Globalizing the health-promoting potential of fermented foods: A culturomics pathway to probiotics

Background: Amplicon and metagenomic studies have consistently shown that naturally fermented foods (FFs) are rich reservoirs of diverse autochthonous microorganisms with significant potential to promote human health. To harness these benefits, it is essential to preserve the complete array of live microbial communities in their most original and unmodified state. Scope and approach: This review begins by exploring the microbial diversity and health-promoting properties of spontaneously FFs. It then provides a comprehensive overview of current probiotic isolation techniques and highlights the potential of culturomics-based strategies for recovering a broader range of microbial taxa from this source. Finally, it discusses the associated health risks and importance of omics-based technologies in enabling detailed characterization of microbial isolates. Key findings and conclusions: Although various strains of lactic acid bacteria, acetic acid bacteria, and yeasts have been isolated from FFs, much of the microbial diversity in these foods still remains unexplored. Most commercial probiotics derived from FFs continue to focus on a narrow range of taxa, primarily due to the widespread reliance on classical culturing methods. However, emerging studies that have adopted culturomics in the context of FFs demonstrate a substantial improvement in the recovery of diverse microbial strains. While this approach holds great promise, its application must be undertaken with caution, particularly regarding the safety of newly isolated strains and their potential to harbor or transmit antibiotic resistance genes. Moreover, although omics-based strain profiling is gaining momentum, the majority of probiotic evaluations in the reviewed literature remain restricted to in vitro non-molecular analyses.