The Multi-Omics Analysis Revealed Microbiological Regulation of Rabbit Colon with Diarrhea Fed an Antibiotic-Free Diet

Simple Summary After being fed an antibiotic-free diet, some rabbits showed typical diarrhea symptoms. In order to explore the reasons, this study used multiple omics analysis. Bacteroidetes and Proteobacteria were significantly upregulated in the colon of diarrhea rabbits, and the ratio of Firmicutes to Bacteroidetes was decreased. The significantly upregulated differential genes were mainly enriched in the IL-17 signaling pathway and were involved in promoting inflammatory response. The different metabolites were mainly enriched in tryptophan metabolism and bile secretion, which affected the anti-inflammatory function. In addition, Bacteroides is positively correlated with 4-Morpholinobenzoic acid and Diacetoxyscirpenol, which is believed to be an important cause of inflammation. The enrichment of Proteobacteria is also related to the high expression of the IL-17 signaling pathway. Diarrhea symptoms appeared after antibiotics were banned from animal feed based on the law of the Chinese government in 2020. The colon and its contents were collected and analyzed from diarrheal and healthy rabbits using three omics analyses. The result of the microbial genomic analysis showed that the abundance of Bacteroidetes and Proteobacteria increased significantly (p-value < 0.01). Transcriptomes analysis showed that differentially expressed genes (DEGs) are abundant in the IL-17 signaling pathway and are highly expressed in the pro-inflammatory pathway. The metabolome analysis investigated differential metabolites (DMs) that were mainly enriched in tryptophan metabolism and bile secretion, which were closely related to the absorption and immune function of the colon. The results of correlation analysis showed that Bacteroidetes was positively correlated with 4-Morpholinobenzoic acid, and 4-Morpholinobenzoic acid could aggravate inflammation through its influence on the bile secretion pathway. The enriched DMs L-Tryptophan in the tryptophan metabolism pathway will lead to the functional disorder of inhibiting inflammation by affecting the protein digestion and absorption pathway. Thus, the colonic epithelial cells were damaged, affecting the function of the colon and leading to diarrhea in rabbits. Therefore, the study provided an idea for feed development and a theoretical basis for maintaining intestinal tract fitness in rabbits.