Identification and characterization of novel Faecalibacterium prausnitzii strains from infant gut microbiota with potential pharmabiotic applications

Faecalibacterium prausnitzii is a dominant commensal bacterium in the human gut, widely known for its production of bioactive metabolites and currently considered a potential pharmabiotic for the treatment of various human diseases. In this study, ten novel strains of Faecalibacterium prausnitzii were isolated from stool samples of Russian infants and characterized using whole genome sequencing and metabolomic analyses. Comparative genomic analysis revealed an open pangenome structure and significant strain-specific variability, reflecting the strains’ high adaptive potential within the human host and confirming the heterogeneity of this species. Four isolates (MSK-01, MSK-05, MSK-07, MSK-09) exhibited elevated butyrate production, and MSK-01 additionally displayed enhanced formate synthesis. The previously developed catalog of genes with anti-inflammatory, immune, and neuromodulatory activity was used for in silico analysis and targeted annotation of sequenced genomes. In silico analysis confirmed the presence of genes associated with anti-inflammatory, antioxidant, and neuromodulatory metabolites. Strains MSK-07 and MSK-09 were selected as the top candidates for development as infant pharmabiotics. These results expand on previously described findings on the genetic diversity of Faecalibacterium prausnitzii and identify promising strains with high pharmabiotic potential for future human therapy. These findings allow us to proceed to the next stages of selection and development of pharmabiotics for microbiome correction.