Comparative genomic and functional analysis of 100 Lactobacillus rhamnosus strains and their comparison with strain GG

PLoS Genet. 2013;9(8):e1003683. doi: 10.1371/journal.pgen.1003683. Epub 2013 Aug 15.


Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanal and industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity and ecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strains isolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG reference genome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling and functional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated with their ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydrate transport and metabolism, production of mucus-binding pili, bile salt resistance, prophages and CRISPR adaptive immunity. Integration of the phenotypic and genomic data revealed that some L. rhamnosus strains possibly resided in multiple niches, illustrating the dynamics of bacterial habitats. The present study showed two distinctive geno-phenotypes in the L. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivative products, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stress resistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequate traits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density and host effects.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Genetic Association Studies
  • Genome, Bacterial*
  • Genomics
  • Lacticaseibacillus rhamnosus / classification
  • Lacticaseibacillus rhamnosus / genetics*
  • Milk / microbiology
  • Phenotype
  • Phylogeny*
  • Population Density

Grants and funding

This study was supported by the grant ERC 250172 - Microbes Inside from the European Research Council, the Center of Excellence in Microbial Food Safety Research (CoE-MiFoSa), Academy of Finland (grant 141140) and the University of Helsinki. FPD was also financially supported by a postdoctoral research fellowship from the Academy of Finland (grant 252123). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.