Aging of Citri Reticulatae pericarpium: Flavonoid metabolite dynamics, fungal community succession, and functional analysis of key transformation strains

Citri Reticulatae Pericarpium (Xinhui Chenpi) , a representative product with a protected geographical indication from Xinhui District, Guangdong Province, China, is a dual-use medicinal and edible material and a traditional medicinal resource whose quality is traditionally believed to improve with prolonged aging. Increasing evidence indicates that the succession of surface microbial communities and their metabolic activities play pivotal roles in these transformations. This study systematically investigated Xinhui Chenpi aged 1–10 years to elucidate the dynamics of dominant fungal genera and experimentally verify their involvement in flavonoid transformation. Ultra-performance liquid chromatography (UPLC), third-generation full-length ITS sequencing (PacBio) , and strain isolation with culture assays were employed to characterize flavonoid profiles, fungal community succession, and the transformation capabilities of key isolates. Flavonoids exhibited a “degradation to resynthesis” trajectory, with polymethoxyflavones (PMFs) steadily accumulating throughout the aging process. Late-stage samples were dominated by the xerophilic genus Xeromyces (Aspergillaceae), which showed strong positive correlations with PMF enrichment, whereas correlations with Penicillium progressively declined over time. Importantly, Aspergillus tubingensis was isolated and confirmed to convert nobiletin into 3′-demethylnobiletin, providing direct mechanistic evidence for fungal-driven PMF structural modification. Community profiling further revealed that multiple Aspergillaceae genera ( Aspergillus , Penicillium , Xeromyces ) may participate in flavonoid transformation. These findings elucidate the microbial mechanisms underlying quality enhancement in aged Chenpi and provide a scientific basis for microbial-assisted optimization of modern aging processes, thereby offering theoretical support for the traditional principle that “aged Chenpi becomes more efficacious.”