Abstract
The fruit microbiome is crucial for fruit quality and postharvest characteristic. This study characterized the microbiome and metabolome of two bayberry cultivars (Myrica rubra cv. DongKui and Dingao) across three orchardsusing high-throughput sequencing and GC-MS metabolomics. The results indicated Dongkui showed lower microbial diversity dominated by Hyphozyma and Papiliotrema and bacterial genus 1174_901_12, whereas Dingao exhibited greater microbial diversity with Hannaella, Uwebraunia, and Pantoea. Fungal diversity was cultivar-dependent, while bacterial composition varied by orchard. Metabolomics revealed higher amino acid in Dingao and elevated myricetin in Dongkui correlating with microbiome differencs. GC-MS identified 16 differntial metabolites between cultivars, linked to microbial variations. Notably, core microbiome analysis identified Aureobasidium as a potential biocontrol agent. However, Dingao hosted more phytopathogens (Colletotrichum, Uwebraunia), implying heightened disease susceptibility and the need for targeted postharvest interventions. These findings provide insights for improving bayberry quality and developing microbiome-based strategies for crop improvement and preservation.