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

Abstract

Amplicon and metagenomic studies have consistently shown that traditional fermented foods (TFFs) 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. This review begins by exploring the microbial diversity and health-promoting properties of TFFs. 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. Although various strains of lactic acid bacteria, acetic acid bacteria, and yeasts have been isolated from TFFs, much of the microbial diversity in these foods still remains unexplored. Most commercial probiotics derived from TFFs 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 TFFs 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. • Traditional fermented foods (TFFs) hold significant potential as probiotic sources. • Probiotic isolation from TFFs is focused primarily on lactic acid bacteria. • Classical isolation methods dominate current isolation practices from TFFs. • Culturomics techniques offer a promising approach to preserve microbial diversity in TFFs.