chlorobacteria" (Cavalier-Smith 1992) Cavalier-Smith 2020. Publication: Cavalier-Smith T, Chao EE. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma 2020; 257:621-753.
- 🧕 Luketa (2012) assigned this phylum to the kingdom "Terrabacterida" Luketa 2012. Publication: Luketa S. New views on the megaclassification of life. Protistology 2012; 7:218-237.
- 🧕 Rinke et al. (2013) assigned this phylum to the superphylum "Terrabacteria" Battistuzzi et al. 2004. Publication: Rinke C, Schwientek P, Sczyrba A, Ivanova NN, Anderson IJ, Cheng JF, Darling A, Malfatti S, Swan BK, Gies EA, et al. Insights into the phylogeny and coding potential of microbial dark matter. Nature 2013; 499:431-437.
- 🧒 Boone et al. (2001) assigned the class "Chloroflexi" to this phylum. Publication: Garrity GM, Holt JG. Phylum BVI. Chloroflexi phy. nov. In: Boone DR, Castenholz RW, Garrity GM (eds), Bergey's Manual of Systematic Bacteriology, 2nd edn, vol. 1 (The Archaea and the Deeply Branching and Phototrophic Bacteria), Springer, New York, 2001, p. 427-446.
- 🧒 Botero et al. (2004) assigned the genus "Thermobaculum" Botero et al. 2004 to this phylum. Publication: Botero LM, Brown KB, Brumefield S, Burr M, Castenholz RW, Young M, McDermott TR. Thermobaculum terrenum gen. nov., sp. nov.: a non-phototrophic gram-positive thermophile representing an environmental clone group related to the Chloroflexi (green non-sulfur bacteria) and Thermomicrobia. Arch Microbiol 2004; 181:269-277.
- 🧒 Cavaletti et al. (2006) assigned the class Ktedonobacteria corrig. Cavaletti et al. 2007 to this phylum. Publication: Cavaletti L, Monciardini P, Bamonte R, Schumann P, Rohde M, Sosio M, Donadio S. New lineage of filamentous, spore-forming, gram-positive bacteria from soil. Appl Environ Microbiol 2006; 72:4360-4369.
- 🧒 Cavalier-Smith and Chao (2020) assigned the subphylum "Chloroflexotia" Cavalier-Smith 2020 to this phylum. Publication: Cavalier-Smith T, Chao EE. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma 2020; 257:621-753.
- 🧒 Cavalier-Smith and Chao (2020) assigned the subphylum "Dehalococcoidotia" Cavalier-Smith 2020 to this phylum. Publication: Cavalier-Smith T, Chao EE. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma 2020; 257:621-753.
- 🧒 Cavalier-Smith and Chao (2020) assigned the subphylum "Caldilineotia" Cavalier-Smith 2020 to this phylum. Publication: Cavalier-Smith T, Chao EE. Multidomain ribosomal protein trees and the planctobacterial origin of neomura (eukaryotes, archaebacteria). Protoplasma 2020; 257:621-753.
- 🧒 Dodsworth et al. (2014) assigned the class Thermoflexia Dodsworth et al. 2014 to this phylum. Publication: Dodsworth JA, Gevorkian J, Despujos F, Cole JK, Murugapiran SK, Ming H, Li WJ, Zhang G, Dohnalkova A, Hedlund BP. Thermoflexus hugenholtzii gen. nov., sp. nov., a thermophilic, microaerophilic, filamentous bacterium representing a novel class in the Chloroflexi, Thermoflexia classis nov., and description of Thermoflexaceae fam. nov. and Thermoflexales ord. nov. Int J Syst Evol Microbiol 2014; 64:2119-2127.
- 🧒 Gupta et al. (2013) assigned the class Chloroflexia corrig. Gupta et al. 2013 to this phylum. Publication: Gupta RS, Chander P, George S. Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov. Antonie Van Leeuwenhoek 2013; 103:99-119.
- 🧒 Hugenholtz and Stackebrandt (2004) assigned the class Thermomicrobia Garrity and Holt 2002 to this phylum. Publication: Hugenholtz P, Stackebrandt E. Reclassification of Sphaerobacter thermophilus from the subclass Sphaerobacteridae in the phylum Actinobacteria to the class Thermomicrobia (emended description) in the phylum Chloroflexi (emended description). Int J Syst Evol Microbiol 2004; 54:2049-2051.
