DNA was isolated from 30 samples of breast milk and infant feces, and sequencing of the V1-V3 region of the 16S rRNA gene was performed. By taxonomic analysis of the obtained sequences, a correlation in the composition of the microbiome of breast milk and infant feaces was found. 28 genetically distinct strains were selected by hierarchical cluster analysis of RAPD-PCR electrophoresis profiles of 100 strains isolated from breast milk. The SDS-PAGE analysis revealed for the first time the presence of S-proteins in 4 strains isolated from breast milk, and PCR analysis confirmed the presence of 3 genes (plnJ, plnA and plnEF) involved in bacteriocin biosynthesis in 6 Lactobacillus plantarum strains. Lb. brevis SF9B and Lb. plantarum SF9C, probiotic strains producing potential therapeutic biomolecules isolated from sauerkraut brine, were also characterized in detail. WGS analysis of the SF9B strain revealed 3 genes (slpB, slpC and slpD) encoding S-proteins. LC-MS analysis of the protein bands obtained by SDS-PAGE and 2D-EF revealed the expression of only one, the slpB gene. Prediction of the secondary structure of the S-protein was performed using the PSIPRED method, and that of the tertiary structure using the I-TASSER server. It was confirmed that the strain SF9C contains 9 bacteriocin-encoding genes. The SWISS-MODEL server was used to predict the tertiary structure of PlnJK and PlnEF plantaricins, whereas physicochemical properties of their α-helices were determined using the HeliQuest server. DGGE analyses and faecal microbiome analyses confirmed the in vivo impact of SF9B and SF9C co-culture application on the faecal microbiome composition of 18 rats.