Identification of “Bacillus cellulasensis” strain NIO-1130T as a member of Bacillus altitudinis and emendation of the latter

Phylogeny of the Bacillus altitudinis Complex and Characterization of a Newly Isolated Strain with Antilisterial Activity

ABSTRACT

Bacillus strain UTK D1-0055 was isolated from a laboratory environment and appeared to have antilisterial activity. The genome was sequenced, the strain was identified as Bacillus altitudinis, and a high-quality complete annotated genome was produced. The taxonomy was evaluated for this and related Bacillus species (B. aerophilus, B. pumilus, B. safensis, B. stratosphericus, and B. xiamenensis) because the taxonomy is unclear and contains errors in public databases such as NCBI. The included strains grouped into seven clusters based on average nucleotide identity. Strains designated as B. aerophilus, B. altitudinis, and B. stratosphericus grouped together in the cluster containing the B. altitudinis type strain, suggesting that these three species should be considered a single species, B. altitudinis. The antimicrobial activity of UTK D1-0055 was evaluated against a panel of 15 Listeria strains (nine Listeria monocytogenes serotypes, Listeria innocua, and Listeria marthii), other foodborne pathogens (six Salmonella enterica serotypes and Escherichia coli), and three representative fungi (Saccharomyces cerevisiae, Botrytis cinerea, and Hyperdermium pulvinatum). Antibacterial activity was observed against all Listeria strains, but no antibacterial effects were found against the other tested bacterial and fungal strains. Biosynthetic gene clusters were identified in silico that may be related to the observed antibacterial activity, and these clusters included genes that putatively encode bacteriocins and nonribosomally synthesized peptides. The B. altitudinis strain identified in this investigation had a broad range of antilisterial activity, suggesting that it and other related strains may be useful for biocontrol in the food industry.

HIGHLIGHTS

Genomic insights into the phylogeny of Bacillus strains and elucidation of their secondary metabolic potential

The genus Bacillus constitutes a plethora of species that have medical, environmental, and industrial applications. While genus Bacillus has been the focus of several studies where genomic data have been used to resolve many taxonomic issues, there still exist several ambiguities. Through the use of in-silico genome-based methods, we tried to resolve the taxonomic anomalies of a large set of Bacillus genomes (n = 178). We also proposed species names for uncharacterized strains and reported genome sequence of a novel isolate Bacillus sp. RL. In the hierarchical clustering on genome-to-genome distances, we observed 11 distinct monophyletic clusters and investigated the functional pathways annotated as the property of these clusters and core-gene content of the entire dataset. Thus, we were able to assert the possible outlier strains (n = 17) for this genus. Analyses of secondary metabolite potential of each strain helped us unravel still unexplored diversity for various biosynthetic genes.