Comparative genomics of Lactobacillus sakei with emphasis on strains from meat

Abstract

Lactobacillus sakei is a lactic acid bacterium important in food microbiology mainly due to its ability to ferment and preserve meat. The genome sequence of L. sakei strain 23K has revealed specialized metabolic capacities that reflect the bacterium's adaption to meat products, and that differentiate it from other LAB. An extensive genomic diversity analysis was conducted to elucidate the core features of the species, and to provide a better comprehension of niche adaptation of the organism. Here, we describe the genomic comparison of 18 strains of L. sakei originating mainly from processed meat against the 23K strain by comparative genome hybridization. Pulsed field gel electrophoresis was used to estimate the genome sizes of the strains, which varied from 1.880 to 2.175 Mb, and the 23K genome was among the smallest. Consequently, a large part of the genome of this strain belongs to a common gene pool invariant in this species. The majority of genes important in adaption to meat products, the ability to flexibly use meat components, and robustness during meat processing and storage were conserved, such as genes involved in nucleoside scavenging, catabolism of arginine, and the ability to cope with changing redox and oxygen levels, which is indicative of the role these genes play in niche specialization within the L. sakei species. Moreover, an additional set of sequenced L. sakei genes beyond the 23K genome was present on the microarray used, and it was demonstrated that all the strains carry remnants of or complete bacteriocin operons. The genomic divergence corresponded mainly to five regions in the 23K genome, which showed features consistent with horizontal gene transfer. Carbohydrate-fermentation profiles of the strains were evaluated in light of the CGH data, and for most substrates, the genotypes were consistent with the phenotypes. We have demonstrated a highly conserved organization of the L. sakei genomes investigated, and the 23K strain is a suitable model organism to study core features of the L. sakei species.

Expression of the Arginine Deiminase Pathway Genes in Lactobacillus sakei Is Strain Dependent and Is Affected by the Environmental pH

“…For example, the conversion of arginine, an alternative energy source abundantly present in meat due to endogenous protease activity, through the ADI pathway renders this species with an improved survival in the stationary growth phase (4,5,31,43). Arginine conversion is a common metabolic trait for the species L. sakei and is encoded by the arc operon (24,41,42). In L. sakei CTC 494, the arc operon (arcABCTDR) shows the same gene order and organization as that of L. sakei 23K (42).…”

“…Fresh meat contains a relatively restricted amount and diversity of carbohydrates, consisting mostly of glucose at levels of between 0.2% and 1.0% (16,20). To effectively cope with this environment, a flexible use of all available energy sources and nutrients present in meat is of importance (20,24). In this sense, an efficient catabolism of nucleosides by L. sakei provides this species with an additional energy source (31).…”

“…Moreover, genome analysis of L. sakei 23K has shown that this strain harbors a putative second arc operon (2,24), suggesting that L. sakei heavily relies on the ADI pathway for competitiveness and survival in a meat environment. Initial annotation of this putative second arc operon predicted two putative peptidyl arginine deiminases (releasing peptide-bound arginine), a putative catabolic ornithine carbamoyltransferase, a putative carbamate kinase, and two putative transport proteins (2).…”

Health and Safety Considerations of Fermented Sausages

“…The second-generation LAB starter cultures, now widely used, are often based on these [69]. Molecular characterization by, for example, genome sequencing and comparative genomics has shown that strains of L. sakei isolated from meat and meat fermentation have evolved to be perfectly adapted to this particular environment [70][71][72]. L. plantarum lacks this specific adaptation but is a fast-growing, highly flexible bacterium with the largest genome size of the lactobacilli.…”

Identification of lactose phosphotransferase systems in Lactobacillus gasseri ATCC 33323 required for lactose utilization

“…The only lactobacillus with a characterized lactose PTS is Lactobacillus zeae (Alpert & Chassy, 1990;Chassy et al, 1976;Chassy & Thompson, 1983;Gosalbes et al, 1999). However, lactose-specific PTS genes have recently been indentified using bioinformatics in Lactobacillus sakei (Nyquist et al, 2011) and Lactobacillus iners (Macklaim et al, 2011), suggesting that lactose-specific PTSs are not rare amongst lactobacilli.…”