Bacillus subtilis genome diversity

Abstract

Microarray-based comparative genomic hybridization (M-CGH) is a powerful method for rapidly identifying regions of genome diversity among closely related organisms. We used M-CGH to examine the genome diversity of 17 strains belonging to the nonpathogenic species Bacillus subtilis. Our M-CGH results indicate that there is considerable genetic heterogeneity among members of this species; nearly one-third of Bsu168-specific genes exhibited variability, as measured by the microarray hybridization intensities. The variable loci include those encoding proteins involved in antibiotic production, cell wall synthesis, sporulation, and germination. The diversity in these genes may reflect this organism's ability to survive in diverse natural settings.

FIG. 1.

Maximum parsimony tree derived using CLUSTALX and PAUP analysis of 754-bp gyrA sequences (34, 36). The E. coli K-12 outgroup is forced. The numbers at nodes indicate bootstrap support values, as calculated by PAUP.

FIG. 2.

M-CGH composite view of genome diversity exhibited by 18 B. subtilis strains and one B. vallismortis strain. Each row shows the results for one strain, and each column represents genes as they are found along the length of the Bsu168 genome, starting at the origin of replication and proceeding clockwise (dnaA to rpmH). Blue indicates a gene that is likely present in the test strain (average Cy control/Cy test log₂ ratio, ≤1), and yellow indicates a gene that is either absent or too highly divergent to hybridize with equal efficiency to the gene of Bsu168 (average Cy control/Cy test log₂ ratio, >1). The image was generated using the CLUSTER and TREEVIEW programs (11).

FIG. 3.

Number of “variable” loci exhibited by each strain as determined by M-CGH. The white and black bars show data for B. subtilis subsp. subtilis and B. subtilis subsp. spizizenii strains, respectively, and the hatched bar shows data for B. vallismortis.