Integrated metabolomics and metagenomics reveal plant-microbe interactions driving aroma differentiation in flue-cured tobacco leaves.

Current research on tobacco aroma predominantly focuses on single-omics approaches. In this study, we conducted a comprehensive investigation of the relationships between tobacco metabolite profiles, microbial communities, and aroma characteristics. Untargeted metabolomics and metagenomic analyses were performed on flue-cured upper tobacco leaves to compare light aromatic tobacco (LAT) and strong aromatic tobacco (SAT). The results showed that sugar metabolite levels in LAT were significantly higher than those in SAT, whereas levels of specific acids and amino acid metabolites in SAT exceeded those in LAT. Redundancy analysis (RDA) and metabolomic correlation analyses indicated that the genera and may promote sugar metabolite accumulation, while potentially regulates both sugar and acid metabolites. In contrast, and were associated with acid and amino acid metabolism, with additionally exhibiting inhibitory effects on sugar metabolism. Metagenomic analysis revealed that , , and were abundant in LAT, whereas and dominated in SAT. Notably, the bidirectional regulation of aromatic metabolites by microbial genera such as highlights the universality of plant-microbe interactions in shaping metabolic networks-a mechanism potentially applicable to other crop systems. These findings reveal conserved microbial functional traits (e.g., metabolic pathway modulation) that may drive plant phenotypic differentiation beyond tobacco, offering insights into microbiome-mediated crop quality improvement. The results provide theoretical guidance for tobacco aging and aroma regulation and underscore the broader significance of microbial community engineering in agriculture for manipulating plant metabolic outputs.