First multilocus sequence typing scheme to study Propionibacterium freudenreichii population structure

Propionibacterium freudenreichii is used as a ripening culture in Swiss cheese manufacture, in which it is involved in the formation of flavour and opening. The concentrations of flavour compounds produced by P. freudenreichii proved highly strain-dependant. Whether this phenotypic biodiversity is related to high molecular diversity is unknown. The aim of this work was to develop a Multilocus Sequence Typing (MLST) scheme to study the molecular diversity and the population structure of P. freudenreichii. Internal fragments of seven genes – rpoB, adk, pf1637, recA, pf169, fumC, gtf – were amplified by PCR and sequenced for 113 strains from different origins. Allele types and sequence types (STs) were assigned according to MLST standards and phylogenetic analyses were performed. Forty-six distinct STs were resolved. Twenty-nine STs were unique (i.e. displayed by only one strain). The number of single nucleotide polymorphisms (SNPs) in allelic sequences ranged from 3 (gtf) to 15 (pf1637). Most of the SNPs were synonymous. The sequences seemed to evolve by interlocus recombination rather than by intralocus recombination. No bond between STs and the strains origins was detected. Thirty-seven STs were assembled in one clonal complex (CC1) with ST-31 as ancestral founder. CC1 represented the core of the population with 92% of the strains. This work results in the design of the first MLST scheme for a Propionibacterium species. It is useful to study P. freudenreichii molecular diversity. The MLST results will next be related to the ability of strains to produce flavour compounds