Genomic Diversity of Lactobacillus salivarius

Lactobacillus spp. are lactic acid bacteria (LAB) that display phylogenetic, phenotypic, and ecological heterogeneity that is reflected in their taxonomic diversity (13). Lactobacilli have complex nutritional requirements that are reflected in the diverse, carbon-rich habitats in which they are found (59). Lactobacilli have been studied extensively because of their importance for the production of fermented foods and beverages (59). Some well-characterized lactobacilli are generally regarded as safe (GRAS), and in more recent times, they have been used as probiotics and vaccine carriers (30). Administration of probiotic cultures benefits the host through a wide variety of mechanisms that are increasingly recognized as being species and strain specific (34). Knowledge of the genetic basis for strain diversity in potentially probiotic species is thus called for. Comparative genomics has emerged as a powerful approach in this era of high-throughput sequencing technologies, and it provides a technological platform to identify strain-specific traits (13). Lactobacillus salivarius (38) is part of the indigenous microbiota of the gastrointestinal tract (GIT) and oral cavity of humans and hamsters (49). The species has also been isolated from human breast milk (41) and from the intestinal tracts of swine (10) and chickens (1). There has been a recent increase in the number of studies in which the probiotic utility of diverse L. salivarius strains was explored (44). However, there is no detailed information on the genomic variability of the species to serve as a reference for identifying strain-specific properties. In this study, we examined the diversity of L. salivarius by applying multilocus sequence typing (MLST) and comparative genomic hybridization (CGH) to a collection of strains. They were derived from a range of ecological niches and were diverse in plasmid content and phenotypic traits (21, 37, 38). The panel included the strain UCC118, whose genome has been sequenced (12) and which has been extensively studied for its probiotic properties (44). MLST is a powerful sequence-based typing method that has been applied to more than 48 bacterial taxa (2). It utilizes the internal nucleotide sequences of multiple housekeeping genes to infer the genetic relatedness of bacterial strains and species. MLST has been applied to industrially relevant LAB strains (15) and to Lactobacillus species, including L. plantarum (16), L. casei (8, 18) and L. sanfranciscensis (46). CGH facilitates the comparison of unsequenced strains on a genome-wide level and can enable the correlation of phenotypic patterns within a species with the genomic content. Horizontal gene transfer (HGT) is often associated with niche adaptation and was detected by CGH studies of other Lactobacillus species, which have revealed strain-specific traits, including carbohydrate utilization and bacteriocin and exopolysaccharide (EPS) production (5, 43). One of the aims of the current study was therefore to investigate whether niche adaptation or probiotic potential was evident in the general L. salivarius population. EPS produced by LAB has been used in the dairy industry to improve the texture, viscosity, and rheological properties of fermented products (26). EPS is also credited with health-promoting properties, such as cholesterol lowering, immunomodulation, antitumorogenic effects, and prebiotic effects (26). Thus, L. salivarius strain clusters, defined by EPS gene content, were further analyzed for EPS production and surface properties.