Transcriptomics Analysis Reveals the Immune Response Mechanism of Rabbits with Diarrhea Fed an Antibiotic-Free Diet

Abstract

China officially promulgated the announcement of banning the use of antibiotics in the animal industry in 2020. However, the prohibition of antibiotics in the animal industry would reduce the feed conversion rate and increase the mortality of animals. In order to obtain information about the pathogenesis and host immune response of rabbits with diarrhea after being fed an antibiotic-free diet, we first analyzed the intestinal tissue sections of rabbits. Secondly, the gene expression differences of rabbit intestinal segments were analyzed by high-throughput sequencing. Our analysis identified 168, 593, 2069, 334, 321, and 1423 DEGs in the comparison groups S_Z (the duodenum of healthy rabbits) vs. S_B (diarrhea in the duodenum of rabbits), K_Z (healthy rabbit jejunum) vs. K_B (rabbits with diarrhea in the jejunum), H_Z (healthy rabbit ileum) vs. H_B (rabbits with diarrhea in the ileum), M_Z (healthy cecum of rabbits) vs. M_B (rabbits with diarrhea in the cecum), J_Z (healthy rabbit colon) vs. J_B (colon of rabbits with diarrhea), and Z_Z (healthy rabbit rectum) vs. Z_B (rectum of rabbits with diarrhea), respectively. The reproducibility and repeatability of the results were validated by RT-qPCR. Enrichment analyses of GO annotations and KEGG pathways revealed the host DEGs that are potentially related to acute inflammation, stress response, tissue dehydration, adaptive immune response, protein binding, activation of related enzymes, migration of immune cells, and so on. In this descriptive study, our findings revealed the changes in the host transcriptome expression profile after feeding an antibiotic-free diet and suggested that feeding an antibiotic-free diet alters the host’s metabolic network and the expression of antiviral proteins, which provides a theoretical basis for further study on the immune response of animals fed an antibiotic-free diet.

A Parasite Odyssey: An RNA virus concealed inToxoplasma gondii

“…Due to a paucity of data within the family Narnaviridae , and the divergent nature of Ao, we re-queried Serratus for Ao-like RdRp palmprints. We retrieved and assembled 166 matching runs from 46 BioProjects with 32 species-like operational taxonomic units (sOTUs) (186 distinct virus-run observations, Supplementary Table S3) (Chen et al, 2022; Zhou et al, 2021; Gil and Hird, 2022; Gao et al, 2021; He et al, 2021; Chen et al, 2021b; Rhie et al, 2021; Bittner et al, 2022; Chen et al, 2021a; Xie et al, 2021; Cui et al, 2022; Wen et al, 2022; Zhou et al, 2022b; Sun et al, 2022; Wu et al, 2021). We recovered relevant Narnavirus RdRp contigs for all 32/32 (100%) sOTU, of which 22/32 (75%) contained a sufficiently long RdRp sequence ( ≈ 390 amino acids, motif F-E (Venkataraman et al, 2018) and thumb) for robust phylogenetic reconstruction.…”

Microbiome, Transcriptome, and Metabolomic Analyses Revealed the Mechanism of Immune Response to Diarrhea in Rabbits Fed Antibiotic-Free Diets

“…As a result, six healthy rabbits were randomly selected as the healthy group, and six rabbits with diarrhea were randomly selected as the diarrhea group. The selection of the diarrhea standard was based on the liver, intestinal, and sacculus rotundus histopathological diagnosis (Chen et al, 2021 ). The Animal Ethical Committee of Sichuan Agricultural University approved all the experimental procedures (approval number: 20210236).…”

“…The intestinal tissue of duodenum specimens was fixed with 4% paraformaldehyde, trimmed, dehydrated, embedded in paraffin, sectioned, dewaxed with xylene, stained with hematoxylin and eosin (HE), dehydrated with alcohol, and sealed with resin. The histological changes of the whole tissue sections were observed under a microscope (HE, bar = 100 μm, power = × 100), and normal areas and obvious lesion areas were recorded with a microscope imaging system (Chen et al, 2021 ).…”

Microbiomics Revealed the Disturbance of Intestinal Balance in Rabbits with Diarrhea Caused by Stopping the Use of an Antibiotic Diet

“…In addition, the expression profile of the host transcriptome of rabbits fed without antibiotics changed, and the differentially expressed genes may be related to model inflammation, adaptive immune response, etc. [ 23 ]. The intestinal flora of animals is necessary for the conversion of bile acids: a previous study found that the level of lithocholic acid produced by bile acid metabolism was significantly reduced in a group with diarrhea; lithocholic acid has a protective effect on the intestinal epithelial barrier and may be related to the pathogenesis of inflammatory bowel disease, meaning that metabolites and gut microbes interact [ 24 ].…”