Microbial Bioactives
Microbial Bioactives | Online ISSN 2209-2161
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Volume 8 Number 1 2025
REVIEWS (Open Access)
Unlocking the Hidden Microbial World in Traditional Chinese Fermented Foods: From Microbial Dark Matter to Functional Exploration
Ravi Goyal 1*, Rajni Bala 1, Reecha Madaan 1
Microbial Bioactives 8 (1) 1-8 https://doi.org/10.25163/microbbioacts.8110656
Submitted: 20 November 2024 Revised: 18 January 2025 Accepted: 26 January 2025 Published: 28 January 2025
Abstract
Traditional Chinese fermented foods (TCFF) harbor extraordinarily diverse microbial communities that underpin their flavor, nutritional value, and safety. Despite decades of research, the majority of microorganisms in these systems remain uncultured, representing a vast microbial dark matter with untapped biotechnological potential. This review systematically examines advances in the identification, characterization, and functional exploration of uncultured microbes in TCFF. By integrating metagenomic sequencing, culturomics, in situ cultivation techniques, and computational tools, researchers have begun to reveal the roles of previously hidden bacteria and archaea in fermentation processes. Notably, uncultured species contribute to the production of key metabolites, including alcohols, esters, acids, and pigments, which shape the sensory qualities of fermented foods. Novel strategies such as resuscitation-promoting factors, microencapsulation, and the iChip device have improved cultivation success rates, facilitating natural product discovery and functional analysis. Furthermore, functional genomics and bioinformatics approaches have provided insights into microbial interactions, gene cluster potentials, and biosynthetic capabilities, highlighting applications in food quality enhancement, environmental bioremediation, and therapeutic discovery. Despite these advances, challenges persist in cultivating slow-growing or symbiotic microbes and in linking genomic potential to in situ functionality. The convergence of traditional knowledge, advanced microbiology, and computational methodologies is transforming our understanding of TCFF microbiomes, bridging the gap between microbial dark matter and applied biotechnology. By systematically elucidating microbial diversity and function, this research not only enhances food science and industrial fermentation but also provides a foundation for exploring novel bioactive compounds from previously inaccessible microbial taxa.
Keywords: Traditional Chinese fermented foods, uncultured microbes, microbial dark matter, metagenomics, culturomics, in situ cultivation, functional metabolites
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