Introduction: A Global Look at Traditional Fermentation
Traditional fermented foods across Asia and Africa capture a remarkable spectrum of microbial life, from the tang of lab-borne LABs to the savory notes shaped by yeasts and molds. In a study sampling 90 foods spanning 24 types from Nepal, South Korea, Ethiopia, and Kazakhstan, researchers explored how ecological factors mold the microbial communities within these ferments. The results reveal that the substrate type—what the food is made from—acts as a primary driver of bacterial community structure, while fungi show a distinct, substrate-insensitive pattern more heavily influenced by fermentation practices and starter cultures. This article synthesizes these findings to explain how ecological context sculpts microbial ecosystems that underpin flavor, texture, and potential health effects in traditional ferments.
What Substrates Do to Bacterial Communities
Analysis of 104 bacterial ASVs across 90 samples showed that bacterial communities cluster strongly by substrate. Vegetables, cereals, and legumes each harbor characteristic bacterial assemblages, with dairy and animal products forming their own profiles. In particular, LABs (lactic acid bacteria) and Bacillales accounted for the majority of reads, with LABs and Saccharomycetales (fungi) dominating many plant-based ferments, and Bacillales being more prevalent in legumes and animal-derived products.
Functional predictions (via PICRUSt2) indicated that plant-based ferments (vegetables, cereals) are enriched for carbohydrate metabolism pathways, folate biosynthesis, and vitamins such as retinol and thiamine. In contrast, dairy, legumes, and animal products showed higher pathways for amino acid metabolism and vitamin B6. This alignment between substrate macronutrient profiles and microbial function highlights how the available nutrients direct both who colonizes a ferment and how they metabolize substrates to shape final product characteristics.
Geography vs. PUFF Microbes: What Explains Regional Differences?
Geography initially appeared to structure bacterial communities when considering all ASVs. However, removing PUFF (previously unexplained, or poorly characterized) microbes markedly reduced this geographic signal. This suggests that regional flavor differences may largely reflect contributions from microbes whose roles in fermentation remain underexplored, rather than well-known canonical fermenters alone. PUFF taxa—including Brevibacterium, Corynebacterium, Salinivibrio, and Debaryomyces species—were distributed across regions and substrates, implying they are key shapers of regional terroir in traditional ferments.
Substrate as the Primary Ecological Filter
Across analyses, substrate type emerged as the strongest ecological filter for bacterial community assembly. Fermented vegetables, dairy, legumes, cereals, and animal products each host distinct bacterial ecologies, with substrate-driven nutrient availability steering which taxa thrive. Fermentation duration, the use of oil or salt, and shelf-life also contributed to differences in bacterial composition, illustrating a dynamic, substrate-mediated ecosystem that evolves over time and processing choices.
Fungal Communities: Practices and Starters Take Center Stage
Unlike bacteria, fungal community structure did not show a strong association with geography or substrate. Instead, fermentation duration and starter cultures were major determinants of fungal assemblages. A notable pattern: starter-assisted ferments tended to show greater uniformity in fungal composition, suggesting that deliberate inoculation can stabilize fungal communities across environments. This contrasts with bacteria, where substrate and geographic history more strongly sculpt the community.
Microbial Networks: Interactions Shape Ferment Quality
Co-occurrence network analyses revealed densely connected bacterial and fungal networks with clearly defined co-abundance groups (CAGs). Interactions were both synergistic and antagonistic, reflecting a complex ecology where certain taxa promote others (e.g., LABs with yeasts) while others suppress competitors. In dairy, L. delbrueckii-CAG dominated, while legume/meat/seafood substrates favored a Bacillus-centric CAG. Cross-kingdom links showed that bacteria and fungi can co-stabilize low-pH environments, enabling the development of distinctive flavors and textures in traditional ferments.
Implications and Future Directions
The study underscores that macronutrient profiles of raw ingredients exert powerful selection pressures on microbial communities in traditional ferments. It also highlights the importance of PUFF microbes as potential keystone players driving regional diversity. Future work using shotgun metagenomics, longitudinal sampling through fermentation, and culture-based validation could reveal strain-level dynamics, enhance functional predictions, and enable targeted manipulation to improve flavor, safety, and health benefits. The integration of metabolomics and co-culture experiments may unlock strategies to engineer multi-strain consortia that optimize palatability, shelf-life, and nutritional value while respecting cultural heritage.
Conclusion
Traditional fermented foods serve as living repositories of microbial diversity shaped by substrate type, processing methods, and regional practices. By disentangling these ecological factors, researchers can better understand how flavor profiles arise, how microbial communities contribute to safety and nutrition, and how to sustainably steward these ancient culinary traditions for future generations.
