Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches

Abstract

Lactobacillus plantarum is a ubiquitous microorganism that is able to colonize several ecological niches, including vegetables, meat, dairy substrates and the gastro-intestinal tract. An extensive phenotypic and genomic diversity analysis was conducted to elucidate the molecular basis of the high flexibility and versatility of this species. First, 185 isolates from diverse environments were phenotypically characterized by evaluating their fermentation and growth characteristics. Strains clustered largely together within their particular food niche, but human fecal isolates were scattered throughout the food clusters, suggesting that they originate from the food eaten by the individuals. Based on distinct phenotypic profiles, 24 strains were selected and, together with a further 18 strains from an earlier low-resolution study, their genomic diversity was evaluated by comparative genome hybridization against the reference genome of L. plantarum WCFS1. Over 2000 genes were identified that constitute the core genome of the L. plantarum species, including 121 unique L. plantarum-marker genes that have not been found in other lactic acid bacteria. Over 50 genes unique for the reference strain WCFS1 were identified that were absent in the other L. plantarum strains. Strains of the L. plantarum subspecies argentoratensis were found to lack a common set of 24 genes, organized in seven gene clusters/operons, supporting their classification as a separate subspecies. The results provide a detailed view on phenotypic and genomic diversity of L. plantarum and lead to a better comprehension of niche adaptation and functionality of the organism.

GtfA and GtfB Are Both Required for Protein O -Glycosylation in Lactobacillus plantarum

“…argentoratensis, for analysis of whole-cell extracts by SDS-PAGE and GlcNAc-specific sWGA blotting. Notably, these 9 strains were selected to maximize the coverage of the phylogenetic tree based on the whole-genome comparative genome hybridization data sets (56), as well as to include strains isolated from diverse niches ( Table 1). All selected strains, including NCIMB12120, displayed sWGA-recognized glycosylated proteins that showed similar banding patterns on SDS-PAGE gels (Fig.…”

Impact of microbial variability on food safety and quality

“…The strain variability observed in L. plantarum might be related to the high genetic diversity reported for this species (Sanders et al, 2015;Siezen et al, 2010;Siezen and van Hylckama Vlieg, 2011), which corresponded to the observed phenotypic diversity, including the strain diversity in stress tolerance. A clear example for the observed strain variability in growth kinetics is given for strain FBR26.…”

“…Moreover, the strain variability is obtained by taking measurement using different strains from the same species or more widely known as between strain variability. Although belonging to one species, each strain might show different genotypic and phenotypic characteristics (De Jesús and Whiting, 2003;Donaldson et al, 2009;Nelson et al, 2004;Sanders et al, 2015;Siezen et al, 2010;Siezen and van Hylckama Vlieg, 2011;Whiting and Golden, 2002). Since one species consists of a wide range of strains, one might expect that strain variability is higher than reproduction variability and experimental error.…”

“…To extend the knowledge of variability in growth and thermal resistance of spoilage microorganisms, Lactobacillus plantarum was chosen as a model species. Although high diversity in genomic and phenotypic levels of L. plantarum have been reported (Sanders et al, 2015;Siezen et al, 2010;Siezen and van Hylckama Vlieg, 2011), none of the studies focused on quantification of strain variability in growth and thermal resistance. Therefore, the objectives of the present study were to quantify strain variability, reproduction (biological) variability and experimental variability with respect to growth and thermal inactivation kinetics of L. plantarum and to quantify the variability in thermal resistance attributed to growth history.…”

“…Lactic acid bacteria are an important group of spoilage microorganisms and are abundant in the environment. They can be found in diverse niches (Siezen et al, 2010) and are commonly isolated from plant and plant material (Hammes and Vogel, 1995), soil (Chen et al, 2005), silage (Yang et al, 2010), meat (Hamasaki et al, 2003), vegetables (Tournas, 2005), and milk (Khedid et al, 2009). Since they are natural contaminants of raw food ingredients, controlling their presence and growth are critical steps to control shelf life of food products.…”