Rice bran is a premium agricultural byproduct rich in nutrients and bioactive substances. The aim of this study was to compare the effects of fermentation with Bacillus subtilis, Lactobacillus plantarum, and a mixture of both on the bacterial communities and metabolic functions of rice bran based on omics techniques. The results showed that probiotic fermentation decreased crude fiber (CF) content, phytic acid, and trypsin inhibitor activity (TIA), and increased trichloroacetic acid soluble protein (TCA-SP), reducing sugar (RS), and total phenol (TP) in rice bran. Ten dominant genera with relative abundances greater than 1% were successfully identified, and probiotic fermentation significantly reduced the relative abundances of Enterobacter, Kasakonia, and Pantoea. A total of 63 differentially expressed metabolites (DEMs) were identified and further analysis revealed that probiotic fermentation increased essential amino acids, phenolic compounds, and organic acids in rice bran. Additionally, the di-strain probiotic fermentation of Bacillus subtilis and Lactobacillus plantarum facilitated the growth of beneficial microbiota (Limosilactobacillus, Prevotella and Dialister) and the production of bioactive substances (lactic acid, catechol, beta-tyrosine, etc.). In conclusion, co-fermentation of di-strain probiotics is a valuable method to produce functional compounds and enhance the health-promoting properties of rice bran.
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