The Thermotogota are a phylum of the domain Bacteria. The phylum Thermotogota is composed of Gram-negative staining, anaerobic, and mostly thermophilic and hyperthermophilic bacteria. Characteristics 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 Thermotogota existing at moderate temperatures have also been identified. Although Thermotogota 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 Thermotogota species to thrive at high temperatures, they are considered attractive targets for use in industrial processes. The metabolic ability of Thermotogota 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. Molecular signatures Until recently, no biochemical or molecular markers were known that could distinguish the species from the phylum Thermotogota 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 Thermotogota species or a number of its subgroups. Many of these CSIs in important housekeeping proteins such as Pol1, RecA, and TrpRS, and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in different sequenced Thermotogota species providing novel molecular markers for this phylum. These studies also identified CSIs specific for each order and each family. These indels are the premise for the current taxonomic organization of the Thermotogota, and are strongly supported by phylogenomic analyses. Additional CSIs have also been found that are specific for Thermotoga, Pseudothermotoga, Fervidobacterium, and Thermosipho. These CSIs are specific for all species within each respective genus, and absent in all other bacteria, thus are specific markers. A clade consisting of the deep-branching species Petrotoga mobilis, Kosmotoga olearia, and Thermotogales bacterium mesG1 was also supported by seven CSIs. Additionally, some CSIs that provided evidence of LGT among the Thermotogota and other prokaryotic groups were also reported. The newly discovered molecular markers provide novel means for identification and circumscription of species from the phylum in molecular terms and for future revisions to its taxonomy. Additionally, a 51 aa insertion CSI was identified to be specific for all Thermotogales as well as Aquificales, another order comprising hyperthermophilic species. Phylogenetic studies demonstrated that the presence of