Genomic subpopulations within the species Pediococcus acidilactici detected by multilocus typing analysis: relationships between pediocin AcH/PA-1 producing and non-producing strains

A high degree of genetic polymorphism among P. acidilactici strains was hig hlighted by a multilocus typing approach analysing several housekeeping gen es and by sampling the whole genome using random amplified polymorphic DNA (RAPD) fingerprint analysis performed by using a single primer pedA gene ta rgeted in low-stringency amplification conditions. Restriction fragment len gth polymorphism of the rpoC, IdhD/L and mle genes, and a modified RAPD ana lysis, permitted the grouping of Pediococcus acidilactici strains in seven genotypes (I-VII). Genotypic results obtained by analysing housekeeping gen es involved in the transcription/translation machinery and in primary metab olism were supported by phylogenetic analysis based on the partial 16S rDNA sequencing of a reference strain of each of the seven clusters obtained. T hree of the seven genotypes detected showed relationships with pediocin AcH /PA-1 production and carbohydrate fermentation patterns: all pediocin-produ cing and sucrose-positive strains were grouped in genotype VII, melibiose-, sucrose- and raffinose-positive strains in genotype VI, and arabinose-posi tive strains in genotype V.