The Variable Regions ofLactobacillus rhamnosusGenomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires

Abstract

Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence–absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains’ core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.

Genomic and Proteomic Characterization of Bacteriophage BH1 Spontaneously Released from Probiotic Lactobacillus rhamnosus Pen

“…A lower level of homology was revealed with two L. rhamnosus phages-Lrm1 (NC_011104.1, identity 94%, query coverage 59%) and Lc-Nu (NC_007501.1, identity 91%, query coverage 28%) ( Figure 4) and other bacteriophages and prophages described for the L. casei group (Dataset S1, S3, S4). These findings, in conjunction with other reports, suggest a high diversity of L. rhamnosus phage genomic sequences, highlighting that sequences of a bacteriophage origin may be a very interesting source of information regarding bacteria phylogenetics [9,25]. Moreover, our results also confirm earlier works by Brandt and Allatosava [26] and Zago et al [27], demonstrating that phage sequences have a high potential for the identification of bacteria of the genus Lactobacillus, even at the strain level.…”

“…However, it remains important to conduct further studies on the safety of using bacteria as dietary supplements, as there are also reports of negative features of some microorganisms considered to be probiotics [6,7]. Additionally, prophage sequences are widespread in genomes of Lactobacillus bacteria [8,9]. In general, the presence of sequences encoding bacteriophage proteins in the genome was considered a negative phenomenon.…”

Comparative analysis of Lactobacillus gasseri from Chinese subjects reveals a new species-level taxa

“…Additionally, the G + C contents in L. paragasseri (34.9%) and L. gasseri (34.82%) were lower than that in other Lactobacillus species. For instance, average G + C contents were 38.96% in L. reuteri [19], 46.1-46.6% in L. casei, 46.5% in L. paracasei [20], and 46.5-46.8% in L. rhamnosus [33], and the average G + C content among lactobacilli genera is estimated at 42.4%. As previously found in bifidobacterial genomes, that the preferred start codon was ATG, also analysis of start codons in L. paragasseri and L. gasseri showed that they preferably used ATG as start codon [34].…”

Biotechnology of health-promoting bacteria

“…This provided insights into the phylogenetic diversity of LAB and bifidobacteria. For example, Lactobacillus rhamnosus, Lactobacillus salivarius or Lactobacillus sakei were found to have a high intra-species diversity (Ceapa et al, 2016;Chaillou et al, 2013;Douillard et al, 2013;Harris et al, 2017), underlying that functional properties towards the host are very much strain-dependent.…”