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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. [ABSTRACT FROM AUTHOR]

Bacteriophages are the most common biological entity, establishing complex phage-bacteria interactions. Keywords: mobile elements (MEs); evolution; adaptability; bacteriophage; virulence factors; insertion sequence (Is); restriction and modification EN mobile elements (MEs) evolution adaptability bacteriophage virulence factors insertion sequence (Is) restriction and modification 1 2 2 02/24/22 20220221 NES 220221 The bacterial mobilome, i.e., the group of all mobile elements present in a bacterial genome, are important players in bacterial evolution, shaping the host genome through complex interactions between the mobile element and host bacteria. Wang et al. investigated the diversity of CRISPR-Cas systems and the presence of prophages in the genomes of 66 I Bifidobacterium pseudocatenulatum i strains. [Extracted from the article]

We report here experiments carried out with nonpathogenic Escherichia coli bacterial strains and their phages. This research yielded interesting insights into their activities, occasionally producing genetic variants of different types. In order to not interfere with the genetic stability of the parental strains involved, we found that the bacteria are genetically equipped to only rarely produce a genetic variant, which may occur by a number of different approaches. On the one hand, the genes of relevance for the production of specific genetic variants are relatively rarely expressed. On the other hand, other gene products act as moderators of the frequencies that produce genetic variants. We call the genes producing genetic variants and those moderating the frequencies of genetic variation "evolution genes". Their products are generally not required for daily bacterial life. We can, therefore, conclude that the bacterial genome has a duality. Some of the bacterial enzymes involved in biological evolution have become useful tools (e.g., restriction endonucleases) for molecular genetic research involving the genetic set-up of any living organism. [ABSTRACT FROM AUTHOR]