Integrated Microbiome and Metabolomics Analysis of the Effects of Dietary Supplementation with Corn-Steep-Liquor-Derived Candida utilis Feed on Black Pigs

Simple Summary Yeast protein feeds have the potential to replace other protein source feeds. Accordingly, in this paper, we used the industrial and agricultural byproducts of glucose master liquor and corn steep liquor as substrates, and utilized Candida utilis for fermentation. Firstly, the medium components of yeast protein feed were optimized, and then the optimized yeast protein feed was fed to weaned Dongliao black piglets; the feeding effect was analyzed using 16S rDNA and metabolomics. We found that Candida utilis feed has no adverse effects on the growth performance of the pigs and that it improves blood lipids and other indicators. A total of 10 plasma metabolites were correlated with 27 genera of bacteria, as revealed by the results of the combined multi-omics analysis, which were mainly enriched in the pathways of primary bile acid metabolism, histidine metabolism, and tryptophan metabolism. The results show that Candida utilis feed can maintain the growth performance of the pigs and enhance their immunity and maintenance of gut flora homeostasis; this likely occurs through amino acid metabolism. Abstract In this experiment, glucose master liquor and corn steep liquor were used as carbon and nitrogen sources, and Candida utilis was used as a strain to ferment yeast feed. The OD value and number of yeast cells were used as response values to optimize the medium components of the yeast feed through a response surface methodology. The optimal medium components were a glucose master liquor concentration of 8.3%, a corn steep liquor concentration of 1.2%, and a KH2PO4 concentration of 0.14%. Under this condition of fermentation, the OD value was 0.670 and the number of yeast cells was 2.72 × 108/mL. Then, we fed Candida utilis feed to Dongliao black piglets, and the effects of the yeast feed on the piglets’ growth performance, fecal microbiota, and plasma metabolic levels were investigated through 16S rDNA sequencing and metabolomics. In total, 120 black piglets with an average initial weight of 6.90 ± 1.28 kg were randomly divided into two groups. One group was fed the basic diet (the CON group), and the other was supplemented with 2.5% Candida utilis add to the basic diet (the 2.5% CU group). After a pre-feeding period, the formal experiments were performed for 21 days. The results showed that the addition of Candida utilis to the diet did not affect growth performance compared with the control group. Meanwhile, no significant differences were observed in the serum biochemical indices. However, piglets in the 2.5% CU group had a significantly altered fecal microbiota, with an increased abundance of Clostridium_sensu_stricto_1, Lactobacillus, and Muribaculaceae_unclassified. Regarding the plasma metabolome, the 12 differential metabolites detected were mainly enriched in the histidine, tryptophan, primary bile acid, and caffeine metabolic pathways. Regarding the integrated microbiome–metabolome analysis, differential metabolites correlated with fecal flora to variable degrees, but most of them were beneficial bacteria of Firmicutes. Collectively, dietary Candida utilis feed had no adverse effect on growth performance; however, it played an important role in regulating fecal flora and maintaining metabolic levels.