Population Genetics of Lactobacillus sakei Reveals Three Lineages with Distinct Evolutionary Histories

Abstract

Lactobacillus sakei plays a major role in meat fermentation and in the preservation of fresh meat. The large diversity of L. sakei strains represents a valuable and exploitable asset in the development of a variety of industrial applications; however, an efficient method to identify and classify these strains has yet to be developed. In this study, we used multilocus sequence typing (MLST) to analyze the polymorphism and allelic distribution of eight loci within an L. sakei population of 232 strains collected worldwide. Within this population, we identified 116 unique sequence types with an average pairwise nucleotide diversity per site (π) of 0.13%. Results from Structure, goeBurst, and ClonalFrame software analyses demonstrated that the L. sakei population analyzed here is derived from three ancestral lineages, each of which shows evidence of a unique evolutionary history influenced by independent selection scenarios. However, the signature of selective events in the contemporary population of isolates was somewhat masked by the pervasive phenomenon of homologous recombination. Our results demonstrate that lineage 1 is a completely panmictic subpopulation in which alleles have been continually redistributed through the process of intra-lineage recombination. In contrast, lineage 2 was characterized by a high degree of clonality. Lineage 3, the earliest-diverging branch in the genealogy, showed evidence of both clonality and recombination. These evolutionary histories strongly indicate that the three lineages may correspond to distinct ecotypes, likely linked or specialized to different environmental reservoirs. The MLST scheme developed in this study represents an easy and straightforward tool that can be used to further analyze the population dynamics of L. sakei strains in food products.

Multilocus Sequence Typing of Leuconostoc gelidum subsp. gasicomitatum, a Psychrotrophic Lactic Acid Bacterium Causing Spoilage of Packaged Perishable Foods

“…A similar population structure was found for the wine-associated species Oenococcus oeni (31). Conversely, recombination both within and between subpopulations was common for Lactobacillus sakei (30).…”

“…Previous studies on the population genetics of food-associated bacterial species have shown that division into subpopulations reflects adaptations to different niches rather than geographical isolation (30,31). The strains in this study were from food products manufactured at 22 production plants located across Finland.…”

Sourdough microbial community dynamics: An analysis during French organic bread-making processes

“…Hence, the genome of L. sanfranciscensis enables it to grow easily in this environment and contributes to its ability to out-compete other bacteria in traditional sourdough (Vogel et al, 2011). Unlike L. sanfranciscensis, the other LAB species detected in this study, L pentosus, L. sakei, L. plantarum and L. kimchii, have already been detected in sourdough and are also frequently isolated from other habitats (Botta and Cocolin, 2012;Chaillou et al, 2013;Corsetti and Gobbetti, 2002;Yoon et al, 2000).…”

High Genetic Diversity among Strains of the Unindustrialized Lactic Acid Bacterium Carnobacterium maltaromaticum in Dairy Products as Revealed by Multilocus Sequence Typing

“…The dissociation index was calculated with Start2 (32). Recombination analysis and phylogenetic tree inference under the neutral coalescent model were performed with ClonalFrame as previously described (37).…”