Multi-omics reveals metabolic shifts by Candida-enhanced fermentation in improving cigar tobacco quality

Traditional natural fermentation of cigar tobacco leaves is stochastic and often yields inconsistent quality. To elucidate how Candida inoculation improves cigar tobacco quality, we performed integrated metagenomic and metabolomic analyses on leaves fermented with or without Candida metapsilosis . Inoculation significantly increased reducing sugar (+23.2%), organic acids (+14.2%), terpenoids (+6.2%), and amino acid derivatives (+11.4%), while decreasing nicotine (−16.4%) and tobacco‑specific nitrosamines (TSNAs) (−18.4%). These changes correlated with improved sensory quality. Microbial α-diversity remained unchanged, whereas β-diversity was clearly separated between groups. LEfSe analysis revealed co-enrichment of Candida and flavor-associated taxa ( Kosakonia , Bacillus , Staphylococcus ) in the inoculation group, while spoilage-related microbes ( Aspergillus , Penicillium , Fusarium ) were reduced. Time-course absolute quantification further confirmed that the inoculated Candida actively proliferated and persisted through fermentation. Functional enrichment showed that the inoculation group was enriched for pathways involved in central carbon metabolism, terpenoid precursor biosynthesis, nicotine degradation, and nitrate reduction, consistent with the observed flavor improvement and nicotine reduction. Species contribution analysis revealed that nicotine degradation genes were predominantly carried by Glutamicibacter (95.3%). Candida and Kosakonia showed significantly increased contributions to the TCA cycle ( Kosakonia: from 3.6 to 4.3% to 8.5–10.0%; Candida : from 0% to 2.0–2.1%), nitrate reduction ( Kosakonia : from 10.2% to 24.1%), and C10‑C20 isoprenoid biosynthesis ( Kosakonia : from 4.2% to 10.9%; Candida : from 0% to 1.8%) ( p < 0.05). Collectively, Candida inoculation reshaped the microbial community and metabolic functions in a manner coincident with improved flavor quality and reduced nicotine content, providing a foundation for developing more consistent fermentation processes.