Endophytic microbiome and metabolome contribution to flavor development in Cucurbitaceae crops: a case study on melon and bitter gourd

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Abstract
Endophytic microbiome and metabolome are known to influence plant physiology, but their specific roles in fruit flavor development remain poorly understood. To explore microbial and metabolic factors linked to distinct flavor phenotypes, we compared stem endophytic microbiome composition and untargeted metabolomes between melon (Cucumis melo, CM) and bitter gourd (Momordica charantia, MC). Our goal was to identify candidate taxa, metabolites and pathways potentially related to sweetness and bitterness. Results showed that fungal diversity and richness were significantly higher in CM than in MC. CM stems were characterized by enrichment of Ascomycota and unique dominance of Sphingomonas, whereas MC exhibited significant enrichment of Botryosporium and a higher relative abundance of Bacteroidota. Metabolomic and pathway analyses revealed that CM displayed upregulation of phenylalanine, tyrosine and tryptophan biosynthesis, flavonoid biosynthesis, and cofactor biosynthesis, along with accumulation of sweet-enhancing metabolites such as naringin dihydrochalcone. By contrast, MC showed elevated activity in plant hormone signal transduction and higher levels of (S)-abscisic acid and dihydrozeatin. This study demonstrates distinct stem endophytic microbiomes and metabolomes between melon and bitter gourd, and highlights candidate functional microorganisms, key metabolites and metabolic pathways that correlate with sweetness and bitterness phenotypes. Further experimental validation is needed to confirm the causal roles of these candidates. These findings provide new insights into the mechanisms underlying melon sweetness and bitter gourd bitterness, and lay a methodological foundation for multi-omics investigations and the future development of microbiome- or metabolite-based strategies for modulating fruit quality and flavor.

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