Introduction
Traditional fermented foods from Nepal, South Korea, Ethiopia, and beyond are vibrant archives of microbial life. Researchers analyzed 90 samples across 24 food types — including vegetables, legumes, cereals, dairy, meat, and seafood — to understand what ecological factors drive the microbial communities that give these ferments their unique flavors, textures, and health implications. The study highlights how substrate type, processing methods, and environmental context interact to shape a complex microbial ecosystem that extends far beyond the canonical fermenters you often hear about.
Substrate as the primary architect of bacterial communities
Across all samples, the food substrate emerged as the strongest determinant of bacterial composition. Plant-based ferments (vegetables, cereals, and legumes) showed distinct microbial profiles from animal-based products (dairy, meat, seafood). When PUFF microbes — a group of abundant yet functionally under-characterized bacteria and fungi — were excluded, geography’s influence on bacterial communities diminished, underscoring that nutrient availability provided by the substrate largely dictates which bacteria thrive.
Specific substrates shaped different bacterial lineages. Vegetable- and cereal-based fermentations enriched carbohydrate-processing pathways, while dairy, legumes, and animal products favored amino-acid metabolism and vitamin-related pathways. This functional alignment with substrate macronutrient profiles suggests microbes adapt their metabolism to the food’s nutrients, driving fermentation flavors, textures, and aromas.
Geography, time, and processing: other ecological levers
Geography initially appeared to modulate microbial structure, but removing PUFF taxa revealed that regional differences largely reflect the presence of those lesser-understood microbes rather than deeply divergent core communities. Fermentation duration, oil and salt usage, and shelf-life also correlated with community structure. Longer fermentations and those lacking oil tended to harbor fewer lactic acid bacteria and more Bacillales, revealing how traditional techniques sculpt the microbial landscape over time.
Salt levels were linked to distinct bacterial signatures: Salinivibrio and several Bacillus- and Leuconostoc-related taxa flourished in salted foods. This aligns with the idea that salinity builds selective pressure, shaping which microbes can persist in a given ferment.
Canonical fermenters and PUFF microbes: a two-tier view of communities
Canonical fermenters such as LABs, Bacillales, and Saccharomycetales (yeasts) dominated many samples, but a substantial fraction of reads came from PUFF microbes with undefined roles in fermentation. PUFF taxa, detected across broad geographies, may be the hidden drivers of regional flavor and aroma profiles. They also formed key nodes in co-occurrence networks, sometimes acting as keystone species, indicating their potential importance in shaping fermentation ecosystems.
Biotic interactions and network architecture
Microbial communities in these ferments are tightly interconnected. Bacteria- and fungi-based networks reveal co-abundance groups (CAGs) with high connectivity and varying centrality. In dairy-rich clusters, L. delbrueckii-linked CAGs interact with PUFF members, while Bacillus-dominant clusters associated with legumes, meat, and seafood show distinct fungal co-structures. Cross-kingdom networks reveal both cooperation and competition: LABs can support yeasts by providing nutrients, whereas certain molds and bacteria can suppress competitors through competitive exclusion or antimicrobial compounds. These intricate networks help explain why even similar substrates from different regions can yield different flavor outcomes.
Functional potential and implications for health and culture
Predictive functional profiling showed substrate-specific metabolic potential. Plant-based ferments emphasized carbohydrate-processing enzymes and vitamins such as folate, retinol, and thiamine, while animal- and legume-based ferments favored amino-acid metabolism and B6-related pathways. These patterns hint at how traditional fermentation not only preserves food but also modulates its nutritional value.
Beyond flavor, some microbes associated with traditional ferments may interact with human health, including gut-associated taxa found in these foods. While the study used amplicon sequencing, it highlights the need for shotgun metagenomics and longitudinal sampling to resolve strain-level functions and track microbial dynamics throughout fermentation.
Need for broader exploration and future directions
The work underscores the value of studying non-European fermentation traditions to uncover microbial diversity and novel interactions. Expanding sampling to more regions and substrates, coupled with metagenomics, metabolomics, and culture-based validation, will deepen our understanding of how microbes contribute to taste, safety, and nutrition in traditional ferments. Longitudinal studies could reveal how microbial interactions evolve across fermentation stages, offering opportunities to engineer multi-strain communities that improve palatability, shelf-life, and health benefits.
Conclusion
Traditional fermented foods are living ecosystems shaped primarily by substrate chemistry, with geography and processing methods adding layers of influence. By mapping bacterial and fungal networks, and by recognizing the prominent role of PUFF microbes, researchers are beginning to decode how culture, cuisine, and microbiology intertwine to create the remarkable diversity of fermented foods enjoyed around the world.
