The name of this phylum is derived from the existence of many of these organisms at high temperatures along with the characteristic sheath structure, or “toga”, surrounding the cells of these species. Recently, some Thermotogae existing in mesophilic temperatures have also been identified. Although Thermotogae species exhibit Gram-negative staining, they are bounded by a single unit lipid membrane, hence they are monoderm bacteria. Because of the ability of some Thermotogae species to thrive at high temperatures, they are considered attractive targets for use in industrial processes. The metabolic ability of Thermotogae to utilize different complex-carbohydrates for production of hydrogen gas led to these species being cited as a possible biotechnological source for production of energy alternative to fossil fuels.
This phylum presently consists of a single class (Thermotogae), order (Thermotogales) and family (Thermotogaceae). It contains a total of nine genera (viz. Thermotoga, Petrotoga, Thermosipho, Fervidobacterium, Marinitoga, Kosmotoga, Geotoga, Thermopallium and Thermococcoides), all of which currently are part of the family Thermotogaceae. In the 16S rRNA trees the Thermotogae have been observed to branch with the Aquificae (another phylum comprising hyperthermophilic organisms) in close proximity to the archaeal-bacterial branch point. However, a close relationship of Thermotogae to Aquificae, and the deep branching of the latter group of species, is not supported by phylogenetic studies based upon other gene/protein sequences and also by conserved signature indels in several highly conserved universal proteins. The Thermotogae have also been scrutinized for their supposedly profuse Lateral gene transfer with Archaeal organisms. However, recent studies based upon more robust methodologies suggest that incidence of LGT between Thermotogae and other groups including Archaea is not as high as suggested in earlier studies.
Molecular Signatures for the Phylum Thermotogae and its Subgroups
Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogae from all other bacteria. However, a recent comparative genomic study has identified large numbers of conserved signature indels (CSIs) in important proteins that are specific for either all Thermotogae species or a number of its sub-groups. Eighteen of these conserved indels in important housekeeping proteins such as Pol1, RecA, TrpRS and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in different sequenced Thermotogae species providing novel molecular markers for this phylum. Additionally, these studies also identified 14 conserved indels that were specific for a clade consisting of the Fervidobacterium and Thermosipho genera, 12 conserved indels that were specific for the genus Thermotoga (except Thermotoga lettingae), 8 conserved indels that provided molecular markers for species from the genus Thermosipho. A clade consisting of the deep branching species Petrotoga mobilis, Kosmotoga olearia and Thermotogales bacterium mesG1 was also supported by 7 conserved indels. Additionally, some CSIs that provided evidence of LGT among the Thermotogae and other prokaryotic groups were also reported. The newly discovered molecular markers provide novel means for identification and circumscription of species from the Thermotogae phylum in molecular terms and for future revisions to the taxonomy of this phylum.
The currently accepted taxonomy is based on the List of Prokaryotic names with Standing in Nomenclature (LPSN)  and the phylogeny is based on 16S rRNA-based LTP release 111 by The All-Species Living Tree Project 
♠ Strain found at the National Center for Biotechnology Information (NCBI) but not listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
♥ No strains lodged at National Center for Biotechnology Information NCBI and or listed in the List of Prokaryotic names with Standing in Nomenclature (LPSN)
- Huber, R. and Hannig, M. (2006) Thermotogales. Prokaryotes 7: 899-922.
- Reysenbach, A.-L. (2001) Phylum BII. Thermotogae phy. nov. In: Bergey's Manual of Systematic Bacteriology, pp. 369-387. Eds D. R. Boone, R. W. Castenholz. Springer-Verlag: Berlin.
- Nesbo C.L.; Kumaraswamy R.; Dlutek M.; Doolittle W.F. & Foght J. (2010). "Searching for mesophilic Thermotogales bacteria: "mesotogas" in the wild". Appl Environ Microbiol 76: 4896–4900. PMID 20495053. doi:10.1128/AEM.02846-09.
- Gupta R.S. (1998). "Protein phylogenies and signature sequences: A reappraisal of evolutionary relationships among archaebacteria, eubacteria, and eukaryotes". Microbiol Mol Biol Rev 62 (4): 1435–1491. PMC 98952. PMID 9841678.
