Data from: De novo assembly of genomes from long sequence reads reveals uncharted territories of Propionibacterium freudenreichii

Background: Propionibacterium freudenreichii is an industrially important
bacterium granted the Generally Recognized as Safe (the GRAS) status, due
to its long safe use in food bioprocesses. Despite the recognized role in
the food industry and in the production of vitamin B12, as well as its
documented health-promoting potential, P. freudenreichii remained poorly
characterised at the genomic level. At present, only three complete genome
sequences are available for the species. Results: We used the PacBio RS II
sequencing platform to generate complete genomes of 20 P. freudenreichii
strains and compared them in detail. Comparative analyses revealed both
sequence conservation and genome organisational diversity among the
strains. Assembly from long reads resulted in the discovery of additional
circular elements: two putative conjugative plasmids and three active,
lysogenic bacteriophages. It also permitted characterisation of the
CRISPR-Cas systems. The use of the PacBio sequencing platform allowed
identification of DNA modifications, which in turn allowed
characterisation of the restriction-modification systems together with
their recognition motifs. The observed genomic differences suggested
strain variation in surface piliation and specific mucus binding, which
were validated by experimental studies. The phenotypic characterisation
displayed large diversity between the strains in ability to utilise a
range of carbohydrates, to grow at unfavourable conditions and to form a
biofilm. Conclusion: The complete genome sequencing allowed detailed
characterisation of the industrially important species, P. freudenreichii
by facilitating the discovery of previously unknown features. The results
presented here lay a solid foundation for future genetic and functional
genomic investigations of this actinobacterial species.