Comparative analysis of metabolite and microbial community dynamics during spontaneous fermentation of Lonicera caerulea berries

Spontaneous fermentation of <i>Lonicera caerulea</i> berries was monitored using integrated widely targeted metabolomics and high-throughput microbiome sequencing to elucidate the dynamic changes in metabolites and microbial communities. Throughout fermentation, 90 non-volatile metabolites and 52 volatile compounds were identified with variable importance in projection (VIP) ≥ 1 and <i>p</i> ≤ 0.05. The evolution of distinct flavor profiles of the fermented <i>L. caerulea</i> berries was attributed to significant changes in the transformation and accumulation of organic acids, lipids, saccharides, phenolic compounds, and amino acids. Metabolic pathway analysis indicated that linoleic acid and phenylalanine metabolism were dominant in the early fermentation stage, whereas aminoacyl-tRNA biosynthesis, cyanoamino acid metabolism, and arginine biosynthesis prevailed in the later phase. Fungal communities were prevalent throughout fermentation. Early fermentation was dominated by <i>Valsa</i>, <i>Actinobacillus</i>, <i>Mortierella</i>, and <i>Ascomycota</i>, and late fermentation was <i>Gluconobacter</i> and <i>Wickerhamomyces</i> enrichment. Notably, strong and significant correlations (|r| > 0.8, <i>p</i> < 0.05) were observed between specific microorganisms, such as <i>Wickerhamomyces</i> and <i>Gluconobacter</i>, and key metabolites, including glucose-6-phosphate, methionine, leucine, isoleucine, and glutamic acid. These findings offer fundamental insights into the biochemical mechanisms of spontaneous fermentation of L. <i>caerulea</i> and provide a scientific basis for developing controlled fermentation strategies to improve the quality of fruit-based foods.