- 🧒 Kawaichi et al. (2013) assigned the class Ardenticatenia Kawaichi et al. 2013 to this phylum. Publication: Kawaichi S, Ito N, Kamikawa R, Sugawara T, Yoshida T, Sako Y. Ardenticatena maritima gen. nov., sp. nov., a ferric iron- and nitrate-reducing bacterium of the phylum 'Chloroflexi' isolated from an iron-rich coastal hydrothermal field, and description of Ardenticatenia classis nov. Int J Syst Evol Microbiol 2013; 63:2992-3002.
- 🧒 Klappenbach and Pierson (2004) assigned the genus "Kouleothrix" to this phylum. Publication: Klappenbach JA, Pierson BK. Phylogenetic and physiological characterization of a filamentous anoxygenic photoautotrophic bacterium ' Candidatus Chlorothrix halophila' gen. nov., sp. nov., recovered from hypersaline microbial mats. Arch Microbiol 2004; 181:17-25.
- 🧒 Kochetkova et al. (2020) assigned the class Tepidiformia Kochetkova et al. 2020 to this phylum. Publication: Kochetkova TV, Zayulina KS, Zhigarkov VS, Minaev NV, Chichkov BN, Novikov AA, Toshchakov SV, Elcheninov AG, Kublanov IV. Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14. Int J Syst Evol Microbiol 2020; 70:1192-1202.
- 🧒 Kochetkova et al. (2020) assigned the order Tepidiformales Kochetkova et al. 2020 to this phylum. Publication: Kochetkova TV, Zayulina KS, Zhigarkov VS, Minaev NV, Chichkov BN, Novikov AA, Toshchakov SV, Elcheninov AG, Kublanov IV. Tepidiforma bonchosmolovskayae gen. nov., sp. nov., a moderately thermophilic Chloroflexi bacterium from a Chukotka hot spring (Arctic, Russia), representing a novel class, Tepidiformia, which includes the previously uncultivated lineage OLB14. Int J Syst Evol Microbiol 2020; 70:1192-1202.
- 🧒 Landry et al. (2017) assigned the class "Candidatus Monstramaria" Landry et al. 2017 to this phylum. Publication: Landry Z, Swan BK, Herndl GJ, Stepanauskas R, Giovannoni SJ. SAR202 Genomes from the Dark Ocean Predict Pathways for the Oxidation of Recalcitrant Dissolved Organic Matter. mBio 2017; 8:0.
- 🧒 Loeffler et al. (2013) assigned the class Dehalococcoidia Löffler et al. 2013 to this phylum. Publication: Loffler FE, Yan J, Ritalahti KM, Adrian L, Edwards EA, Konstantinidis KT, Muller JA, Fullerton H, Zinder SH, Spormann AM. Dehalococcoides mccartyi gen. nov., sp. nov., obligately organohalide-respiring anaerobic bacteria relevant to halogen cycling and bioremediation, belong to a novel bacterial class, Dehalococcoidia classis nov., order Dehalococcoidales ord. nov. and family Dehalococcoidaceae fam. nov., within the phylum Chloroflexi. Int J Syst Evol Microbiol 2013; 63:625-635.
- 🧒 McIlroy et al. (2016) assigned the genus "Candidatus Promineifilum" corrig. McIlroy et al. 2016 to this phylum. Publication: McIlroy SJ, Karst SM, Nierychlo M, Dueholm MS, Albertsen M, Kirkegaard RH, Seviour RJ, Nielsen PH. Genomic and in situ investigations of the novel uncultured Chloroflexi associated with 0092 morphotype filamentous bulking in activated sludge. ISME J 2016; 10:2223-2234.
- 🧒 Mehrshad et al. (2018) assigned the class "Candidatus Bathosphaeria" Mehrshad et al. 2018 to this phylum. Publication: Mehrshad M, Salcher MM, Okazaki Y, Nakano SI, Simek K, Andrei AS, Ghai R. Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi. Microbiome 2018; 6:176.
- 🧒 Mehrshad et al. (2018) assigned the class "Candidatus Umbricyclopia" Mehrshad et al. 2018 to this phylum. Publication: Mehrshad M, Salcher MM, Okazaki Y, Nakano SI, Simek K, Andrei AS, Ghai R. Hidden in plain sight-highly abundant and diverse planktonic freshwater Chloroflexi. Microbiome 2018; 6:176.
