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

doi: 10.1186/s12866-018-1159-y.

Laura J Marinelli 3 4, Noël Grosset 5, Sorel T Fitz-Gibbon 6, Charles A Bowman 7, Brian Q Dang 7, Daniel A Russell 7, Deborah Jacobs-Sera 7, Baochen Shi 8, Matteo Pellegrini 6, Jeff F Miller 2 9, Michel Gautier 5, Graham F Hatfull 7, Robert L Modlin 1 2

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

Lucy Cheng et al. BMC Microbiol. 2018.

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.

Keywords: Bacteriophage; Cheese microbiota; Cutibacterium acnes; Phage genomics; Propionibacterium freudenreichii.

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Figures

Fig. 1

Fig. 1

Morphology of P. freudenreichii bacteriophages. Electron micrographs of Anatole and B22 (as indicated) showing both have siphoviral morphologies with isometric heads and long flexible tails. Scale markers are 100 nm

Fig. 2

Fig. 2

Dot plot nucleotide comparisons of P. freudenreichii bacteriophages. The genome sequences of seven P. freudenreichii bacteriophages (varying from 35,209 bp to 38,555 bp) were compared with each other, as well as the previously sequenced P. freudenreichii phage, PFR1 (38,071 bp) [19] and the C. acnes phage, P100.1 (29,612 bp) [5], using the dotplot program Gepard, with standard parameter settings (word length = 10, window = 0) [39]. Cluster BW includes Doucette, B22, E6, and G4. Cluster BV includes Anatole, E1, and B3. PFR1 and P100.1 group in the separate clusters, BX and BU, respectively

Fig. 3

Fig. 3

Genome map of P. freudenreichii phages Anatole and Doucette. Predicted genes are shown as boxes either above or below the genome corresponding to rightwards- and leftwards-transcription, respectively. The gene numbers are shown within each colored box, and its phamily number is shown above, with the number of phamily members shown in parentheses; coloring reflects the phamily assignment. Grouping of genes into phamily of related sequences and map generation was performed using Phamerator [40] and the database ‘Actinobacteriophage_685’. Putative gene functions are listed above the genes

Fig. 4

Fig. 4

Whole genome comparisons of P. freudenreichii bacteriophages. The genome organizations of seven P. freudenreichii bacteriophages are shown with the pairwise nucleotide sequence similarities displayed as colored segments between the genomes. The strength of sequence similarity is represented according to a color spectrum in which violet is the most similar and red is the least (above a threshold BLASTN E-value of 10− 5). Predicted genes are shown as colored boxes either above or below each genome, representing leftwards- and rightwards-transcription, respectively. The gene numbers are shown within each colored box, and its phamily number is shown above, with the number of phamily members shown in parentheses; coloring reflects the phamily assignment. The maps were generated using the program Phamerator [40] and database Actinobacteriophage_685

Fig. 5

Fig. 5

Relationships between Propionibacteriophages and Cutibacteriophages. a Heat map representation of shared gene content between seven P. freudenreichii phage genomes and seven C. acnes phage genomes. The proteins encoded by C. acnes phages (P101A, P100.1, P100D, P100A, P14.4, P1.1) and P. freudenreichii phages (Cluster BW: G4, E6, B22, Doucette; Cluster BV: B3, E1, Anatole) were assorted into phamilies using Phamerator [40] and the proportions of shared genes calculated. The scale on the right shows heat map colors with percent of shared genes. b Gene content relationships between P. freudenreichii phages and phages of related hosts. The relationships between the seven P. freudenreichii phages and a selection of phages that infect other bacteria in the Actinobacteria phylum were compared according to shared gene content using Phamerator and displayed using the Neighbor Network function of SplitsTree [34]. Cluster BW phages of P. freudenreichii are shown in the green circle, Cluster BV phage of P. freudenreichii in the blue circle, and C. acnes phages in the orange circle. Galaxy and Min1 are phages of Mycobacterium and Microbacterium, respectively, and REQ2 and REQ3 are Rhodococcus phages

Fig. 6

Fig. 6

The mosaic prophage of P. freudenreichii CIRM-BIA 139. The whole genome sequence project of P. freudenreichii contains two contigs (contigs 1 and 17; Accession numbers CCYX01000001 and CCYX01000017, respectively) with similarities to Cluster BW phages. The predicted organization of the prophage is shown aligned to phages G4 and B22 presenting them in two tiers, and organization from attL through to attR reflecting the integrated prophage structure. Segments corresponding to the two contigs are shown, which overlap in the middle of the tape measure protein gene; the reverse complement of contig 1 is shown. The prophage genes are colored according to their homologues in G4 and B22. The genes in prophage contig 1 are either shared with both phages or only with phage B22, whereas the genes at the right end of contig 1 are shared uniquely with phage G4

References

    1. Pope WH, Bowman CA, Russell DA, Jacobs-Sera D, Asai DJ, Cresawn SG, Jacobs WR, Hendrix RW, Lawrence JG, Hatfull GF. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife. 2015;4:e06416. doi: 10.7554/eLife.06416. -DOI -PMC -PubMed
    1. Kwan T, Liu J, Dubow M, Gros P, Pelletier J. The complete genomes and proteomes of 27 Staphylococcus aureus bacteriophages. Proc Natl Acad Sci U S A. 2005;102(14):5174–5179. doi: 10.1073/pnas.0501140102. -DOI -PMC -PubMed
    1. Kwan T, Liu J, Dubow M, Gros P, Pelletier J. Comparative genomic analysis of 18 Pseudomonas aeruginosa bacteriophages. J Bacteriol. 2006;188(3):1184–1187. doi: 10.1128/JB.188.3.1184-1187.2006. -DOI -PMC -PubMed
    1. Scholz CF, Kilian M. The natural history of cutaneous propionibacteria, and reclassification of selected species within the genus Propionibacterium to the proposed novel genera Acidipropionibacterium gen. nov., Cutibacterium gen. nov. and Pseudopropionibacterium gen. nov. Int J Syst Evol Microbiol. 2016;66(11):4422–4432. doi: 10.1099/ijsem.0.001367. -DOI -PubMed
    1. Marinelli LJ, Fitz-Gibbon S, Hayes C, Bowman C, Inkeles M, Loncaric A, Russell DA, Jacobs-Sera D, Cokus S, Pellegrini M, et al. Propionibacterium acnes bacteriophages display limited genetic diversity and broad killing activity against bacterial skin isolates. MBio. 2012;3(5):e00279–e00212. doi: 10.1128/mBio.00279-12. -DOI -PMC -PubMed

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