Genomic diversity of 24 Propionibacterium freudenreichii 1 strains
Résumé
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. AEM 2010) were (i) sequenced by Solexa-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 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 (ability to lactose degradation for exemple). 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.