- Gupta R.S. (2011). "Origin of diderm (Gram-negative) bacteria: antibiotic selection pressure rather than endosymbiosis likely led to the evolution of bacterial cells with two membranes". Antonie van Leeuwenhoek 100: 171–182. PMC 3133647. PMID 21717204. doi:10.1007/s10482-011-9616-8.
- Eriksen N.T.; Riis M.L.; Holm N.K. & Iversen N. (2010). "H(2) synthesis from pentoses and biomass in Thermotoga spp.". Biotechnol Lett 33 (2): 293–300. PMID 20960218. doi:10.1007/s10529-010-0439-x.
- Conners S.B.; Mongodin E.F.; Johnson M.R.; Montero C.I.; Nelson K.E. & Kelly R.M. (2006). "Microbial biochemistry, physiology, and biotechnology of hyperthermophilic Thermotoga species". FEMS Microbiol Rev 30 (6): 872–905. PMID 17064285. doi:10.1111/j.1574-6976.2006.00039.x.
- NCBI Taxonomy. http://www.ncbi.nlm.nih.gov/taxonomy
- Euzeby JP. List of prokaryotic names with standing in nomenclature. http://www.bacterio.cict.fr/t/thermotogales .
- Klenk H.P.; Meier T.D.; Durovic P. et al. (1999). "RNA polymerase of Aquifex pyrophilus: Implications for the evolution of the bacterial rpoBC operon and extremely thermophilic bacteria". J Mol Evol 48 (5): 528–541. PMID 10198119. doi:10.1007/pl00006496.
- Gupta R.S. (2000). "The phylogeny of Proteobacteria: relationships to other eubacterial phyla and eukaryotes". FEMS Microbiol Rev 24 (4): 367–402. PMID 10978543. doi:10.1111/j.1574-6976.2000.tb00547.x.
- Ciccarelli F.D.; Doerks T.; von Mering C.; Creevey C.J.; Snel B. & Bork P. (2006). "Toward automatic reconstruction of a highly resolved tree of life". Science 311: 1283–1287. PMID 16513982. doi:10.1126/science.1123061.
- Di Giulio M. (2003). "The universal ancestor was a thermophile or a hyperthermophile: Tests and further evidence". J Theor Biol 221 (3): 425–436. PMID 12642117. doi:10.1006/jtbi.2003.3197.
- Griffiths E. & Gupta R.S. (2004). "Signature sequences in diverse proteins provide evidence for the late divergence of the order Aquificales.". International Microbiol 7 (1): 41–52. PMID 15179606.
- Nelson K.E.; Clayton R.; Gill S. et al. (1999). "Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima". Nature 399 (6734): 323–329. PMID 10360571. doi:10.1038/20601.
- Nesbo C.L.; L'Haridon S.; Stetter K.O. & Doolittle W.F. (2001). "Phylogenetic analyses of two "Archaeal" genes in Thermotoga maritima reveal multiple transfers between Archaea and Bacteria". Mol Biol Evol 18 (3): 362–375. PMID 11230537. doi:10.1093/oxfordjournals.molbev.a003812.
- Ochman H.; Lawrence J.G. & Groisman E.A. (2000). "Lateral gene transfer and the nature of bacterial innovation". Nature 405 (6784): 299–304. PMID 10830951. doi:10.1038/35012500.
- Zhaxybayeva O.; Swithers K.S.; Lapierre P. et al. (2009). "On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales". Proc Natl Acad Sci U S A 106: 5865–5870. PMID 19307556. doi:10.1073/pnas.0901260106.
- Gupta R.S. & Bhandari V. (2011). "Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups". Antonie Van Leeuwenhoek 100: 1–34. PMID 21503713. doi:10.1007/s10482-011-9576-z.
- Kunisawa T (2011). "Inference of the phylogenetic position of the phylum Deferribacteres from gene order comparison". Antonie van Leeuwenhoek 99: 417–422. PMID 20706870. doi:10.1007/s10482-010-9492-7.
- Sayers et al. "Thermotogae". National Center for Biotechnology Information (NCBI) taxonomy database . Retrieved 2013-03-20.
- All-Species Living Tree Project."16S rRNA-based LTP release 111 (full tree)" (PDF). Silva Comprehensive Ribosomal RNA Database . Retrieved 2013-03-20.