Completed Genomic Sequence ofBacillus thuringiensisHER1410 Reveals aCry-Containing Chromosome, Two Megaplasmids, and an Integrative Plasmidial Prophage

Abstract

Bacillus thuringiensis is the most used biopesticide in agriculture. Its entomopathogenic capacity stems from the possession of plasmid-borne insecticidal crystal genes (cry), traditionally used as discriminant taxonomic feature for that species. As such, crystal and plasmid identification are key to the characterization of this species. To date, about 600 B. thuringiensis genomes have been reported, but less than 5% have been completed, while the other draft genomes are incomplete, hindering full plasmid delineation. Here we present the complete genome of Bacillus thuringiensis HER1410, a strain closely related to B. thuringiensis entomocidus and a known host for a variety of Bacillus phages. The combination of short and long-read techniques allowed fully resolving the genome and delineation of three plasmids. This enabled the accurate detection of an unusual location of a unique cry gene, cry1Ba4, located in a genomic island near the chromosome replication origin. Two megaplasmids, pLUSID1 and pLUSID2 could be delineated: pLUSID1 (368 kb), a likely conjugative plasmid involved in virulence, and pLUSID2 (156 kb) potentially related to the sporulation process. A smaller plasmidial prophage pLUSID3, with a dual lifestyle whose integration within the chromosome causes the disruption of a flagellar key component. Finally, phylogenetic analysis placed this strain within a clade comprising members from the B. thuringiensis serovar thuringiensis and other serovars and with B. cereus s. s. in agreement with the intermingled taxonomy of B. cereus sensu lato group.

The Distribution of Several Genomic Virulence Determinants Does Not Corroborate the Established Serotyping Classification of Bacillus thuringiensis

“…Taken together, the use of more than one locus, as in the case of multilocus sequence typing (MLST) [ 20 , 78 ] or phylogenomic approach [ 71 , 83 ], shows that the distribution of phenotypic features among the strains of Bc species, including the Bt serological groups, does not confine to any of the established phenotypic classifications. In the present work, none of the phylogenetic inferences virtually supported the serotyping-based division, which further urges the re-evaluation of the established classification and adherence to the large-scale phylogenetic approaches.…”

Unraveling protein interactions between the temperate virus Bam35 and its Bacillus host using an integrative Yeast two hybrid-High throughput sequencing approach

“…Besides, six out of the seven confirmed interactions belong to this cluster (Supplementary Figure 6). Remarkably, within those, the enterotoxin/SH3 domain protein (Iap in Supplementary Figure 6) was also annotated as the conserved virulent factor EntA [56,78]. SH3 domains are known to be involved in protein-protein interactions and cell wall recognition and binding [79].…”

“…In our case, the latter proved more appropriate since Bam35 has a limited number of viral genes, that were already available and tested for autoactivation in Y2H [20]. We also generated and thoroughly analyzed a random fragments genomic library of B. thuringiensis HER1410, a well characterized strain at the genomic level which is entomopathogenic and highly sensitive to Bacillus phage infections [18,56]. Based on this, our custom HER1410 library and the 32 encoded proteins from phage Bam35 have been screened using Y2H.…”

Genomics of an endemic cystic fibrosis Burkholderia multivorans strain reveals low within-patient evolution but high between-patient diversity

“…The aim of the current study was to investigate the genomic epidemiology and evolution of B. multivorans ST-742 that were isolated from respiratory samples of four Belgian CF patients over a period of at least ten years. We combined sequencing technologies to enable an optimal resolution in the de novo reconstruction of the genomes and elucidation of structural variations [29,30], with clinical and antibiotic resistance data to discriminate between ST-742 isolates. We show that ST-742 isolates of different patients have distinct genomic profiles and propose that each patient has been colonized independently from a natural reservoir of ST-742 where recombination events diversify the population of this microdiverse endemic B. multivorans strain.…”