Dynamic changes in microbiome during traditional Vietnamese fish sauce fermentation revealed by metagenomics analysis

“Nước m˘ a´ ắm” is a traditional Vietnamese fish sauce made from fish and salt through natural fermentation. The fish sauce fermentation process is regulated by complex metabolic activities driven by the combined effects of enzymes and microbial communities. We performed metagenomic analyses on four samples to reveal the role of specific microbes in protein degradation and flavor production within the bacterial community. Among the four analyzed fish sauce samples, Tetragenococcus halophilus was the dominant species in the bacterial communities. The relative abundance of Tetragenococcus halophilus increased after six months of fermentation, reaching its highest level at 66.07%. Protease profiling in fish sauce samples (1, 3 and 6 months of fermentation) identified various enzymes from Tetragenococcus, Staphylococcus and Bacillus species, including prolidase and Xaa-Pro aminopeptidase. These enzymes enhanced proline release, which is important for osmotic balance and flavor formation. Several abundant proteases might contribute to degrade proteins efficiently under high salinity conditions, releasing free amino acids essential for bacterial growth and flavor development. Supporting this, pangenome analysis of Tetragenococcus halophilus revealed a high prevalence of genes for salt stress adaptation, compatible solute synthesis, transporters and amino acid biosynthesis, supporting survival and metabolic activity in fermented fish sauce. These findings provide valuable insights into the bacterial composition and functional roles during fish sauce fermentation, and promote the exploration of potential proteolytic strains involved in flavor development to enhance production quality.