Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages
Cheng, Lucy | Marinelli, Laur J. | Grosset, Noel | Fitz-Gibbon, Sorel T. | Bowman, Charles A. | Dang, Brian Q. | Russel, Daniel A. | Jacobs-Sera, Deborah | Shi, Baochen | Pelligrini, Matteo | Miller, Jeff F. | Gautier, Michel | Hatfull, Graham F. | Modlin, Robert L. | David Geffen School of Medicine [Los Angeles] ; University of California [Los Angeles] (UCLA) ; University of California (UC)-University of California (UC) | Science et Technologie du Lait et de l'Oeuf (STLO) ; Institut National de la Recherche Agronomique (INRA)-AGROCAMPUS OUEST | Department of Molecular, Cell, and Developmental Biology Los Angeles ; University of California (UC) | Department of Biological Sciences ; Dartmouth College [Hanover] | Department of Molecular, Cell, and Developmental Biology ; University of California [Los Angeles] (UCLA) ; University of California (UC)-University of California (UC) | California NanoSystems Institute ; University of California [Los Angeles] (UCLA) ; University of California (UC)-University of California (UC)
Background:A remarkable exception to the large genetic diversity often observed for bacteriophages infecting aspecific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is also a member of the Propionibacteriaceae family, Propionibacterium freudenreichii , a bacterium used in production of Swiss-type cheeses, have also been described and are common contaminants of the cheese manufacturing process. However, little is known about their genetic composition and diversity.Results:We obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-typecheese samples, and determined their complete genome sequences. These data revealed that all seven phage isolates are of similar genomic length and GC% content, but their genomes are highly diverse, including genes encoding the capsid, tape measure, and tail proteins. In contrast to C. acnes phages, all P. freudenreichii phage genomes encode a putative integrase protein, suggesting they are capable of lysogenic growth. This is supported by the finding of related prophages in some P. freudenreichii strains. The seven phages could further be distinguished as belonging to two distinct genomic types, or ‘ clusters ’ , based on nucleotide sequences, and host range analyses conducted on a collection of P. freudenreichii strains show a higher degree of host specificity than is observed for the C. acnes phages.Conclusions:Overall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, asevidenced by their higher genetic diversity, potential for lysogenic growth, and more restricted host ranges. This suggests substantial differences in the evolution of these related species from the Propionibacteriaceae family and their phages, which is potentially related to their distinct environmental niches.
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