Abstract
Bacteriophage infection of Lactococcus species can cause serious disruption of dairy fermentation processes. The most common isolates from the dairy environment are Siphoviridae lytic 936-type phages. To gain specific knowledge about this group of phages in Polish dairies, we examined 90 isolates from 8 different locations. Based on restriction fragment length polymorphism analysis, coupled with physiological and molecular studies, the isolated phages were divided into 8 distinct groups. Whole-genome sequencing of single representatives from each phage group provided data about their biology and genetic composition. The phages present an overall conserved genome organization. High sequence homology to another Polish isolate, Lactococcus phage bIBB29, indicates their close phylogenetic relatedness to this strain. Such similarity may be suggestive of a general genome conservation among phages persisting in Polish dairies. Comparative genome analyses with other 936-type phages revealed several discriminative traits, including the presence and position of HNH endonuclease genes, varying number of orfs in the early gene region, and a putative TpeX gene. Interestingly, host range of the sequenced phages was restricted to L. lactis subsp. lactis biovar. diacetylactis strains. The results provide new data regarding phages present in the Polish dairy environment and permit analysis of their biology, genome composition and relatedness to other Lactococcus 936-type phages.
Highlights
The majority of starter cultures used in the dairy industry for the production of sour cream, buttermilk, kefir or cheese contain, among other microorganisms, a mixture of Lactococcus lactis (L. lactis) strains
While host range and DNA restriction fragment length polymorphism (RFLP) analyses are the principal techniques used in phage typing, phage characterization through whole-genome sequencing is far more valuable for providing information on newly emerged phages and for understanding the population dynamics of phages in the dairy environment[8,9,28,49]
Recent studies postulate the engagement of other factors, such as the neck protein structure (NPS) or tail protein extension (TpeX), in infection[28,43]
Summary
The majority of starter cultures used in the dairy industry for the production of sour cream, buttermilk, kefir or cheese contain, among other microorganisms, a mixture of Lactococcus lactis (L. lactis) strains. According to the classification proposed by Deveau et al.[10], lactococcal phages are grouped into ten distinct types based on nucleotide sequence homology. Eight of these phage types belong to the Siphoviridae family (with long, non-contractile tails and isometric or prolate heads), and the remaining two belong to Podoviridae (with short, non-contractile tails and isometric heads). Time-based studies on the evolution of phages in a single dairy plant provide proof of the prevalence of 936-type phages in this environment over long periods of time[17]. In an attempt to characterize 936-type phages collected during a 3-year period from 8 dairies located in various geographical regions in Poland, we initially screened 90 isolates for RFLPs. Based on distinct restriction patterns, phages were divided into 8 groups, and a representative from each group was subjected to whole-genome sequencing. The obtained data provide further information about the phages present in the milk environment, allowing the elucidation of their biology and genetic components and their comparison to already known 936-type phages that infect Lactococcus spp
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