Synthetic microbial communities enhance tobacco quality by driving bacterial community succession and modulating metabolite profiles

The fermentation of cigar tobacco leaves (CTLs) is a critical process driven by microbial activity, which directly influences the degradation of macromolecules and the development of distinctive aromas. However, mechanisms for the directional regulation of this process using defined microbial consortia remain underexplored. This study aimed to construct a synthetic microbial community (SynCom) to enhance the fermentation efficiency and quality of cigar tobacco leaves. Bacillus safensis and Bacillus velezensis with high extracellular cellulase, amylase and protease activities were screened out, and synthetic communities were constructed. This microbial community was applied to cigar tobacco leaves (cultivar QX204) during a 42-day fermentation. The SynCom significantly accelerated the degradation of key macromolecules, reducing cellulose, protein, and starch contents by 52.48 %, 56.36 %, and 68.47 %, respectively, which were markedly greater reductions than those observed in the uninoculated control. Microbiome analysis revealed that inoculation shifted the bacterial community structure, increasing the relative abundance of Firmicutes and significantly enriching the genus Bacillus . Metabolomic profiling identified 31 differentially accumulated volatile flavor compounds, including phenylacetic acid, phytol, and farnesol, which were upregulated in the BsBv group and contributed to enhanced honey, floral, and baked aromas, while reducing irritancy. Integrated multi-omics analysis indicated that these improvements were associated with key metabolic pathways, notably pyruvate metabolism, the pentose phosphate pathway, and glycerolipid metabolism. Furthermore, partial least squares path modeling (PLS-PM) elucidated that the SynCom consortium directly modulated chemical components and indirectly improved sensory quality by mediating shifts in microbial β-diversity. These findings provide mechanistic insights into how functional SynComs can directionally improve tobacco leaf quality and offer a practical strategy for achieving efficient, high-quality cigar tobacco production. • 31 key aroma compounds upregulated, imparting honey, floral, and baked notes while reducing irritancy. • Multi-omics and PLS-PM reveal direct and microbiome-mediated pathways improving tobacco quality. • First demonstration of targeted microbial consortia driving flavor formation via core metabolic networks.