Recently the phylogenetic relationship of the group Thermotogota was characterized based on the CSI approach. Previously no biochemical or molecular markers were known that could clearly distinguish the species of this phylum from all other bacteria. More than 60 CSIs that were specific for the entire Thermotogota phylum or its different subgroups were discovered. 18 CSIs are uniquely present in various Thermotogota species and provide molecular markers for the phylum. Additionally there were many CSIs that were specific for various Thermotogota subgroups. 12 CSIs were specific for a clade consisting of various Thermotogota species except Tt. Lettingae. 14CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and 18 CSIs were specific for the genus Thermosiphon.
Lastly 16 CSIs were reported that were shared by either some or all Thermotogota species or some species from other taxa such as Archaea, Aquificota, Bacillota, Pseudomonadota, Deinococcota, Fusobacteriota, Dictyoglomota, Chloroflexota, and eukaryotes. The shared presence of some of these CSIs could be due to lateral gene transfer (LGT) between these groups. However the number of CSIs that are commonly shared with other taxa is much smaller than those that are specific for Thermotogota and they do not exhibit any specific pattern. Hence they have no significant effect on the distinction of Thermotogota.