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The Thermotogae is a phylum level division in the bacterial kingdom composed of gram-negative staining, anaerobic, mostly thermophilic and hyperthermophilic bacteria. Among the first bacterial species identified to exist in temperatures greater than 80°C, the name of the 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. Nevertheless, due to the ability of some Thermotogae to thrive at high temperatures, they are considered attractive targets for use in industrial processes. Within genome sizes around 2 Mb, the Thermotogae also contain several proteins which are utilized in the metabolism of a variety of different complex-carbohydrates. Their metabolic ability 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. Thermotogae taxonomy In 16S rRNA trees the Thermotogae have been observed to branch with the Aquificales in close proximity to the archaeal-bacterial branch point. This branching in the 16S rRNA led to the hypothesis of life’s origin in high temperature environments as Aquificales and Thermotogae are both bacterial phyla with species that are able to survive and reproduce at extremely high temperatures (> 80°C). The relationship among these two phyla along with their branching within the bacterial kingdom has been disputed by phylogenetic analysis based on multiple genes/protein based analysis which places the Thermotogae closer to the Firmicutes and Aquificae closer to Proteobacteria. The Thermotogae have also been scrutinized for their supposedly profuse Lateral gene transfer with Archaeal organisms. The first Thermotogales genome sequenced (T. maritima in 1999) was estimated to share 24% of its genome with Archaeal species based on best-BLAST hits. However, recent estimates based on more robust methodologies suggest lower incidence of LGT. The species of the Thermotogae phylum are currently confined to a single class (Thermotogae), order (Thermotogales) and family (Thermotogaceae). They are currently identified mainly on the basis of their unique toga and branching in the 16S rRNA and other phylogenetic trees. Until recently, no biochemical or molecular markers were known that clearly distinguish the species in the phylum from each other or from bacteria of other phyla. Recent comparative genomic analysis based methodologies have identified several conserved amino acid inserts and deletions (or indels) as molecular markers that are specific for the Thermotogae or its sub-groups. Based on the genomic analysis for several Thermotogae for which complete genome were available, several subdivisions of the phylum have been defined through commonly shared molecular markers. Other than consolidation of the phylum-level division, these include the strong relationships among Thermosipho genus species, among most species of the Thermotoga genus except Thermotoga lettingae, the cladal relationship among species of the Fervidobacterium and Thermosipho genera and that among Kosmotoga-Petrotoga and Thermotogales bacterium MesG1.Ag.4.2. Additionally, based on molecular markers, few cases of LGT among the Thermotogae and other prokaryotic groups were discovered (Outlined in Figure 2).