Abstract
BackgroundPropionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. PF is also extremely adaptable to several ecological niches and can grow on a variety of carbon and nitrogen sources. The aim of this work was to discover the genetic basis for strain-dependent traits related to its ability to use specific carbon sources. High-throughput sequencing technologies were ideal for this purpose as they have the potential to decipher genomic diversity at a moderate cost.Results21 strains of PF were sequenced and the genomes were assembled de novo. Scaffolds were ordered by comparison with the complete reference genome CIRM-BIA1, obtained previously using traditional Sanger sequencing. Automatic functional annotation and manual curation were performed. Each gene was attributed to either the core genome or an 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 strains whereas eight sugars were degraded by all of them. The corresponding genes were present in the core genome. Lactose, melibiose and xylitol were only used by some strains. In this case, the presence/absence of genes responsible for carbon uptake and degradation correlated well with the phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence of these genes was in line the metabolic pathways described previously in other species. We also considered the genetic origin (transduction, rearrangement) of the corresponding genomic islands. Ribose and gluconate were degraded to a greater or lesser extent (quantitative phenotype) by some strains. For these sugars, the phenotypes could not be explained by the presence/absence of a gene but correlated with the premature appearance of a stop codon interrupting protein synthesis and preventing the catabolism of corresponding carbon sources.ConclusionThese results illustrate (i) the power of correlation studies to discover the genetic basis of binary strain-dependent traits, and (ii) the plasticity of PF chromosomes, probably resulting from horizontal transfers, duplications, transpositions and an accumulation of mutations. Knowledge of the genetic basis of nitrogen and sugar degradation opens up new strategies for the screening of PF strain collections to enable optimum cheese starter, probiotic and white biotechnology applications.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1467-7) contains supplementary material, which is available to authorized users.
Highlights
Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties
Results relative to 21 strains Twenty-one strains of Propionibacterium freudenreichii were chosen according to MLST results [12] and in order to represent the diversity of the species (Table 1)
We show here for the first time that gluconate degradation is strain-dependent and that strains unable to degrade this sugar accumulate nonsense mutations in different genes of the pathways
Summary
Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. Propionibacterium freudenreichii is a food-grade actinobacterium (gram positive, high GC content) known for its low nutritional requirements. It is responsible for the holes and aroma of Swiss-type cheese and for the biotechnological production of propionate and vitamin B12. Propionibacterium freudenreichii was first isolated a century ago from Emmental cheese [2] but the species is found in various biotopes such as silage, soil, rumen and waste water [3]. These observations indicate its ability to adapt to different environmental conditions. Strains able to degrade nitrate should be avoided in a setting of probiotic supply because such strains may cause the release of toxic nitroso compounds in the gut
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