The shortage of feed protein has plagued the development of the animal husbandry industry in China. In this study, a new three-stage fermentation technology for producing distillers’ grain feed protein was developed by introducing Aspergillus niger, yeast, and lactic acid bacteria. During the aerobic stage, there was a negative correlation between the reducing sugar content in the distillers’ grains and the amount of Aspergillus niger. The maximum reducing sugar concentration (36.89 mg g−1) was obtained when the oxygen supply was 30 mL min−1 and the fermentation time was two days. During the microaerophilic stage, the natural exchange of oxygen achieved optimal true protein enhancement (from 10.8% to 16.4%) among the three oxygen supply modes (natural exchange, forced ventilation, and filling supplement). During the anaerobic stage, lactic acid bacteria were inoculated for feed protein preservation and flavor enhancement. Our results provided insight and practical guidance for the high-value use of distillers’ grains.
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