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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 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.
Chloroflexi 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, the class Chloroflexi. Since 2001, however, new classes have been created thanks to newly discovered species, and the phylum Chloroflexi is now divided as follows:
Ktedonobacteria Cavaletti et al., 2007 emend. Yabe et al., 2010
"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 Chloroflexi 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.
Genus Oscillochloris Gorlenko & Pivovarova 1989 emend. Keppen et al. 2000
Species O. chrysea ? Gorlenko & Pivovarova 1989(type sp.)
Species O. trichoides ? (ex Szafer) Gorlenko & Korotkov 1989 emend. Keppen et al. 2000 ["Oscillatoria trichoides" (Szafer) Lauterborn 1915]
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 (, -?, -), 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 Chlorobi, whereas Cyanobacteria has the root cyanos (), meaning "blue-green."
Unlike some other phyla, there is no theme root in the name of genera of Chloroflexi, and in fact many genera beginning with "Chloro-" or ending in "-chloris" are either cyanobacteria or chlorobi.
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