Nevertheless, because the individual gene phylogenies are congruent to one another and to the concatenated gene phylogeny, we discuss relationships within the B. subtilis species complex in reference to the concatenated phylogenies only (Fig. 1 and Supplementary Fig. S1). We addressed the relationships from the most basal member of the complex to the most derived. Thus, we began with Bacillus pumilus. This species was found at the base of the B. subtilis species complex phylogeny. Interestingly, Gordon et al. (1973) speculated that it might one day be considered a ‘variety of B. subtilis rather than a separate species’ once more data were collected on a large number of B. pumilus strains. However, our results clearly indicate that B. pumilus forms a clade distinct from B. subtilis.