###### Abstract  
Jerusalem artichoke juice is valued for its nutritional content and health benefits. Spontaneous fermentation enhances its flavor, quality, and functional components through microbial metabolic activities. This study used high-throughput sequencing to analyze microbial community changes, and LC-MS and GC-MS to detect secondary metabolites and flavor compounds during fermentation. During natural fermentation, beneficial bacteria like _Lactobacillus_ and _Pediococcus_ increased, promoting lactic acid production and inhibiting harmful bacteria, while environmental bacteria decreased. Similarly, fungi shifted from environmental types like _Geosmithia_ and _Alternaria_ to fermentation-associated _Pichia_ and _Penicillium_. A total of 1666 secondary metabolites were identified, with 595 upregulated and 497 downregulated. Key metabolic pathways included phenylpropanol biosynthesis, with significant increases in phenylalanine, tryptophan, and related metabolites. Lipid and nucleotide metabolism also showed significant changes. Flavor compounds, including 134 identified alcohols, esters, acids, and ketones, mostly increased in content after fermentation. Notable increases were seen in Phenylethyl Alcohol, Ethyl Benzenproponate, 3-Methylbutyl Butanoate, Ethyl 4-Methylpentanoate, 5-Ethyl-3-Hydroxy-4-Methyl-2(5H)-Furanone, Ethyl Decanoate, Hexanoic Acid, and 1-Octanol. \(\gamma\)-aminobutyric acid (GABA) and other functional components enhanced the health value of the juice. This study provides insights into microbial and metabolic changes during fermentation, aiding in optimizing processes and improving the quality of fermented Jerusalem artichoke juice for functional food development. Jerusalem artichoke; spontaneous fermentation; microbial diversity; secondary metabolites; flavor compounds +
Footnote †: journal: _plants_  
0000-0001-9993-3499-3499-34999-  
artichoke extracts can be used in fermented fruit and vegetable juices to boost probiotic content and functionality [15; 18; 19]. Jerusalem artichoke tubers improve the moisture retention and texture of fermented bread, increasing dietary fiber content and catering to health-conscious consumers [20; 21; 22; 23]. The components of Jerusalem artichoke juice, rich in inulin and other fermentable sugars, serve as substrates for microbial metabolism, leading to the production of various primary and secondary metabolites [24]. Spontaneous fermentation is an effective food processing method that utilizes natural microbial communities from raw materials, equipment, and the environment [25; 26]. This method preserves the original flavor of the ingredients while producing beneficial metabolites through microbial activity, thereby enhancing the nutritional and health value of the food [27; 28]. Secondary metabolites play crucial roles in fermentation. Phenolic acids, flavonoids, and alkaloids exhibit antioxidant, antimicrobial, and anticancer properties. For example, flavonoids have strong antioxidant activity, protecting cells from oxidative stress [29; 30]. Phenolic acids like chlorogenic acid and caffe acid have anti-inflammatory and antimicrobial effects, enhancing food preservation and safety [31; 32; 33]. Additionally, alkaloids produced during fermentation, such as biotin and pyridoxine, improve the nutritional value of the food and enhance its health benefits [34; 35]. Studies have shown that adding inulin to spontaneously fermented products like yogurt, kimchi, and fermented fruit and vegetable juices increases probiotic content and enhances health benefits. Inulin addition significantly improves the survival rate of probiotics and sensory properties in yogurt. During fermentation, inulin is metabolized by lactic acid bacteria, producing organic acids (e.g., lactic and acetic acids) and other metabolites that enhance the taste and nutritional value of yogurt [36; 37; 38; 39; 40]. The flavor of spontaneously fermented foods primarily arises from the various metabolites produced by microbes during fermentation.