Intraspecies genomic diversity and natural population structure of the meat-borne lactic acid bacterium Lactobacillus sakei

Stephane Chaillou (1) , Marie Daty (1) , Fabienne F. Baraige (1) , Anne Marie Dudez (2, 3) , Patricia Anglade (1) , Rhys Jones (1, 4) , Carl-Alfred Alpert (5, 6) , Marie-Christine Champomier-Verges (1) , Monique Zagorec (1)

1 UFLEC - Unité de recherche Flore Lactique et Environnement Carné
2 UR 0309 Unité Flore Lactique et Environnement Carné (FLEC)
3 Unité mixte de recherche interactions plantes-microorganismes
4 AgResearch Ltd
5 UR 309 Unité Flore Lactique et Environnement Carné (FLEC)
6 German Institute of Human Nutrition

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.

Mots clés: primers; pcr; emended descriptions; dry fermented sausages; curvatus subsp melibiosus; abo-elnaga; dna; identification; pediococcus; products; expression

Domaines: Sciences du Vivant [q-bio]

Stephane Chaillou, Marie Daty, Fabienne F. Baraige, Anne Marie Dudez, Patricia Anglade, et al.. Intraspecies genomic diversity and natural population structure of the meat-borne lactic acid bacterium Lactobacillus sakei. Applied and Environmental Microbiology, 2009, 75 (4), pp.970-980. ⟨10.1128/AEM.01721-08⟩. ⟨hal-01190024⟩