Multi-omics insights into linalool-mediated modulation of microbial metabolism during cigar tobacco solid-state fermentation

Mold contamination in solid-state fermentation (SSF) severely compromises product stability and safety, leading to spoilage and off-flavor formation. Although synthetic preservatives are used, they often induce ecological instability and residual risks, prompting a shift toward natural alternatives. However, the mechanisms by which natural compounds modulate microbial interactions and affect metabolism remain elusive. Here, we characterized the divergent ecological and metabolic trajectories of linalool-mediated biocontrol versus chemical preservation (sodium dehydroacetate) treatment in a cigar tobacco solid-state fermentation model using an integrated multi-omics framework combining volatile/non-targeted metabolomics, amplicon sequencing and metagenomics. Our analysis showed that sodium dehydroacetate was associated with a centralized co-occurrence structure and distinct functional profiles, together with a late-stage accumulation of off-flavor precursors, including total acids (1619.07 µg/kg) and nitrogen-containing heterocycles (5763.58 µg/kg), both significantly higher than in the control ( P < 0.05). In this boom-bust pattern, Pseudomonas and Aspergillus were identified as central nodes, and their co-occurrence with amino acid metabolism was linked to late-stage metabolite accumulation. In contrast, linalool was associated with a more modular and less centralized co-occurrence architecture and phase-dependent metabolic changes: early cycles were characterized by the enrichment of specific metabolites, including long-chain fatty acid methyl esters (e.g., methyl hexadecanoate at 527.65 µg/kg, P < 0.05 vs. control) and alkaloid biosynthesis pathway. Concurrently, a positive co-occurrence between Pantoea and Diaporthe , together with biofilm-associated functions (ko02026), was observed. At mid-to-late cycles, a microbial consortium associated with fatty acid metabolism and aromatic degradation was enriched. Moreover, linalool-associated secondary metabolic pathways were negatively correlated with potential spoilage bacteria, providing molecular-level associations consistent with its potential role in microbial modulation. This study indicates that linalool-mediated treatment was associated with a shift in microbial community structure from a centralized to a more modular co-occurrence pattern, offering insights into microbial and metabolic modulation and providing a basis for further evaluation of plant-derived strategies to reduce chemical inputs in cigar tobacco solid-state fermentation.