Expanding the diversity of oenococcal bacteriophages: Insights into a novel group based on the integrase sequence

Temperate bacteriophages are a contributor of the genetic diversity in the lactic acid bacterium Oenococcus oeni We used a classification scheme for oenococcal prophages based on integrase gene polymorphism, to analyze a collection of Oenococcus strains mostly isolated in the area of Bordeaux, which represented the major lineages identified through MLST schemes in the species. Genome sequences of oenococcal prophages were clustered into four integrase groups (A to D) which were related to the chromosomal integration site. The prevalence of each group was determined and we could show that members of the int(B)- and int(C)-prophage groups were rare in our panel of strains. Our study focused on the so far uncharacterized members of the int(D)-group. Various int(D) viruses could be easily isolated from wine samples, while int(D) lysogens could be induced to produce phages active against two permissive O. oeni isolates. These data support the role of this prophage group in the biology of O. oeni. Global alignment of three relevant int(D)-prophages revealed significant conservation and highlighted a number of unique ORFs that may contribute to phage and lysogen fitness. C) 2013 Elsevier B.V. All rights reserved.