Metagenomic and metabolite analysis reveals microbial community and metabolite dynamics in fermented Indigo naturalis

• Published in: Heliyon Vol. 10; no. 17; p. e36733
• Main Authors: Yuan, Xinyi, Zhang, Dayan, Li, Duanyang, Ji, QiSen, Gao, Jihai, Hou, Feixia, Chen, Yang'er
• Format: Journal Article
• Language: English
• Published: England Elsevier Ltd 15.09.2024; Elsevier
• Subjects: Indigo Naturalis; Metabolites; Metagenome; Microbial community structure; Metabolites; Metagenome; Indigo Naturalis; Microbial community structure
• ISSN: 2405-8440; 2405-8440
• DOI: 10.1016/j.heliyon.2024.e36733

The soaking and fermentation of the stems and leaves is an important intermediate step in the processing of Indigo Naturalis. However, the relationship between microbiota and Indigo Naturalis yields is still poorly understood. This study aimed to compare microbial communities and metabolite profiles at various stages of soaking fermentation, followed by validation of the results using HPLC. A total of 731 compounds were identified through metabolite analysis, with the levels of indigo and indirubin peaking after 36 h of fermentation. Metagenomes revealed Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria were identified as the most abundant microbial phyla in soaking fermentation. Correlation analysis indicated that the yields of indigo and indirubin may be affected by Lactococcus, Clostridium, and Enterobacter through the regulation of related synthetic enzymes. The findings offered novel perspectives on the relationship of microorganisms and Indigo Naturalis yields. [Display omitted] •The content of indigo reached its highest after 36 h.•Clostridium, Escherichia and Lactobacillus was the dominant bacterial genera.•It's possible to increase indigo yield by adjusting the content of microorganisms.