Lactobacillus helveticus is a versatile dairy bacterium found to possess heterogeneous genotypes depending on the ecosystem from which it was isolated. The recently published genome sequence showed the remarkable flexibility of its structure, demonstrated by a substantial level of insertion sequence (IS) element expansion in association with massive gene decay. To assess this diversity and examine the level of genome plasticity within the L. helveticus species, an array-based comparative genome hybridization (aCGH) experiment was designed in which 10 strains were analyzed. The aCGH experiment revealed 16 clusters of open reading frames (ORFs) flanked by IS elements. Four of these ORFs are associated with restriction/modification which may have played a role in accelerated evolution of strains in a commercially intensive ecosystem undoubtedly challenged through successive phage attack. Furthermore, analysis of the IS-flanked clusters demonstrated that the most frequently encountered ISs were also those most abundant in the genome (IS1201, ISL2, ISLhe1, ISLhe2, ISLhe65, and ISLhe63). These findings contribute to the overall viewpoint of the versatile character of IS elements and the role they may play in bacterial genome plasticity.Lactobacillus helveticus is a gram-positive, homofermentative lactic acid bacterium which is widely used in the manufacture of cheeses, such as Swiss cheese and some Cheddar-type cheeses (22,25). It is also commonly used in the production of different types of Italian cheeses, such as Parmigiano Reggiano (18) and Grana Padano, where it contributes to the formation of specific flavor compounds (42).Phylogenetic analysis of ribosomal protein sequences derived from lactobacilli and streptococci classified L. helveticus in the same group along with both gastrointestinal (GI) tract and dairy-specific species (14). Comparative analysis of the 16S rRNA of L. helveticus DPC4571 revealed 98.4% identity with Lactobacillus acidophilus NCFM and indicated that this probiotic strain was closely related to strain DPC4571, despite the different environments these two lactobacilli inhabit (4). The results of genomic analysis of L. helveticus suggested that two major events have occurred in the diversification process of L. helveticus from a common ancestor with L. acidophilus, selective gene loss and acquisition of a large number of insertion sequence (IS) elements (4). IS elements are DNA sequences capable of independent transposition within and between bacterial genomes (31). Their capacity for independent mobility demonstrates the parasitic nature of these elements (11); however, they can also be regarded as having a positive influence, as they assist in promoting genetic variation (1). Thus, even though the primal character of these elements remains unclear in that they may be considered simply as selfish DNA elements, their impact on the architecture of microbial genomes is undeniable. It has already been demonstrated that IS-related mutations occur in Escherichia coli (44), Lactococcus lactis (10)...