Table S1. P. freudenreichii strains used in this study. Table S2. Average nucleotide identities of P. freudenreichii phages. (DOCX 71Â kb

Baochen Shi (16761)

Brian Dang (4901188)

Charles Bowman (4901176)

Daniel Russell (2094130)

Deborah Jacobs-Sera (199566)

Graham Hatfull (3402956)

Jeff Miller (4901182)

Laura Marinelli (4901185)

Lucy Cheng (4901179)

Matteo Pellegrini (2078)

Michel Gautier (492401)

NoĂŤl Grosset (4901173)

Robert Modlin (4535785)

Sorel Fitz-Gibbon (3251946)

BMC Microbiology

Lucy Cheng

Laura J. Marinelli

Noël Grosset

Sorel T. Fitz-Gibbon

Charles A. Bowman

Brian Q. Dang

Daniel A. Russell

Deborah Jacobs-Sera

Baochen Shi

Matteo Pellegrini

Jeff F. Miller

Michel Gautier

Graham F. Hatfull

Robert L. Modlin

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Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

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Additional file 1: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Figure S2. Genome organization of phage E6. See Additional file 2: Figure S1 for details. (PDF 161Â kb

Additional file 3: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

Abstract Background 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 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-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. Conclusions Overall, 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

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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

Cheng, Lucy

Marinelli, Laura J

Grosset, Noël

Fitz-Gibbon, Sorel T

Bowman, Charles A

Dang, Brian Q

Russell, Daniel A

Jacobs-Sera, Deborah

Shi, Baochen

Pellegrini, Matteo

Miller, Jeff F

Gautier, Michel

Hatfull, Graham F

Modlin, Robert L

eScholarship - University of California

English

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

Additional file 1: of Complete genomic sequences of Propionibacterium freudenreichii phages from Swiss cheese reveal greater diversity than Cutibacterium (formerly Propionibacterium) acnes phages

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