Comparative genomic studies have identified several
conserved signature indels (CSIs) that are specific for all species belonging to the phylum
Aquificota and provide potential molecular markers. Several CSIs have also been identified that are specific for the species from the
Aquificota and provide potential molecular markers for this phylum. Phylogenetic studies demonstrated that the presence of the same CSI within these two unrelated groups of bacteria is not due to
lateral gene transfer, rather the CSI likely developed independently in these two groups of thermophiles due to
selective pressure. and also by CSIs in several highly conserved universal proteins 16S-23S-5S operons. In contrast to the very high G+C content of their rRNAs (i.e. more than 62%), which is required for stability of their secondary structures at high growth temperatures, the inference that the
Aquificota do not constitute a deep-branch lineage is also independently strongly supported by CSIs in a number of important proteins (viz. Hsp70, Hsp60, RpoB, RpoB and AlaRS), which support its placement in the proximity of the phylum Proteobacteria, particularly the
Campylobacterota. In contrast to the above cited analyses that are based on a few indels or on single genes, analyses on informational genes, which appeared to be less often transferred to the
Aquifex lineage than noninformational genes, most often placed the Aquificales close to the Thermotogales. These authors explain the frequently observed grouping of
Aquificota with Campylobacterota as result of frequent
horizontal gene transfer due to shared ecological niches. Along with the Thermotogota, the
Aquificota are
thermophilic eubacteria. ==Phylogeny==