Bacterial community dynamics reveal its key bacterium, Bacillus amyloliquefaciens ZB, involved in soybean meal fermentation for efficient water-soluble protein production

Abstract Microbial fermentation can increase the water-soluble protein (WSP) contents of soybean meal, but the microbial community compositions and its functions remain unclear during the fermentation of soybean meal. In this study, the soybean meal was naturally fermented and the dynamics of bacterial community structure were determined. The results showed that natural fermentation can significantly increase the WSP content and digestive enzyme activities of soybean meal. The bacterial diversity indexes of soybean meal were increased and the community structure was significantly changed after fermentation. The bacterial community composition mainly consisted of Pseudomonas before fermentation, but it was almost completely replaced by Bacillus after 24 h of fermentation. The key operational taxonomic unit (OTU) for fermentation was screened as OTU161 from Bacillus, and its candidate strain was isolated from the fermented soybean meal and identified as Bacillus amyloliquefaciens ZB. Bioaugmented inoculation of ZB significantly increased the WSP content by 110.0%, 47.2%, and 473.7%, respectively, after 24, 72, and 96 h of fermentation and digestive enzyme activities by 16.1–41.8% during 24–48 h of fermentation, and shorten the fermentation time, compared to natural fermentation.