# The Analysis of Transcriptomes and Microorganisms Reveals Differences Between the Intestinal Segments of New Zealand Rabbits

## TL;DR

This study explores how different parts of the rabbit intestine differ in nutrient transport, immune responses, and microbes, revealing specialized functions along the intestinal tract.

## Contribution

The study provides transcriptome-based evidence for regional specialization in rabbit intestinal physiology and host–microbe interactions.

## Key findings

- Small intestine shows higher expression of genes for amino acid, sugar, and bile salt transport.
- Large intestine is enriched in genes related to water absorption and short-chain fatty acid metabolism.
- Microbial diversity is higher in the large intestine, dominated by Firmicutes and Bacteroidetes.

## Abstract

We collected five different intestinal segments from the intestinal tract of New Zealand rabbits, analyzed the key differences in nutrient transport, immune responses, and microbial ecology among different segments of the intestine, and explored the interaction between the transcriptome and microbiota, providing important insights into rabbit intestinal physiology and laying the foundation for understanding host–microbe crosstalk in the New Zealand rabbit model.

This study systematically characterized functional compartmentalization along the intestinal tract of New Zealand rabbits by analyzing mucosal tissue and luminal contents from distinct segments, including the duodenum, jejunum, ileum, cecum, and colon, using RNA-seq and 16S rRNA sequencing. Transcriptomic analysis revealed that differentially expressed genes identified between the small and large intestines were mainly enriched in digestion, absorption, and immune functions. Genes associated with the transport of amino acids, sugars, vitamins, and bile salts showed significantly higher expression in the small intestine, whereas genes related to water absorption, short-chain fatty acids (SCFAs), nucleotides, and metal ion transport were preferentially expressed in the large intestine. From an immunological perspective, genes involved in fungal responses were enriched in the small intestine, while bacterial response pathways and pattern recognition receptor (PRR) signaling genes were upregulated in the large intestine. Microbiota analysis demonstrated significantly greater diversity and abundance in the large intestine compared with the small intestine. Specifically, Proteobacteria and Actinobacteria were enriched in the small intestine, whereas Firmicutes, Verrucomicrobia, and Bacteroidetes dominated the large intestine. Correlation analysis further identified significant associations between gut microbiota composition and host genes involved in nutrient digestion and absorption. Together, these findings provide transcriptome-based evidence for regional specialization of nutrient transport, immune responses, and microbial ecology along the rabbit intestine.