Genome analysis of the temperate bacteriophage PMBT6 residing in the genome of Bifidobacterium thermophilum MBT94004

  • Sabrina SprotteEmail author
  • Wilhelm Bockelmann
  • Erik Brinks
  • Peer Schleifenbaum
  • Gyu-Sung Cho
  • Gregor Fiedler
  • Knut J. Heller
  • Charles M. A. P. Franz
  • Horst Neve
Annotated Sequence Record


The Siphoviridae phage PMBT6 was identified by transmission electron microscopy in the supernatant of Bifidobacterium thermophilum MBT94004 bioreactor fermentation culture, where it occurred at a moderately high titer. Genome analysis of the bacterial DNA confirmed the presence of this prophage within the genome of the lysogenic host. Under laboratory conditions, the prophage could not be induced by mitomycin C, ultraviolet C irradiation or hydrogen peroxide, suggesting that the prophage was released by spontaneous induction under (yet unknown) bioreactor conditions. Genome sequencing of the virion resulted in a linear, double-stranded DNA molecule of 36,561 bp with a mol% G + C content of 61.7 and 61 predicted open reading frames with low similarity to other Bifidobacterium spp. genomes, confirming that PMBT6 represents a novel temperate phage for this genus.



We kindly thank Angela Back, Inka Lammertz and Gesa Gehrke for technical assistance.

Compliance with ethical standards

Conflict of interest

None of the authors has any conflict of interest to declare.

Ethical approval

This article does not contain any studies with human participants or animals performed by any of the authors.

Supplementary material

705_2019_4448_MOESM1_ESM.pdf (39 kb)
Supplementary material 1 (PDF 38 kb)


  1. 1.
    Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NewYorkGoogle Scholar
  2. 2.
    Kearse M, Moir R, Wilson A et al (2012) Geneious basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data. Bioinformatics 28(12):1647–1649. CrossRefPubMedPubMedCentralGoogle Scholar
  3. 3.
    Nurk S, Bankevich A, Antipov D et al. (2013) Assembling genomes and mini-metagenomes from highly chimeric reads. In: Deng M, Jiang R, Sun F et al. (eds) Research in computational molecular biology: 17th Annual International Conference, RECOMB 2013, Beijing, China, April 7–10, 2013. Proceedings, vol 7821. Springer Berlin Heidelberg; Imprint; Springer, Berlin, Heidelberg, pp 158–170Google Scholar
  4. 4.
    Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22(22):4673–4680CrossRefPubMedPubMedCentralGoogle Scholar
  5. 5.
    Aziz RK, Bartels D, Best AA et al (2008) The RAST server: rapid annotations using subsystems technology. BMC Genom 9:75. CrossRefGoogle Scholar
  6. 6.
    Altschul SF, Gish W, Miller W et al (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. CrossRefPubMedGoogle Scholar
  7. 7.
    Letunic I, Bork P (2018) 20 years of the SMART protein domain annotation resource. Nucleic Acids Res 46(D1):D493–D496. CrossRefPubMedGoogle Scholar
  8. 8.
    Besemer J, Lomsadze A, Borodovsky M (2001) GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res 29(12):2607–2618CrossRefPubMedPubMedCentralGoogle Scholar
  9. 9.
    Zhou Y, Liang Y, Lynch KH et al (2011) PHAST: a fast phage search tool. Nucleic Acids Res 39((Web Server issue)):W347-52. CrossRefPubMedGoogle Scholar
  10. 10.
    Lugli GA, Milani C, Turroni F et al (2016) Prophages of the genus Bifidobacterium as modulating agents of the infant gut microbiota. Environ Microbiol 18(7):2196–2213. CrossRefPubMedGoogle Scholar
  11. 11.
    Mahony J, Lugli GA, van Sinderen D et al (2018) Impact of gut-associated bifidobacteria and their phages on health: two sides of the same coin? Appl Microbiol Biotechnol 102(5):2091–2099. CrossRefPubMedGoogle Scholar
  12. 12.
    Ventura M, Lee J-H, Canchaya C et al (2005) Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis. Appl Environ Microbiol 71(12):8692–8705. CrossRefPubMedPubMedCentralGoogle Scholar
  13. 13.
    Ventura M, Turroni F, Foroni E et al (2010) Analyses of bifidobacterial prophage-like sequences. Antonie Van Leeuwenhoek 98(1):39–50. CrossRefPubMedGoogle Scholar
  14. 14.
    Ventura M, Turroni F, Lima-Mendez G et al (2009) Comparative analyses of prophage-like elements present in bifidobacterial genomes. Appl Environ Microbiol 75(21):6929–6936. CrossRefPubMedPubMedCentralGoogle Scholar
  15. 15.
    Mavrich TN, Casey E, Oliveira J et al (2018) Characterization and induction of prophages in human gut-associated Bifidobacterium hosts. Sci Rep 8(1):12772. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Jans C, Lacroix C, Follador R et al (2013) Complete genome sequence of the probiotic Bifidobacterium thermophilum strain RBL67. Genome Announc 1(3):e00191-13–e00191-13. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
    Groth AC, Calos MP (2004) Phage integrases: biology and applications. J Mol Biol 335(3):667–678CrossRefPubMedGoogle Scholar
  18. 18.
    Koberg S, Mohamed MDA, Faulhaber K et al (2015) Identification and characterization of cis- and trans-acting elements involved in prophage induction in Streptococcus thermophilus J34. Mol Microbiol 98(3):535–552. CrossRefPubMedGoogle Scholar
  19. 19.
    Ptashne M (2004) A genetic switch: phage lambda revisited, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New YorkGoogle Scholar
  20. 20.
    Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25(5):955–964CrossRefPubMedPubMedCentralGoogle Scholar
  21. 21.
    Kala S, Cumby N, Sadowski PD et al (2014) HNH proteins are a widespread component of phage DNA packaging machines. Proc Natl Acad Sci USA 111(16):6022–6027. CrossRefPubMedGoogle Scholar
  22. 22.
    Merrill BD, Ward AT, Grose JH et al (2016) Software-based analysis of bacteriophage genomes, physical ends, and packaging strategies. BMC Genomics 17:679. CrossRefPubMedPubMedCentralGoogle Scholar

Copyright information

© Springer-Verlag GmbH Austria, part of Springer Nature 2019

Authors and Affiliations

  • Sabrina Sprotte
    • 1
    Email author
  • Wilhelm Bockelmann
    • 1
  • Erik Brinks
    • 1
  • Peer Schleifenbaum
    • 1
  • Gyu-Sung Cho
    • 1
  • Gregor Fiedler
    • 1
  • Knut J. Heller
    • 1
  • Charles M. A. P. Franz
    • 1
  • Horst Neve
    • 1
  1. 1.Department of Microbiology and Biotechnology, Max Rubner-InstitutFederal Research Institute of Nutrition and FoodKielGermany

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