Comparative Genomic and Functional Analysis of 100 Lactobacillus rhamnosus Strains and Their Comparison with Strain GG

Lactobacillus rhamnosus is a lactic acid bacterium that is found in a large variety of ecological habitats, including artisanaland industrial dairy products, the oral cavity, intestinal tract or vagina. To gain insights into the genetic complexity andecological versatility of the species L. rhamnosus, we examined the genomes and phenotypes of 100 L. rhamnosus strainsisolated from diverse sources. The genomes of 100 L. rhamnosus strains were mapped onto the L. rhamnosus GG referencegenome. These strains were phenotypically characterized for a wide range of metabolic, antagonistic, signalling andfunctional properties. Phylogenomic analysis showed multiple groupings of the species that could partly be associated withtheir ecological niches. We identified 17 highly variable regions that encode functions related to lifestyle, i.e. carbohydratetransport 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 theL. rhamnosus species. The geno-phenotype A suggests an adaptation to stable nutrient-rich niches, i.e. milk-derivativeproducts, reflected by the alteration or loss of biological functions associated with antimicrobial activity spectrum, stressresistance, adaptability and fitness to a distinctive range of habitats. In contrast, the geno-phenotype B displays adequatetraits to a variable environment, such as the intestinal tract, in terms of nutrient resources, bacterial population density andhost effects.