Genomic diversity of 24 Propionibacterium freudenreichii strains

High-throughput sequencing technologies have the potential to decipher genomic diversity at a moderate cost. Propionibacterium freudenreichii is an Actinobacterium used in cheese technology (responsible for aroma and holes in Swiss cheese) and that has probiotic properties (bifidogenic and with anti-inflammatory properties in human and animal).

23 strains of Propionibacterium freudenreichii covering 18 different sequence types out of 46 (Dalmasso et al. IJFM 2011) were (i) sequenced by Illumina paired-end sequencing and (ii) de novo assembled using Velvet software.

Depending on strain, 63 to 166 scaffolds were obtained. These scaffolds were arranged with MAUVE along the reference genome CIRM-BIA1, previously obtained from traditional Sanger sequencing (Falentin et al. PlosOne 2010). For each strain, single nucleotide polymorphism and insertion-deletion events were plotted against reference genome.

Sequences were automatically annotated (by blastp and pattern matching) on the INRA-AGMIAL platform. By bidirectional best-hit, each gene was attributed either to core genome or accessory genome. In some strains, some genes belonging to the accessory genome corresponded with genomic islands and confered peculiar phenotypes. Presence/lack of genes responsible for carbone and nitrogen uptake and degradation correlates with some quantitative traits (nitrate, aspartate, lactose degradation). For qualitative traits, like anti-inflammatory properties, annotation of these 23 genomes, enable the design of a pan-genomic microarray and the provide proteome files for the identification of differentially expressed proteins (ANR SURFING).

In the future, screening of P. freudenreichii (~500 strains) collection on genetic basis at CIRM-BIA biological resource center (Rennes) will help in strain choice for cheese starter and probiotic market.