title: Intraspecies genomic diversity and natural population structure of the meat-borne lactic acid bacterium Lactobacillus sakei.
abstract: Lactobacillus sakei is a food-borne bacterium naturally found in meat and fish products. A study was performed to examine the intraspecies diversity among 73 isolates sourced from laboratory collections in several different countries. Pulsed-field gel electrophoresis analysis demonstrated a 25% variation in genome size between isolates, ranging from 1,815 kb to 2,310 kb. The relatedness between isolates was then determined using a PCR-based method that detects the possession of 60 chromosomal genes belonging to the flexible gene pool. Ten different strain clusters were identified that had noticeable differences in their average genome size reflecting the natural population structure. The results show that many different genotypes may be isolated from similar types of meat products, suggesting a complex ecological habitat in which intraspecies diversity may be required for successful adaptation. Finally, proteomic analysis revealed a slight difference between the migration patterns of highly abundant GapA isoforms of the two prevailing L. sakei subspecies (sakei and carnosus). This analysis was used to affiliate the genotypic clusters with the corresponding subspecies. These findings reveal for the first time the extent of intraspecies genomic diversity in L. sakei. Consequently, identification of molecular subtypes may in the future prove valuable for a better understanding of microbial ecosystems in food products.
authors.affiliation: UR309, Unité Flore Lactique & Environnement Carné (FLEC), Institut National de la Recherche Agronomique (INRA), Domaine de Vilvert, 78350 Jouy-en-Josas, France. Stephane.Chaillou@jouy.inra.fr
authors.forename: Stéphane
authors.initials: S
authors.lastname: Chaillou
authors.forename: Marie
authors.initials: M
authors.lastname: Daty
authors.forename: Fabienne
authors.initials: F
authors.lastname: Baraige
authors.forename: Anne-Marie
authors.initials: AM
authors.lastname: Dudez
authors.forename: Patricia
authors.initials: P
authors.lastname: Anglade
authors.forename: Rhys
authors.initials: R
authors.lastname: Jones
authors.forename: Carl-Alfred
authors.initials: CA
authors.lastname: Alpert
authors.forename: Marie-Christine
authors.initials: MC
authors.lastname: Champomier-Vergès
authors.forename: Monique
authors.initials: M
authors.lastname: Zagorec
mesh_terms: D001426:Bacterial Proteins / Q000032:analysis; D016000:Cluster Analysis; D016172:DNA Fingerprinting; D004269:DNA, Bacterial / Q000737:chemistry / Q000235:genetics*; D016521:Electrophoresis, Gel, Pulsed-Field; D005396:Fish Products / Q000382:microbiology*; D005838:Genotype; D007778:Lactobacillus / Q000737:chemistry / Q000145:classification* / Q000235:genetics* / Q000302:isolation & purification; D008461:Meat Products / Q000382:microbiology*; D008969:Molecular Sequence Data; D010802:Phylogeny; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D020543:Proteome; D017422:Sequence Analysis, DNA
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D020543:Proteome