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

<jats:p>To clarify the evolutionary relationships and classification of <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> species, comprehensive phylogenomic and comparative analyses were performed on >300 <jats:italic>Bacillus/Bacillaceae</jats:italic> genomes. Multiple genomic-scale phylogenetic trees were initially reconstructed to identify different monophyletic clades of <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> 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 <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> species, in addition to the Subtilis and Cereus clades, consistently formed 17 novel distinct clades. Additionally, some <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> species reliably grouped with the genera <jats:italic>Alkalicoccus, Caldalkalibacillus, Caldibacillus, Salibacterium</jats:italic> and <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.23320" xlink:type="simple">Salisediminibacterium</jats:ext-link> </jats:named-content> </jats:italic>. The distinctness of identified <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> 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 <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> species clades should be recognized as novel genera, with the names <jats:italic>Alteribacter</jats:italic> gen. nov.<jats:italic>, Ectobacillus</jats:italic> gen. nov., <jats:italic>Evansella</jats:italic> gen. nov.<jats:italic>, Ferdinandcohnia</jats:italic> gen. nov.<jats:italic>, Gottfriedia</jats:italic> gen. nov.<jats:italic>, Heyndrickxia</jats:italic> gen. nov.<jats:italic>, Lederbergia</jats:italic> gen. nov.<jats:italic>, Litchfieldia</jats:italic> gen. nov.<jats:italic>, Margalitia</jats:italic> gen. nov.<jats:italic>, Niallia</jats:italic> gen. nov.<jats:italic>, Priestia</jats:italic> gen. nov.<jats:italic>, Robertmurraya</jats:italic> gen. nov.<jats:italic>, Rossellomorea</jats:italic> gen. nov.<jats:italic>, Schinkia</jats:italic> gen. nov.<jats:italic>, Siminovitchia</jats:italic> gen. nov., <jats:italic>Sutcliffiella</jats:italic> gen. nov. and <jats:italic>Weizmannia</jats:italic> gen. nov. We also propose to transfer ‘<jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.27572" xlink:type="simple">Bacillus kyonggiensi</jats:ext-link> </jats:named-content> </jats:italic>s’ to <jats:italic>Robertmurraya kyonggiensis</jats:italic> sp. nov. (type strain: NB22=JCM 17569<jats:sup>T</jats:sup>=DSM 26768). Additionally, we report 31 CSIs that are unique characteristics of either the members of the Subtilis clade (containing the type species <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.10618" xlink:type="simple">B. subtilis</jats:ext-link> </jats:named-content> </jats:italic>) or the Cereus clade (containing <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4871" xlink:type="simple">B. anthracis</jats:ext-link> </jats:named-content> </jats:italic> and <jats:italic> <jats:named-content content-type="species"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4885" xlink:type="simple">B. cereus</jats:ext-link> </jats:named-content> </jats:italic>). As most <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> 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 <jats:italic> <jats:named-content content-type="genus"> <jats:ext-link xmlns:xlink="http://www.w3.org/1999/xlink" ext-link-type="uri" xlink:href="http://doi.org/10.1601/nm.4857" xlink:type="simple">Bacillus</jats:ext-link> </jats:named-content> </jats:italic> to restrict it to only the members of the Subtilis and Cereus clades.</jats:p>