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Background   Lysinibacillus sphaericus  (formerly named  Bacillus sphaericus ) is incapable of polysaccharide utilization and some isolates produce active insecticidal proteins against mosquito larvae. Its taxonomic status was changed to the genus  Lysinibacillus  in 2007 with some other organisms previously regarded as members of  Bacillus . However, this classification is mainly based on physiology and phenotype and there is limited genomic information to support it.    Results  In this study, four genomes of  L. sphaericus  were sequenced and compared with those of 24 representative strains belonging to  Lysinibacillus  and  Bacillus . The results show that  Lysinibacillus  strains are phylogenetically related based on the genome sequences and composition of core genes. Comparison of gene function indicates the major difference between  Lysinibacillus  and the two  Bacillus  species is related to metabolism and cell wall/membrane biogenesis. Although  L. sphaericus  mosquitocidal isolates are highly conserved, other  Lysinibacillus  strains display a large heterogeneity. It was observed that mosquitocidal toxin genes in  L. sphaericus  were in close proximity to genome islands (GIs) and mobile genetic elements (MGEs). Furthermore, different copies and varying genomic location of the GIs containing  binA/binB  was observed amongst the different isolates. In addition, a plasmid highly similar to pBsph, but lacking the GI containing  binA/binB , was found in  L. sphaericus  SSII-1.    Conclusions  Our results confirm the taxonomy of the new genus  Lysinibacillus  at the genome level and suggest a new species for mosquito-toxic  L. sphaericus . Based on our findings, we hypothesize that (1)  Lysinibacillus  strains evolved from a common ancestor and the mosquitocidal  L. sphaericus  toxin genes were acquired by horizontal gene transfer (HGT), and (2) capture and loss of plasmids occurs in the population, which plays an important role in the transmission of  binA/binB .    Electronic supplementary material  The online version of this article (doi:10.1186/s12864-015-1359-x) contains supplementary material, which is available to authorized users.

Genome comparison provides molecular insights into the phylogeny of the reassigned new genus Lysinibacillus