title: Phylogenomic re-assessment of the thermophilic genus Geobacillus.
abstract: Geobacillus is a genus of Gram-positive, aerobic, spore-forming obligate thermophiles. The descriptions and subsequent affiliations of the species in the genus have mostly been based on polyphasic taxonomy rules that include traditional sequence-based methods such as DNA-DNA hybridization and comparison of 16S rRNA gene sequences. Currently, there are fifteen validly described species within the genus. The availability of whole genome sequences has provided an opportunity to validate and/or re-assess these conventional estimates of genome relatedness. We have applied whole genome approaches to estimate the phylogenetic relatedness among the sixty-three Geobacillus strains for which genome sequences are currently publicly available, including the type strains of eleven validly described species. The phylogenomic metrics AAI (Average Amino acid Identity), ANI (Average Nucleotide Identity) and dDDH (digital DNA-DNA hybridization) indicated that the current genus Geobacillus is comprised of sixteen distinct genomospecies, including several potentially novel species. Furthermore, a phylogeny constructed on the basis of the core genes identified from the whole genome analyses indicated that the genus clusters into two monophyletic clades that clearly differ in terms of nucleotide base composition. The G+C content ranges for clade I and II were 48.8-53.1% and 42.1-44.4%, respectively. We therefore suggest that the Geobacillus species currently residing within clade II be considered as a new genus.
authors.affiliation: Centre for Microbial Ecology and Genomics, University of Pretoria, 0028, South Africa.
authors.forename: Habibu
authors.initials: H
authors.lastname: Aliyu
authors.affiliation: Centre for Microbial Ecology and Genomics, University of Pretoria, 0028, South Africa.
authors.forename: Pedro
authors.initials: P
authors.lastname: Lebre
authors.affiliation: Bioinformatics & Systems Biology, Justus-Liebig-University Giessen, 35392 Giessen, Hesse, Germany.
authors.forename: Jochen
authors.initials: J
authors.lastname: Blom
authors.affiliation: Centre for Microbial Ecology and Genomics, University of Pretoria, 0028, South Africa; Department of Genetics, University of Pretoria, 0028, South Africa. Electronic address: don.cowan@up.ac.za.
authors.forename: Don
authors.initials: D
authors.lastname: Cowan
authors.affiliation: Centre for Microbial Ecology and Genomics, University of Pretoria, 0028, South Africa; Department of Microbiology, University of Pretoria, 0028, South Africa.
authors.forename: Pieter
authors.initials: P
authors.lastname: De Maayer
mesh_terms: D001482:Base Composition / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics*; D056506:Geobacillus / Q000145:classification* / Q000235:genetics*; D058889:Molecular Typing; D009693:Nucleic Acid Hybridization; D010802:Phylogeny; D012336:RNA, Ribosomal, 16S / Q000235:genetics*
chemical_list: D004269:DNA, Bacterial; D012336:RNA, Ribosomal, 16S
keywords: Average Nucleotide Identity; Digital DNA–DNA hybridization; Geobacillus; Phylogenomic metrics; Thermophile