Impact of Fermentation on Bacterial and Fungal Microbiome Interactions in Pla-Ra, a Traditional Thai Food

Pla-ra, a traditional Thai fermented fish product, undergoes complex microbial and biochemical transformations that contribute to its unique flavor and aroma. This study investigated the effects of fermentation on the microbiome of pla-ra, focusing on bacteria-fungi interactions. Freshwater fish, combined with salt and roasted rice, were sampled after 1 and 6 months of fermentation. Bacterial and fungal communities in these pla-ra samples were characterized using next-generation sequencing of the 16S rRNA (V3-V4 region) and ITS2 regions, respectively. Results demonstrated that initial bacterial contamination levels were within standard limits, while fungal contamination (estimated by culture) exceeded pla-ra guidelines. Both pH and salinity increased slightly during fermentation. A decrease in bacterial alpha diversity and an increase in fungal diversity during fermentation were observed. Bacterial genera such as Candidatus Hydrogenedens, Bellilinea, and various unclassified Acidobacteria groups declined, while Enhydrobacter, Dermacoccus, and Halanaerobium increased, indicating adaptation to increased salinity. Penicillium, the dominant fungal taxon, has a potential role in flavor development. Importantly, microbial network analysis revealed dynamic interactions, including an inhibitory effect of Penicillium on Dermacoccus and Enhydrobacter, but only early in fermentation. KEGG pathway analysis highlighted upregulation of glycerophospholipid metabolism and downregulation of lipid metabolism. In conclusion, our results demonstrate that pla-ra fermentation decreases bacterial and increases fungal diversity, impacting bacteria-fungi interactions and correlations in ways that may influence taste and smell. This information contributes to optimizing traditional fermentation practices and enhancing product quality and safety.