Identification and Characterization of Novel Faecalibacterium prausnitzii Strains with Potential Pharmabiotic Applications

Abstract

Faecalibacterium prausnitzii is a dominant commensal bacterium in the human gut, widely known for its anti-inflammatory and immunomodulatory properties and currently considered a potential pharmabiotic for the treatment of various human diseases. In this study, ten new strains of F. prausnitzii were isolated from stool samples of Russian children and characterized using hybrid genome sequencing and metabolomic analyses. Comparative genomics revealed an open pangenome structure and significant strain-specific variability, reflecting the high adaptive potential of strains in humans and confirming the heterogeneity of this species previously described in the literature. Several isolates (fp1, fp5, fp7, fp9) showed increased butyrate production, while fp1 showed increased formate synthesis. In silico analysis confirmed the presence of genes associated with anti-inflammatory, antioxidant, and neuromodulatory metabolites, as well as the absence of antibiotic resistance genes. These results expand on previously described findings on the genetic diversity of F. prausnitzii and identify promising, safe strains with high pharmabiotics potential for future human therapy.