Rationale of the selection of lactobacilli strains for the development of a probiotic microbial consortium based on their biological safety

Background. Lactobacilli, being representatives of the normobiota, are of great interest as the most important and promising biotechnological targets for the development of probiotics and functional nutrition. The key criterion for strain selection is proven safety, specifically the absence of virulence and antimicrobial resistance (AMR) genes. An important aspect of the biosafety of lactobacilli is the absence of plasmids in the genome.

Aim. To evaluate the safety of lactobacilli strains based on their phenotypic susceptibility to antimicrobials (AMs) and whole-genome analysis for the evidence-based selection of candidate strains for probiotic consortia.

Materials and methods. The study included 34 strains of lactobacilli isolated from the intestinal biotope of healthy and apparently healthy children and adolescents in the Irkutsk region. The strains were identified using MALDI-TOF mass spectrometry and whole-genome sequencing. Susceptibility to AMs was determined using the disk diffusion method. The genomes of lactobacillus strains were screened for the presence of AMR, virulence, and plasmid sequences.

Results. A phenotypic analysis of the susceptibility of lactobacilli strains to AMs revealed both collection-wide characteristics and species-specific features, mainly in relation to oxacillin and penicillin G. The genes for AMR and virulence were absent in the genomes of all analyzed lactobacillus strains. Plasmids were found in the genomes of 26 of the 34 strains. In terms of horizontal transfer, 37 plasmids were non-mobilizable, 22 were mobilizable, and 1 was conjugative. Strains with mobile and conjugative plasmids were excluded from the list of candidate strains for probiotic consortia.

Conclusion. The proposed algorithm for selecting lactobacilli strains, including the assessment of phenotypic susceptibility to AMs, genome screening for the presence of AMR and virulence genes, and mobile plasmid elements, enables the selection of safe strains for the further development of probiotic consortia.

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