- 🧒 Nierychlo et al. (2019) assigned the genus "Candidatus Defluviifilum" Nierychlo et al. 2019 to this phylum. Publication: Nierychlo M, Milobedzka A, Petriglieri F, McIlroy B, Nielsen PH, McIlroy SJ. The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants. FEMS Microbiol Ecol 2019; 95:0.
- 🧒 Nierychlo et al. (2019) assigned the genus "Candidatus Sarcinithrix" Nierychlo et al. 2019 to this phylum. Publication: Nierychlo M, Milobedzka A, Petriglieri F, McIlroy B, Nielsen PH, McIlroy SJ. The morphology and metabolic potential of the Chloroflexi in full-scale activated sludge wastewater treatment plants. FEMS Microbiol Ecol 2019; 95:0.
- 🧒 Rodriguez et al. (2020) assigned the class "Candidatus Limnocylindria" Mehrshad et al. 2018 to this phylum. Publication: Rodriguez-R LM, Tsementzi D, Luo C, Konstantinidis KT. Iterative subtractive binning of freshwater chronoseries metagenomes identifies over 400 novel species and their ecologic preferences. Environ Microbiol 2020; 22:3394-3412.
- 🧒 Spieck et al. (2020) assigned the genus "Candidatus Nitrocaldera" Spieck et al. 2020 to this phylum. Publication: Spieck E, Spohn M, Wendt K, Bock E, Shively J, Frank J, Indenbirken D, Alawi M, Lucker S, Hupeden J. Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs. ISME J 2020; 14:364-379.
- 🧒 Spieck et al. (2020) assigned the genus "Candidatus Nitrotheca" Spieck et al. 2020 to this phylum. Publication: Spieck E, Spohn M, Wendt K, Bock E, Shively J, Frank J, Indenbirken D, Alawi M, Lucker S, Hupeden J. Extremophilic nitrite-oxidizing Chloroflexi from Yellowstone hot springs. ISME J 2020; 14:364-379.
- 🧒 Yamada et al. (2006) assigned the class Anaerolineae Yamada et al. 2006 to this phylum. Publication: Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 2006; 56:1331-1340.
- 🧒 Yamada et al. (2006) assigned the class Caldilineae Yamada et al. 2006 to this phylum. Publication: Yamada T, Sekiguchi Y, Hanada S, Imachi H, Ohashi A, Harada H, Kamagata Y. Anaerolinea thermolimosa sp. nov., Levilinea saccharolytica gen. nov., sp. nov. and Leptolinea tardivitalis gen. nov., sp. nov., novel filamentous anaerobes, and description of the new classes Anaerolineae classis nov. and Caldilineae classis nov. in the bacterial phylum Chloroflexi. Int J Syst Evol Microbiol 2006; 56:1331-1340.
- 🙄 This taxon name is occasionally misprinted (or affected by an OCR error) in some sources as: "Chioroflexi"; "Chlmoflexi"; "Chlorofexi"; "Chlorofltxi"; "Cholroflexi"; "Choroflexi"; "Chroloflexi"; "Cloroflexi".
- 📧 The e-mail address of the corresponding author given in the effective publication is not functional any more.
- 🧍 The formation of this name was discussed in Judicial Opinion 129. Publication: Arahal et al. Judicial Opinion No. 129. Int J Syst Evol Microbiol 2024; 74:6064.
- 🧍 The type order "Chloroflexales" has no standing in bacterial nomenclature. Publication: Gupta RS, Chander P, George S. Phylogenetic framework and molecular signatures for the class Chloroflexi and its different clades; proposal for division of the class Chloroflexia class. nov. [corrected] into the suborder Chloroflexineae subord. nov., consisting of the emended family Oscillochloridaceae and the family Chloroflexaceae fam. nov., and the suborder Roseiflexineae subord. nov., containing the family Roseiflexaceae fam. nov. Antonie Van Leeuwenhoek 2013; 103:99-119.

Parent taxon: Bacteria Woese et al. 2024

Assigned by: LPSN automated production system. The following publication is only one of the sources consulted. It may or may not mention this taxon name. — Oren A, Garrity GM. Valid publication of the names of forty-two phyla of prokaryotes. Int J Syst Evol Microbiol 2021; 71:5056.

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Record number: 779

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Phylum "Chloroflexi"