Comparative genomic analysis of the multispecies probiotic-marketed product VSL#3

Abstract

Several probiotic-marketed formulations available for the consumers contain live lactic acid bacteria and/or bifidobacteria. The multispecies product commercialized as VSL#3 has been used for treating various gastro-intestinal disorders. However, like many other products, the bacterial strains present in VSL#3 have only been characterized to a limited extent and their efficacy as well as their predicted mode of action remain unclear, preventing further applications or comparative studies. In this work, the genomes of all eight bacterial strains present in VSL#3 were sequenced and characterized, to advance insights into the possible mode of action of this product and also to serve as a basis for future work and trials. Phylogenetic and genomic data analysis allowed us to identify the 7 species present in the VSL#3 product as specified by the manufacturer. The 8 strains present belong to the species Streptococcus thermophilus, Lactobacillus acidophilus, Lactobacillus paracasei, Lactobacillus plantarum, Lactobacillus helveticus, Bifidobacterium breve and B. animalis subsp. lactis (two distinct strains). Comparative genomics revealed that the draft genomes of the S. thermophilus and L. helveticus strains were predicted to encode most of the defence systems such as restriction modification and CRISPR-Cas systems. Genes associated with a variety of potential probiotic functions were also identified. Thus, in the three Bifidobacterium spp., gene clusters were predicted to encode tight adherence pili, known to promote bacteria-host interaction and intestinal barrier integrity, and to impact host cell development. Various repertoires of putative signalling proteins were predicted to be encoded by the genomes of the Lactobacillus spp., i.e. surface layer proteins, LPXTG-containing proteins, or sortase-dependent pili that may interact with the intestinal mucosa and dendritic cells. Taken altogether, the individual genomic characterization of the strains present in the VSL#3 product confirmed the product specifications, determined its coding capacity as well as identified potential probiotic functions.

Fig 1. Phylogenetic position of the strains from the VSL#3 product.

This phylogenetic tree was generated based on the genome-predicted core proteome shared between the strains from the VSL#3 product and that of a set of relevant reference and representative strains. The position of the eight strains used for the formulation of the VSL#3 product are shaded in blue.

Fig 2. Defense systems of the multi-species probiotic product VSL#3.

Number of predicted restriction/modification enzymes (blue) and CRISPR-Cas spacers (green). Strains devoid of CRISPR-Cas loci have a number of spacers equal to zero.

Fig 3. CRISPR-Cas loci identified in the strains of the VSL#3 product.

The CRISPR-Cas loci were identified using CRISPRFinder [56] and their gene order and predicted annotations are depicted along with their juxtaposing array of spacers. Legend: *, split gene.

Fig 4. Pilus gene clusters identified in the multispecies product VSL#3.

Both Tad pilus and sortase-dependent pilus gene clusters are shown along with a corresponding pilus gene cluster previously characterized [17]. The percentage indicates the degree of amino acid sequence conservation between the different genes.