Abstract
BackgroundA remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific 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.ResultsWe obtained seven independently isolated bacteriophages that infect P. freudenreichii from Swiss-type cheese 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.ConclusionsOverall, our data demonstrate P. freudenreichii bacteriophages are distinct from C. acnes phages, as evidenced 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.
Highlights
A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes phages, which are highly homogeneous
Isolation of bacteriophages To investigate the diversity of bacteriophages that infect P. freudenreichii, we isolated P. freudenreichii phages from Swiss-type cheese by culturing with, or without, indicator strains of host bacteria (Table 1)
The Propionibacteriaceae family is comprised of a diverse group of organisms, containing species such as C. acnes, a human commensal proposed to be involved in the pathogenesis of acne vulgaris, and P. freudenreichii, which is used in the manufacture of Swiss-type cheeses, as well as in the fermentative production of vitamin B12 and propionic acid
Summary
A remarkable exception to the large genetic diversity often observed for bacteriophages infecting a specific bacterial host was found for the Cutibacterium acnes (formerly Propionibacterium acnes) phages, which are highly homogeneous. Phages infecting the related species, which is a member of the Propionibacteriaceae family, Propionibacterium freudenreichii, a bacterium used in production of Swiss-type cheeses, have been described and are common contaminants of the cheese manufacturing process. Most bacteriophage populations display a wide range of genetic diversity, including those phages infecting Mycobacterium, Staphylococcus, and Pseudomonas spp. Cutibacterium acnes bacteriophages, whose host was formerly a member of the genus Propionibacterium and was recently reclassified [4], have been found to have a surprisingly limited genetic diversity [5]. C. acnes has a lower average percent GC (60% vs. 67%) and encodes a larger proportion of genes involved in processes such as host association, tissue degradation, and iron acquisition [4, 9]
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