title: The Variable Regions of Lactobacillus rhamnosus Genomes 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.
authors.affiliation: Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands corinaceapa@uchicago.edu.
authors.forename: Corina
authors.initials: C
authors.lastname: Ceapa
authors.affiliation: Laboratory of Systems and Synthetic Biology, Wageningen University, the Netherlands.
authors.forename: Mark
authors.initials: M
authors.lastname: Davids
authors.affiliation: RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland.
authors.forename: Jarmo
authors.initials: J
authors.lastname: Ritari
authors.affiliation: Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands.
authors.forename: Jolanda
authors.initials: J
authors.lastname: Lambert
authors.affiliation: NIZO Food Research, Ede, the Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Wels
authors.affiliation: Department of Veterinary Biosciences, University of Helsinki, Finland.
authors.forename: François P
authors.initials: FP
authors.lastname: Douillard
authors.affiliation: Danone Research, Palaiseau, France.
authors.forename: Tamara
authors.initials: T
authors.lastname: Smokvina
authors.affiliation: Laboratory of Microbiology, Wageningen University, the Netherlands RPU Immunobiology, Department of Bacteriology and Immunology, University of Helsinki, Finland Department of Veterinary Biosciences, University of Helsinki, Finland.
authors.forename: Willem M
authors.initials: WM
authors.lastname: de Vos
authors.affiliation: Gut Biology & Microbiology Platform, Nutricia Research Centre, Utrecht, the Netherlands Laboratory of Microbiology, Wageningen University, the Netherlands.
authors.forename: Jan
authors.initials: J
authors.lastname: Knol
authors.affiliation: Host-Microbe Interactomics Group, Department of Animal Sciences, Wageningen University and Research Centre, Wageningen, the Netherlands.
authors.forename: Michiel
authors.initials: M
authors.lastname: Kleerebezem
mesh_terms: D064113:CRISPR-Cas Systems; D050260:Carbohydrate Metabolism / Q000235:genetics*; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing; D052201:Lacticaseibacillus rhamnosus / Q000235:genetics*; D058977:Molecular Sequence Annotation; D010802:Phylogeny
keywords: comparative genomics; core and pan-genome; diversity; niche adaptation; probiotic