Development of an Online Genome Sequence Comparison Resource for Bacillus cereus sensu lato Strains Using the Efficient Composition Vector Method

Abstract

An automated method was developed for differentiating closely related B. cereus sensu lato (s.l.) species, especially biopesticide Bacillus thuringiensis, from other human pathogens, B. anthracis and B. cereus sensu stricto (s.s.). In the current research, four typing methods were initially compared, including multi-locus sequence typing (MLST), single-copy core genes phylogenetic analysis (SCCGPA), dispensable genes content pattern analysis (DGCPA) and composition vector tree (CVTree), to analyze the genomic variability of 23 B. thuringiensis strains from aizawai, kurstaki, israelensis, thuringiensis and morrisoni serovars. The CVTree method was the best option to be used for typing B. thuringiensis strains since it proved to be the fastest method, whilst giving high-resolution data about the strains. In addition, CVTree agrees well with ANI-based method, revealing the relationship between B. thuringiensis and other B. cereus s.l. species. Based on these data, an online genome sequence comparison resource was built for Bacillus strains called the Bacillus Typing Bioinformatics Database to facilitate strain identification and characterization.

Greater wax moth control in apiaries can be improved by combining Bacillus thuringiensis and entrapments

“…Genome annotation was performed by the NCBI Prokaryotic Genome Automatic Annotation Pipeline. Composition vector tree (CVTree) phylogenetic analysis was performed using a free, web-based tool-the Bacillus Typing Bioinformatics Database ( https://btbidb.com ) 67 . The genome data of other B. thuringiensis strains were selected in the database to generate the phylogenetic tree.…”

“…The genome of Bt BiotGm was sequenced and the data were deposited in NCBI at BioProject PRJNA998231 (raw sequence data under accession number SRX22206352 , assembly sequences under accession numbers CP130743 to CP130747). The web-based tool-the Bacillus Typing Bioinformatics Database 67 used in the CVTree phylogenetic analysis can be obtained from https://btbidb.com . US Environmental Protection Agency’s BeeREX model data used in this study could be downloaded from https://www.epa.gov/sites/production/files/2015-11/beerexv1.0.xlsx .…”

The Perpetual Vector Mosquito Threat and Its Eco-Friendly Nemeses

“…Like Ls, Bacillus thuringiensis is an aerobic Gram-positive spore-forming rod that is naturally present in many ecological niches, including soil, plants, stored products, aquatic environments, and insects and their habitats [ 243 ]. The bacterium is classified in the Bacillus cereus sensu lato ( sl ), which contains at least 22 non-pathogenic and pathogenic species, with the most notable of the latter being B. anthracis [ 244 ]. Although these bacteria share a high degree of genetic identity, Bt is distinguished from other members of B. cereus ls by the parasporal crystalline inclusions.…”

Bacillus species are core microbiota of highly resistant maize varieties that induce host metabolic defense against corn stalk rot

“…SPAdes (version 3.15.5) 70 was used to perform genome assembly with gradient k values (21,33,55,77, 99 and 127), and annotation was accomplished using Prokka (version 1.13) 71 . To obtain taxonomy information about the isolates, a neighbor-joining (NJ) phylogenetic tree was reconstructed based on the amino acid sequences of 4,215 genomes using the CVTree Standalone Version with k-string = 6 72 . The abundance of these isolates in the rhizosphere was determined by mapping the metagenomic data to these genomes using Bowtie2 (version 2.1.0).…”