Comparative genomic and functional analysis of Lactobacillus casei and Lactobacillus rhamnosus strains marketed as probiotics

Four Lactobacillus strains were isolated from marketed probiotic products, including L. rhamnosus strains from Vifit (Friesland Campina) and Idoform (Ferrosan), and L.casei strains from Actimel (Danone) and Yakult (Yakult Honsa Co.), respectively. Their genomes and phenotypes were characterized and compared in detail with L. casei strain BL23 and L. rhamnosus strain GG. Phenotypic analysis of the new isolates indicated differences in carbohydrate utilization between L. casei and L. rhamnosus strains, which could be linked to their genotypes. The two isolated L. rhamnosus strains had virtually identical genomes to L. rhamnosus GG, testifying for their genomic stability and integrity in food products. The L. casei strains showed much greater genomic heterogeneity. Remarkably, all strains contained an intact spaCBA pili gene cluster. However, only the L. rhamnosus strains produced mucus-binding SpaCBA pili under the conditions tested. Transcription initiation mapping demonstrated the insertion of an iso-IS30 element upstream of the pili gene cluster in L. rhamnosus strains but absent in L. casei strains had constituted a functional promoter driving the pili gene expression. All L. rhamnosus strains triggered an NF-κB response via the TLR-2 receptor in a reporter cell line, whereas the L. casei strains did not or to a much smaller extent. This study demonstrates that the two L. rhamnosus strains isolated from probiotic products are virtually identical to L. rhamnosus GG and further highlights the differences between these and L. casei strains widely-marketed as probiotics, in terms of genome-content, mucus-binding and metabolic capacity, and host signalling capabilities.