SRA

Propionibacterium freudenreichii (PF) is an Actinobacterium used in cheese technology and for its probiotic properties. PF also displays high adaptability towards several ecological niches and is able to grow on various carbon and nitrogen sources. The aim of this work is to discover the genetic basis of strain-dependent traits related to the ability to utilize specific carbon sources. High-throughput sequencing technologies are ideal for that purpose as they have the potential to decipher genomic diversity at a moderate cost. Twenty one strains of PF were sequenced and the genomes were de novo assembled. Scaffolds were ordered with comparison to the complete reference genome CIRM-BIA1, previously obtained using traditional Sanger sequencing. Automatic functional annotation and manual curation were performed. Each gene was attributed to either core genome or to accessory genome. The ability of the 21 strains to degrade 50 different sugars was evaluated. Thirty-three sugars were degraded by none of the sequenced strain whereas eight sugars were degraded by all of them. The corresponding genes were present in the core genome. Lactose, melibiose and xylitol were utilized by only some strains. In this case, presence/lack of genes responsible for carbon uptake and degradation correlates well with the phenotypes. Furthermore the simultaneous presence of those genes is in agreement with previously described metabolic pathways in other species. The genetic origin (transduction, rearrangement) of the corresponding genetic islands is discussed. Ribose and gluconate were degraded more or less (quantitative phenotype) by some strains. For these sugars, phenotypes was not explained by presence/lack of gene but correlated with premature appearance of a stop codon which interrupts protein synthesis and prevents the catabolism of corresponding carbon sources.