Genome sequence of Lactobacillus helveticus: an organism distinguished by selective gene loss and IS element expansion

Teagasc, Moorepark Food Research Centre, Moorepark, Fermoy, Co. Cork, Ireland; Alimentary Pharmabiotic Centre, Cork, Ireland

^* To whom correspondence should be addressed. Email: tom.beresford{at}teagasc.ie.

	Abstract

Mobile genetic elements are major contributing factors to the generation of genetic diversity in prokaryotic organisms. For example insertion sequence (IS) elements have been shown to specifically contribute to niche adaptation by promoting a variety of genetic rearrangements. The complete genome sequence of the cheese culture Lactobacillus helveticus DPC 4571 was determined and revealed significant conservation when compared to three non-dairy gut lactobacilli. Despite originating from significantly different environments, 65-75% of genes were conserved between the commensal and dairy lactobacilli which allowed key niche-specific gene sets to be described. However, the primary distinguishing feature was two hundred and thirteen IS elements in the DPC 4571 genome, ten times more than the other lactobacilli. Moreover, genome alignments revealed an unprecedented level of genome stability between these four Lactobacillus species considering the number of IS elements in the L. helveticus genome. Comparative analysis also indicated that the IS elements were not the primary agents of niche adaptation for the L. helveticus genome. A clear bias towards the loss of genes reported to be important for gut colonization was observed for the cheese culture but there was no clear evidence of IS-associated gene deletion and decay for the majority of genes lost. Furthermore, an extraordinary level of sequence diversity exists between copies of certain IS elements in the DPC 4571 genome indicating they may represent an ancient component of the L. helveticus genome. These data suggests a special unobtrusive relationship between the DPC 4571 genome and its mobile DNA complement.