The dynamic changes in physicochemical properties, microbial communities, and volatile compounds in kombucha made from Flos sophorae (FLSK) and Elm fruit (EFK) were compared to those of black tea (BTK) and green tea (GTK) over a 12-day fermentation period. The results revealed that overall flavonoid and polyphenol content, as well as antioxidant activity, increased initially and then decreased, accompanied by a steady reduction in pH within the fermentation broths investigated. Notably, the GTK exhibited stronger antioxidant activity than the other fermentation broths. Furthermore, 16S rRNA gene sequencing revealed that Komagataeibacter rhaeticus, Komagataeibacter saccharivorans, and Acidovorax wautersii were the dominating microbial species in the fermentation broths under this study. Komagataeibacter rhaeticus initially reduced and then increased throughout the FLSK fermentation, whereas Komagataeibacter saccharivorans increased from day 0 to day 6, and remain stable by day 12 during the EFK fermentation. Comparative analysis revealed that Komagataeibacter rhaeticus was more abundant in the FLSK and GTK than in the EFK and BTK, whereas Komagataeibacter saccharivorans showed a higher abundance in the EFK relative to the other fermentation broths. Gas chromatography-mass spectrometry identified acetic acid, linalool, ethanol, and ethyl acetate as the major volatile chemicals that rose significantly in fermentation mixtures of the examined substrates. The FLSK had a much higher linalool concentration than the other fermentation broths, although the EFK and GTK had higher ethanol content. Correlation study found that Komagataeibacter rhaeticus was negatively related with alcohol compounds, but Komagataeibacter saccharivorans was positively associated with a diverse spectrum of acids, alcohols, and esters. The study found changes in bioactive chemicals as well as interactions between bacterial populations and volatile compounds throughout fermentation in the substrates investigated.
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