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Several studies have tried to reconstruct the phylogeny of the genus.
The Bacillus-specific study with the most diversity covered is by Xu and Cote ' using 16S and the ITS region, where they divide the genus into 10 groups, which includes the nested genera Paenibacillus, Brevibacillus, Geobacillus, Marinibacillus and Virgibacillus.
However, the tree constructed by the living tree project, a collaboration between ARB-Silva and LPSN where a 16S ( and 23S if available ) tree of all validated species was constructed, the genus Bacillus contains a very large number of nested taxa and majorly in both 16S and 23S it is paraphyletic to Lactobacillales ( Lactobacillus, Streptococcus, Staphylococcus, Listeria, etc.
), due to Bacillus coahuilensis and others.
A gene concatenation study found similar results to Xu and Cote ', but with a much more limited number of species in terms of groups, but used Listeria as an outgroup, so in light of the ARB tree, it may be " inside-out ".

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