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

Abstract

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.ResultsWe 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.ConclusionThe 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.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4165-9) contains supplementary material, which is available to authorized users.

Secretome profiling of Propionibacterium freudenreichii reveals highly variable responses even among the closely related strains

“…Strain‐specific differences in release of SlpA, InlA and FimB as well as in biofilm formation (Deptula et al ., ) imply that the cereal JS114 and the dairy JS22 strains differ in their adherence features. To explore this further, we quantitatively compared both the biofilm formation efficiency and the adherence of the two strains cultured under physiological condition to mucin, BSA and hydrophobic material (resin‐based Polysorp wells optimized to bind hydrophobic proteins).…”

“…As Opp systems are essential for several milk‐adapted bacteria that use casein‐derived peptides/amino acids for growth in milk (Savijoki et al ., ), it could be that increased oligopeptide uptake could help the strain to adapt in environments containing milk. In support of this, we previously reported that these two strains differed also in their preference for different carbohydrates; unlike JS22, the cereal JS14 strain was not able to metabolize the milk‐carbohydrate lactose (Deptula et al ., ). In that study, we also indicated the presence of the galE1‐galP‐lacZ operon in a genomic island in JS22, which is the likely explanation for the ability of this strain to grow on lactose.…”

“…We also demonstrated that neither one of the two strains were able to bind porcine mucus, which is in line with a previous report suggesting that P. freudenreichii interacts with other surface compounds of the epithelial cells rather than mucins (Do Carmo et al ., ). One of the P. freudenreichii strains used in the present study (JS18) was recently shown to harbour a complete fimB ‐ fimA ‐ srtC2 operon capable of producing a surface appendage conferring mucus binding ability on the cells (Deptula et al ., ). As fimbriae have been reported to take part in host–microbe and microbe–microbe interactions in probiotic bifidobacteria (O'Connell Motherway et al ., ; Turroni et al ., ), it could be that fimbrial gene clusters have undergone adaptive mutations reducing their ability to colonize intestinal tract.…”

“…JS4, JS6 and JS279). We have previously reported that the strains selected for this study differed also in terms of their ability to form biofilm (Deptula et al ., ). In particular, the JS14 and JS22 strains showed distinct biofilm phenotypes; JS14 formed biofilm under normal conditions, while JS22 displayed non‐biofilm‐forming phenotype under the same conditions (Deptula et al ., ).…”

“…Compared with the genome of the Acidipropionibacterium strain ATCC4875 (Parizzi et al, 2012), the P. freudenreichii strains have smaller genomes (roughly 3.6 Mbp versus 2.6 Mbp), and although many common genes could be identified, the genomes of the two species vary significantly (Parizzi et al, 2012;Koskinen et al, 2015). We recently compared the genomes of 20 P. freudenreichii strains, of which 16 and 4 were from dairy and cereal environments respectively (Deptula et al, 2017b). Phylogenetic analyses using the whole genomes indicated that the strains with cereal origin cluster away from the dairy strains (Deptula et al, 2017b).…”