Probiotics play an important role in animal production, providing health benefits to the host by improving intestinal microbial balance. In this study, we added three different probiotics, Saccharomyces cerevisiae (SC), Bacillus licheniformis (BL), and lactic acid bacteria (LAB), and compared them with the control group (CON), to investigate the effects of probiotic supplementation on growth performance, gut microbiology, and gut flora of S. trutta. Our results showed that feeding probiotics improved the survival, growth, development, and fattening of S. trutta. Additionally, probiotic treatment causes changes in the gut probiotic community, and the gut flora microorganisms that cause significant changes vary among the probiotic treatments. However, in all three groups, the abundance of Pseudomonas, Acinetobacter, and Rhizophagus bacterial genera was similar to that in the top three comparative controls. Furthermore, differences in the composition of intestinal microbiota among feed types were directly associated with significant changes in the metabolomic landscape, including lipids and lipid-like molecules, organic acids and derivatives, and organoheterocyclic compounds. The probiotic treatment altered the gut microbiome, gut metabolome, and growth performance of S. trutta. Using a multi-omics approach, we discovered that the addition of probiotics altered the composition of gut microbiota, potentially leading to modifications in gut function and host phenotype. Overall, our results highlight the importance of probiotics as a key factor in animal health and productivity, enabling us to better evaluate the functional potential of probiotics.

In this study, we screened the expression stability of six reference genes (18S rRNA, β-actin, GAPDH, EF1a, B2M, and HPRT1) in hybrid yellow catfish (n6), considering the SBM levels, sampling time points, and different tissues. Four different statistical programs, BestKeeper, NormFinder, Genorm, and Delta Ct, combined with a method that comprehensively considered all results, were used to evaluate the expression stability of these reference genes systematically. The results showed that SBM levels significantly impacted the expression stability of most of the reference genes studied and that this impact was time-, dose-, and tissue-dependent. The expression stability of these six reference genes varied depending on tissue, sampling time point, and SBM dosage. Additionally, more variations were found among different tissues than among different SBM levels or sampling time points. Due to its high expression, 18S rRNA was excluded from the list of candidate reference genes. β-actin and GAPDH in the liver and β-actin, HPRT1 and EF1a in the intestine were the most stable reference genes when SBM levels were considered. HPRT1, and EF1a in tissues sampled at 2W and EF1a and β-actin in tissues sampled at 4 and 6W were proposed as two stable reference genes when different tissues were considered. When the sampling time points were considered, β-actin, EF1a, and HPRT1 were the top three stable reference genes in the intestine. In contrast, β-actin and B2M are the most stable reference genes in the liver. In summary, β-actin, EF1a, and HPRT1 were the more stable reference genes in this study. The stability of reference genes depends on the tissues, sampling time points, and SBM diet levels in hybrid yellow catfish. Therefore, attention should be paid to these factors before selecting suitable reference genes for normalizing the target genes.

The effects of berberine (BBR) on intestinal health suffering from soybean meal (SBM)-induced enteritis (SBMIE) in hybrid yellow catfish (Pelteobagrus fulvidraco ♀ × Pelteobagrus vachelli ♂) were investigated in this study, focusing specifically on oxidant-antioxidant capacity, intestinal morphology, microbiota homeostasis and tryptophan catabolites. A total of 270 individuals with the initial body weight (IBW) of 23.27 ± 0.60 g were randomly divided into 9 tanks at the density of 30 fish per tank. Three diets, the SBM diet (75% of fish meal substituted by SBM, SBM), BBR1 (75 mg/kg BBR was added to the SBM diet, BBR1) and BBR2 diet (150 mg/kg BBR was added to the SBM diet, BBR2), were used to feed fish for 42 d. The results indicated that the final body weight (FBW), weight gain rate (WGR) and specific growth rate (SGR) were all significantly increased in BBR2 group compared with SBM group (P < 0.05). Intestinal barrier proteins and genes (ZO-1 and occludin) expression (P < 0.05) and intestinal interleukin-10 (IL-10) content (P = 0.001) were all greatly improved with BBR administration, especially in the BBR2 group. The apoptosis related genes (caspase 3 and caspase 9) (P < 0.05) of intestinal epithelium cells were also significantly reduced by dietary BBR compared with SBM group. Comparative analysis of intestinal microbial composition and tryptophan catabolites between the SBM group and BBR2 group revealed that BBR significantly ameliorated the imbalance of intestinal microbiota and improved the intestinal tryptophan catabolites, especially reflected in the relative abundance of Romboutsia and the levels of L-5-hydroxytryptophan (L-5-HTP), indole-3-acetic acid (IAA) and kynurenine (KYN) in intestinal contents (P < 0.05). As a result, the aryl hydrocarbon receptor (AhR) signaling was then activated. Correlation analyses showed that the relative abundance of Romboutsia was positively correlated with IAA and KYN levels in the intestinal contents (P < 0.05), and negatively correlated with interleukin-1 beta (IL-1β) and interleukin-6 (IL-6) levels in hindgut (P < 0.01). The levels of L-5-HTP, IAA, and KYN in intestinal contents were positively correlated with key factors of hindgut AhR signaling pathway, tight junctions (TJs) and anti-inflammatory cytokines (P < 0.05). Kyoto Encyclopedia of Genes and Genomes (KEGG) functional prediction results showed that the intestinal microbial functions were mainly enriched in metabolic pathways, including amino acid metabolism, carbohydrate metabolism, and metabolism of cofactors and vitamins. In conclusion, BBR ameliorated SBMIE in hybrid yellow catfish by reducing oxidative stress, enhancing antioxidant and anti-inflammatory capacity, alleviating intestinal pathological damage and microbial dysbiosis. The microbiota-tryptophan catabolite-AhR axis may play an essential role in this protective process.