Co-occurrence network of microbes linking growth and immunity parameters with the gut microbiota in Nile tilapia (Oreochromis niloticus) after feeding with fermented soybean meal

The supplementation of fish feed with fermented soybean meal (FSBM) as an additive is widely used to produce aquatic feed. However, the mechanism by which FSBM regulates gut microbes in fish are still largely unknown. In the present work, soybean meal fermented by Lactobacillus fermentum (Lactobacillus group), Bacillus natto (Bacillus group), and Saccharomyces cerevisiae (Saccharomyces group) was added to fish diets, and the effects of these diets on gut microbiota, growth performance [Weight gain rate (WGR) and Specific growth rate (SGR)], and immunity [superoxide dismutase (SOD), lysozyme (LSZ) and alkaline phosphatase (AKP)] of Nile tilapia was assessed. Compared with Nontreated group, Lactobacillus and Saccharomyces fermented soybean meal remarkably improved the WGR, SGR, AKP, and LSZ (p < 0.05). The SOD activity was significantly lower in Bacillus group than other groups (p < 0.05). High-throughput sequencing of the V3-V4 region of the 16S rRNA gene was used to analyze the gut microbiota of Nile tilapia. PCoA and UPGMA showed that the similarity between the Saccharomyces and Lactobacillus groups was higher. Compared with Nontreated group, Lactobacillus fermented soybean meal significantly increased the Chao1 index and number of observed species (p < 0.05), while Bacillus fermented soybean meal remarkably improved the Simpson and Shannon indices (p < 0.01). Corynebacterium and Mycobacterium were significantly enriched in the Saccharomyces and Lactobacillus groups, and Aquabacterium and Acidovorax were significantly enriched in the Bacillus group. LEfSe analysis showed that Rhizobiales, Thermomicrobia, Myxococcales and Gemmatales were the biomarker in Lactobacillus group, Mycobacterium, Clavibacter and Coxiellaceae were the biomarker in Saccharomyces group, and Brevundimonas and Aquabacterium were the biomarker in Bacillus group. More interestingly, the co-occurrence network indicated that fish diets supplemented with L. fermentum or S. cerevisiae fermented soybean meal were more likely to impact some species that played pivotal roles in the network. L. fermentum- or S. cerevisiae- fermented SBM tended to activate similar “big team” species and promote their cooperation to perform certain functions. This research showed that FSBM fermented by L. fermentum, B. natto, and S. cerevisiae exerted different effect on growth, immunity, and gut microbiota of Nile tilapia, and the co-occurrence network of the microbiota could partially explain the relationship between the growth performance and immune parameters and the microbiomic data.