Robust demarcation of 17 distinct Bacillus species clades, proposed as novel Bacillaceae genera, by phylogenomics and comparative genomic analyses: description of Robertmurraya kyonggiensis sp. nov. and proposal for an emended genus Bacillus limiting it only to the members of the Subtilis and Cereus clades of species

Abstract

To clarify the evolutionary relationships and classification of <i>Bacillus</i> species, comprehensive phylogenomic and comparative analyses were performed on >300 <i>Bacillus/Bacillaceae</i> genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of <i>Bacillus</i> species. In parallel, detailed analyses were performed on protein sequences of genomes to identify conserved signature indels (CSIs) that are specific for each of the identified clades. We show that in different reconstructed trees, most of the <i>Bacillus</i> species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some <i>Bacillus</i> species reliably grouped with the genera <i>Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium</i> and <i>Salisediminibacterium</i>. The distinctness of identified <i>Bacillus</i> species clades is independently strongly supported by 128 identified CSIs which are unique characteristics of these clades, providing reliable means for their demarcation. Based on the strong phylogenetic and molecular evidence, we are proposing that these 17 <i>Bacillus</i> species clades should be recognized as novel genera, with the names <i>Alteribacter</i> gen. nov.<i>, Ectobacillus</i> gen. nov., <i>Evansella</i> gen. nov.<i>, Ferdinandcohnia</i> gen. nov.<i>, Gottfriedia</i> gen. nov.<i>, Heyndrickxia</i> gen. nov.<i>, Lederbergia</i> gen. nov.<i>, Litchfieldia</i> gen. nov.<i>, Margalitia</i> gen. nov.<i>, Niallia</i> gen. nov.<i>, Priestia</i> gen. nov.<i>, Robertmurraya</i> gen. nov.<i>, Rossellomorea</i> gen. nov.<i>, Schinkia</i> gen. nov.<i>, Siminovitchia</i> gen. nov., <i>Sutcliffiella</i> gen. nov. and <i>Weizmannia</i> gen. nov. We also propose to transfer '<i>Bacillus kyonggiensi</i>s' to <i>Robertmurraya kyonggiensis</i> sp. nov. (type strain: NB22=JCM 17569^T=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species <i>B. subtilis</i>) or the Cereus clade (containing <i>B. anthracis</i> and <i>B. cereus</i>). As most <i>Bacillus</i> species which are not part of these two clades can now be assigned to other genera, we are proposing an emended description of the genus <i>Bacillus</i> to restrict it to only the members of the Subtilis and Cereus clades.