Flue-cured tobacco (FCT) with irritating and undesirable flavor must be treated with aging process. However, the spontaneous aging usually takes a very long time for the low efficiency. Bioaugmentation with functional strains is a promising method to improve FCT quality with high aging efficiency. To ease the adverse effect of excessive starch or protein content on the FCT quality, we screened B. amyloliquefaciens LB with high alpha-amylase and B. kochii SC with high neutral protease from the FCT microflora with the flow cytometry. The mono, co-culture of strains was subjected to solid-state fermentation with FCT. B. amyloliquefaciens monoculture at 2 days and B. kochii monoculture at 2.5 days achieved the optimum quality. B. amyloliquefaciens-B. kochii co-culture at a ratio of 3:1 fermenting for 2 days demonstrated a more comprehensive quality enhancement and higher functional enzyme activity than mono-cultivation. With the analysis of OPLS-DA model, there were 38 differential compounds between bioaugmentation samples. In co-cultivation, most of Maillard reaction products and terpenoid metabolites were at a higher level than other samples, which promoted an increase in aroma, softness and a decrease in irritation. This result was in line with our design about the quality enhancement of FCT with co-cultivation. In our study, we presented a promising bioaugmentation technique for changing the quality attributes of FCT in a short aging time.
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