Editorial: Diversity, Function, and Application of Microbes in Traditional Food Fermentation

Weiwei Dong¹Shenxi Chen^2*Yuanliang Hu^1*

• ¹Hubei Normal University, Huangshi, China
• ²Jinpai Company Ltd, Huangshi, China

Collectively, the diversity-focused cluster underscores the unique value of traditional fermentations as natural laboratories for microbial ecology. By resolving community structures and dynamics, these studies illuminate the ecological principles underlying fermentation quality and pinpoint key taxa and interactions suitable for targeted application. This thematic cluster centers on core microbes that carry out key biochemical functions and thereby shape flavor or health attributes, together with the biosynthesis of their metabolites. The first thread concerns microbial origins and mechanisms of aroma production and flavor precursors. Li et al. reported that a plant endophytic bacterium, Bacillus velezensis, can produce cyclic dipeptides at high levels. Upon thermal cracking, these compounds release key nutty, roasted, and fruity notes, and their application significantly enhances product flavor. Zhang et al. demonstrated that Lentilactobacillus diolivorans strain ZX6 generates abundant n-propanol in saucearoma Baijiu via the methylglyoxal pathway, that is, proceeding from pyruvate or lactate to 1,2-propanediol and then to propanol, catalyzed by aldehyde dehydrogenase.Quantitative PCR results showed its widespread presence in fermentation pits, identifying it as an important source of higher alcohols. This suggests that monitoring and regulating this bacterium could be leveraged to manage n-propanol levels and Taken together, the functional microbes cluster clearly showcases two parallel value chains. The first involves flavor enhancement driven by specialized metabolites and enzymatic activities. The second involves health promotion mediated by probiotic functions and targeted biotransformation. By establishing reproducible links between specific microbes and defined metabolites or physiological effects, these studies make a transition from descriptive ecology to functional food microbiology and provide industry with directly verifiable, scalable strain candidates and implementation roadmaps. Building on advances in understanding microbial diversity and function, several studies shift toward process innovation and application-focused development, with an emphasis on steering fermentation outcomes through synthetic or well-defined microbial consortia. Gao et al. engineering a synthetic microbial community, SMC-L1, for low-salt soy sauce. Traditionally, foy sauce required ~18% NaCl for microbial control, but by combining Tetragenococcus halophilus, a halophilic lactic acid bacterium, with compatible yeasts, and using multi-omics optimization, they achieved stable fermentation at just 13% salt. The resulting soy sauce contained ~40% more amino nitrogen than the control and exhibited richer flavor metabolites, including elevated succinate that was driven by a Tetragenococcus-mediated anaerobic TCA cycle and short-chain esters. This work effectively decoupled salinity from flavor quality and offered a promising route toward healthier condiments. Similarly, OuYang et al. assembled a defined consortium from metabolically complementary strains, which significantly increased acetoin content and improved overall functional quality in citrus vinegar. Through targeted metabolic optimization, the consortium outperformed traditional monoculture conditions, highlighting the potential of rationally designed communities to enhance food fermentation process.In traditional fermented dairy products and beverages, advances in starter-culture technology are equally notable. Mudoor Sooresh et al. tackled the challenge of preserving the complex microbiota of kefir grains. They showed that Freeze-dried starters derived from authentic grains could inoculate milk to produce products nearly indistinguishable from fresh kefir in both flavor and community structure, which provides a practical solution for standardized production in regions without access to live grains. Chen et al. extended kefir fermentation to a plant-based matrix. During four months of serial transfer in soymilk, the kefir community underwent adaptive reshaping.Lactobacillus kefiranofaciens, initially dominant ~95% in dairy kefir, dropped to 16%, while Lacticaseibacillus paracasei, capable of metabolizing soymilk oligosaccharides such as raffinose and stachyose, rose to ~77% and became the dominant species. This shift reduced kefiran production, grain size, and texture quality and led to declines in sensory attributes and ACE inhibitory activity. Even so, the study establishes a foundation for plant-based kefir development and suggests strategies to maintain functional robustness, such as periodic rejuvenation in dairy matrices or supplementation with exopolysaccharide-producing strains.From a broader perspective, Su et al. demonstrated the potential of cross-scenario strain utilization. Yeasts originating from Chinese mantou fermentation differ markedly from wine yeasts in stress tolerance, which reflects distinct domestication histories.Leveraging such adaptive features may enable targeted selection for conditions such as high sugar, high osmolarity, elevated ethanol, or low pH.Overall, traditional foods worldwide provide a broad strain and process library for application-oriented innovation. Ethiopian fermented foods rich in Bacillus and probiotic-potential lactic acid bacteria, Chinese fermented vegetables with enzymeinhibitory activities, and Baijiu fermented grains yielding novel yeast and mold isolates can all serve as a source pool for next-generation starters and functional food components. Looking forward, traditional food fermentation must move from experiencedriven practice toward predictability and verifiable design. Integrating amplicon, metagenomic, and metabolomic data with kinetic models offers a pathway to constructing simplified digital-twin fermentation systems. Machine learning and other artificial intelligence approaches can further enable pre-screening of community formulations and process parameters before bench-scale experimentation and scale-up.Central to this shift is the use of dose-response relationships that map strain to metabolites and, ultimately, to flavor or functional outcomes, thereby guiding rational parameter selection. Such approaches can reduce trial and error, shorten development timelines, and ensure product quality (Fig. 2). Reproducibility begins with safeguarding microbial diversity. We recommend establishing microbial resource banks that cover traditional starters such as Daqu, koji, sourdough, and kefir, along with standardized protocols for isolation, preservation, revival, and activation, in order to prevent losses of flavor and stability that can accompany industrial simplification. In parallel, practices such as back-slopping and raw-material pretreatment should be documented, with sources and authorizations clearly specified, to form a traceable body of process knowledge.Functional claims must be supported by clear lines of evidence. Begin with in vitro assays to confirm enzymatic inhibition or substrate degradation. Then quantify doseresponse relationships with sensory and physicochemical indices in food models.Finally, verify efficacy and safety in animal or human studies. By combining multiomics with metabolic flux analysis, one can identify which classes of metabolites attain effective concentrations in actual foods and, on this basis, define the minimum effective intake. These data directly inform label compliance and regulatory submissions.On the application front, priority can be given to low-salt, low-sugar, and plantbased scenarios. By combining substrate adaptation, community remodeling, and supplementation with exogenous metabolites, texture and flavor can be improved. For example, in plant-based fermentations, supplementing exopolysaccharide-producing strains or adding flavor precursors can counterbalance deficits in mouthfeel and aroma.Finally, by unifying data recording formats for multi-omics, process parameters, and sensory results, we can construct shareable evaluation datasets that facilitate reproducibility and benchmarking across facilities.In conclusion, this Research Topic systematically elucidates how microbial diversity can be translated into measurable, controllable functions, and further clarifies how these functions can be harnessed through targeted process innovation. Collectively, the studies presented here contribute to a more mature and integrated conceptual framework. Traditional fermentation should be viewed not only as a cultural heritage to be preserved, but also as dynamic frontiers driving scientific discovery and biotechnological progress. Through in-depth profiling and comparative analyses of fermentation microbiomes across diverse regions and raw-material contexts, we can generate actionable strategies for improving product quality, enhancing nutritional value, and advancing sustainability. Such approaches ensure that the microbial resources and functional potential embedded in traditional fermented foods continue to deliver stable, reliable, and health-and-flavor-aligned societal benefits at scale.