Introduction: A Global Look at Traditional Ferments
Traditional fermented foods are more than culinary staples; they are living ecosystems shaped by culture, environment, and time. From Nepal’s achars and gundruk to South Korea’s kimchi and oiji, and Ethiopian ayib and injera, these foods showcase a spectrum of substrates—vegetables, legumes, cereals, dairy, meat, and seafood—and a variety of fermentation techniques. This study maps how ecological factors govern the microbial communities that drive flavor, texture, aroma, and safety in culturally diverse ferments.
Substrate Type as the Primary Architect of Bacterial Communities
Across 90 samples representing 24 fermented foods, substrate emerged as the strongest determinant of bacterial community structure. Plant-based foods (vegetables, cereals, legumes) consistently hosted distinct bacterial assemblages compared with animal-based products. Within plant substrates, cereal-based, legume-based, and vegetable-based ferments formed separate clusters, reflecting macronutrient profiles and the carbohydrate-rich milieu that selects for particular microbes.
Functional predictions aligned with these patterns. Vegetable- and cereal-based ferments favored pathways tied to carbohydrate metabolism and the biosynthesis of folate, retinol, and thiamine, underscoring a substrate-driven functional specialization. Dairy, legumes, and animal-based ferments tended toward amino-acid–related pathways and vitamins such as B6, mirroring their richer protein and lipid content.
Geography and PUFF Microbes: Subtle Yet Important Contributors
Geography significantly influenced bacterial communities when all data were considered. However, removing PUFF microbes—taxa with unclear roles in fermentation—attenuated the geographic signal. This suggests that regional differences in flavors and textures may arise from less-characterized microbes that populate traditional ferments across continents.
PUFF microbes, including Brevibacterium, Corynebacterium, Salinivibrio, and Rhizopus, appeared across broad regions and substrates, hinting at their widespread, yet not fully understood, contributions to fermentation processes. Fungi such as Debaryomyces nepalensis and Tausonia pululans also played central roles in specific substrate groups, shaping aroma and mouthfeel in dairy and vegetable ferments, respectively.
Fermentation Practices: Duration, Salt, Oil, and Shelf-Life as Ecological Levers
Beyond substrate and geography, practical aspects of fermentation—how long it lasts, whether oil or salt is used, and how long products are stored—significantly mold microbial landscapes. Longer fermentations and the absence of oil were linked to reduced LAB abundance and higher Bacillales presence, illustrating how process choices tilt the microbial balance toward different canonical players.
Salt usage also created distinct bacterial profiles. Salinivibrio and several Bacillus, Leuconostoc, and Lacticaseibacillus members thrived in salted foods, aligning with known salt tolerance and niche adaptation. These relationships highlight how traditional practices directly steer microbial succession and, by extension, sensory outcomes.
Co-Occurrence Networks: Bacteria-Fungi Interdependence Shaping Fermentation
Microbial interactions reveal a tapestry of cooperation and competition. Bacterial and fungal ASVs formed densely connected networks with five distinct bacterial and fungal co-abundance groups (CAGs). In dairy, a Lactobacillus delbrueckii–dominated CAG stood out, while legumes, meat, and seafood showcased a Bacillus-centric group. Vegetable and cereal ferments harbored LAB- and yeast-rich CAGs that also housed PUFF taxa, suggesting complex, substrate-specific webs of interaction.
Cross-kingdom analyses showed that L. delbrueckii-CAG bacteria frequently co-occurred with D. nepalensis fungi, yet antagonized Candida-CAG members. These dynamics imply that microbial cooperation can enhance flavor development, while antagonism can suppress competing microbes, collectively steering fermentation toward desired attributes.
Functional Potentials and Health Implications
Predicted functional profiles reinforce the concept that substrate drives microbial metabolism. Plant-based ferments emphasize carbohydrate-active enzymes, while dairy and meat-focused ferments lean toward amino-acid metabolism and vitamin pathways. Some detected taxa align with health-promoting traits, including lactic acid bacteria’s resilience to gut conditions and potential immune modulation. Moreover, traditional ferments may harbor gut-associated bacteria, prompting intrigue about their roles in human microbiomes and long-term health implications.
Limitations and Future Directions
Although amplicon sequencing provided broad taxonomic insights, its resolution limits strain-level conclusions. Shotgun metagenomics, metabolomics, and longitudinal sampling could uncover strain-specific functions, temporal dynamics, and causal interactions. Culturing PUFF microbes for experimental validation would further illuminate their roles in fermentation, aroma, texture, and safety. Understanding these ecosystems could enable engineered multi-strain starters to optimize palatability, shelf-life, and health benefits while respecting cultural heritage.
Conclusion: Substrate-Mediated Microbial Ecologies Shape Traditional Ferments
In traditional fermented foods, macronutrient profiles and preparation methods largely govern microbial community assembly. Geography and less-understood PUFF microbes contribute to regional flavor differences, while microbial networks reveal intricate interdependencies between bacteria and fungi. By decoding these ecological drivers, we can appreciate how culture, environment, and time converge to produce the remarkable diversity of fermented foods enjoyed around the world.
