Impact of storage conditions on microbial dynamics and metabolite profiles in aged Citri Reticulatae Pericarpium

Aging drives the properties and quality of Citri Reticulatae Pericarpium (pericarps of Citrus reticulata ‘Chachi’ (GCP)), which are widely used as food and herbal medicine. However, the mechanisms of microbial-driven chemical transformation remain unclear. This study evaluated the effects of temperature, humidity and aging time on the microbiome and metabolome of GCP using multi-omics approaches. The results showed that dominant bacterial genera like Pseudomonas (68.0–1.1%), Acinetobacter (44.9–0.01%), and Streptococcus (35.1–0.02%), and fungal genera such as Xeromyces (99.9–22.6%), Paraxerochrysium (65.7–0.03%), and Aspergillus (58.2–0%) differentiated between samples and storage conditions. Spearman’s correlation analysis revealed that specific bacterial and fungal genera were distinctly associated with flavonoids, microbial gas exchange, and volatile organic compounds (VOCs). Notably, Streptococcus, Aspergillus , and Cladosporium showed significant positive correlations with hesperidin and didymin levels ( p < 0.05), while Kroppenstedtia , Lactobacillus , and Paenibacillus were positively correlated with C5 carbonyl compounds, the key VOCs ( p < 0.05), suggesting their potential roles in metabolite transformation. Kyoto Encyclopedia of Genes and Genomes (KEGG)-based functional prediction further indicated potential microbial pathways involved in the biosynthesis and degradation of flavonoids and VOCs. Overall, these findings highlight the important role of microbial communities in mediating bioactive compound transformations, providing a theoretical basis for optimizing the aging process and enhancing the quality of GCP. • Aging of Citrus reticulata peels postulated to be driven by microbial dynamics. • Microbial communities in aged peels varied with temperature and humidity. • Flavonoids, gas exchange, and volatiles correlated with various microbial genera. • Functional prediction elucidated microbial metabolism of volatiles and flavonoids.