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

Area of Science:

• Animal Science
• Molecular Biology
• Immunology

Background:

• China's 2020 ban on antibiotic use in animal agriculture presents challenges, potentially reducing feed efficiency and increasing animal mortality.
• Understanding the host's response to antibiotic-free diets is crucial for maintaining animal health and productivity.
• Diarrhea in rabbits fed antibiotic-free diets necessitates research into underlying pathogenesis and immune mechanisms.

Purpose of the Study:

• To investigate the pathogenesis and host immune response in rabbits experiencing diarrhea after transitioning to an antibiotic-free diet.
• To identify differentially expressed genes (DEGs) in various intestinal segments of rabbits under antibiotic-free conditions.
• To elucidate the molecular mechanisms underlying the host's transcriptome alterations in response to an antibiotic-free diet.

Main Methods:

• Analysis of intestinal tissue sections from healthy and diarrheic rabbits on an antibiotic-free diet.
• High-throughput sequencing to analyze gene expression differences across rabbit intestinal segments (duodenum, jejunum, ileum, cecum, colon, rectum).
• Validation of differentially expressed genes (DEGs) using quantitative real-time PCR (RT-qPCR).
• Enrichment analyses of Gene Ontology (GO) annotations and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.

Main Results:

• Identified a significant number of DEGs in all analyzed intestinal segments when comparing healthy rabbits to those with diarrhea on an antibiotic-free diet.
• GO and KEGG pathway analyses indicated that DEGs are associated with acute inflammation, stress responses, tissue dehydration, adaptive immunity, protein binding, enzyme activation, and immune cell migration.
• The antibiotic-free diet altered the host's metabolic network and the expression of antiviral proteins.

Conclusions:

• Feeding an antibiotic-free diet significantly alters the host's transcriptome profile in rabbits, particularly affecting immune and metabolic pathways.
• The observed changes suggest a complex host response involving inflammation, immune activation, and metabolic adjustments.
• Findings provide a foundational understanding for further research into the immune responses and health management of animals on antibiotic-free diets.