title: High-resolution amplified fragment length polymorphism typing of Lactococcus lactis strains enables identification of genetic markers for subspecies-related phenotypes.
abstract: A high-resolution amplified fragment length polymorphism (AFLP) methodology was developed to achieve the delineation of closely related Lactococcus lactis strains. The differentiation depth of 24 enzyme-primer-nucleotide combinations was experimentally evaluated to maximize the number of polymorphisms. The resolution depth was confirmed by performing diversity analysis on 82 L. lactis strains, including both closely and distantly related strains with dairy and nondairy origins. Strains clustered into two main genomic lineages of L. lactis subsp. lactis and L. lactis subsp. cremoris type-strain-like genotypes and a third novel genomic lineage rooted from the L. lactis subsp. lactis genomic lineage. Cluster differentiation was highly correlated with small-subunit rRNA homology and multilocus sequence analysis (MLSA) studies. Additionally, the selected enzyme-primer combination generated L. lactis subsp. cremoris phenotype-specific fragments irrespective of the genotype. These phenotype-specific markers allowed the differentiation of L. lactis subsp. lactis phenotype from L. lactis subsp. cremoris phenotype strains within the same L. lactis subsp. cremoris type-strain-like genomic lineage, illustrating the potential of AFLP for the generation of phenotype-linked genetic markers.
authors.affiliation: NIZO food research, P.O. Box 20, 6710 BA Ede, The Netherlands.
authors.forename: Oylum Erkus
authors.initials: OE
authors.lastname: Kütahya
authors.forename: Marjo J C
authors.initials: MJ
authors.lastname: Starrenburg
authors.forename: Jan L W
authors.initials: JL
authors.lastname: Rademaker
authors.forename: Corné H W
authors.initials: CH
authors.lastname: Klaassen
authors.forename: Johan E T
authors.initials: JE
authors.lastname: van Hylckama Vlieg
authors.forename: Eddy J
authors.initials: EJ
authors.lastname: Smid
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
mesh_terms: D054458:Amplified Fragment Length Polymorphism Analysis / Q000379:methods*; D004269:DNA, Bacterial / Q000235:genetics; D005819:Genetic Markers; D014644:Genetic Variation; D005838:Genotype; D013294:Lactococcus lactis / Q000145:classification* / Q000235:genetics*; D058885:Multilocus Sequence Typing; D010641:Phenotype
chemical_list: D004269:DNA, Bacterial; D005819:Genetic Markers