The Analysis of Transcriptomes and Microorganisms Reveals Differences between the Intestinal Segments of Guinea Pigs

SIMPLE SUMMARY: Functional differences between the various segments of the intestine and differences in the intestines between species have been demonstrated in previous studies. Guinea pigs are commonly used model animals in intestinal-related research. As well as modeling disease states, it is important to study the intestinal tract of guinea pigs to derive basic data for the rational use of guinea pig models. Therefore, we collected six different segments of the intestinal tissue of guinea pigs and analyzed the gene expression profiles and microbial composition of each of these regions. The results revealed the functional regionalization of the intestine, with changes in functional gene expression between different intestinal segments, an association between microbial abundance and gene expression, and differences in intestinal gene expression between different species. Our study provides a reference for future intestinal-related research. ABSTRACT: The intestine is a tubular organ with multiple functions such as digestion absorption and immunity, but the functions of each intestinal segments are different. Intestinal regionalization is necessary for normal physiological function, but it also means the research results obtained at specific sites may not be applicable to other intestinal segments. In order to comprehensively describe the functional changes in the intestine, different intestinal segments and their contents (duodenum, jejunum, ileum, cecum, colon, and rectum) of guinea pigs were collected for RNA seq and 16S rRNA seq, respectively. The results showed differential genes of each intestinal segment mainly involve mucosa, digestion, absorption, and immunity. The gene sets related to fat, bill salts, vitamins, aggregates, amino acids, and water absorption were highly expressed in the small intestine, and the gene sets related to metal ions, nucleotides, and SCFAs were highly expressed in the large intestine. In terms of immunity, the CD8(+) T, Th1, eosinophils, pDCs, and natural killer (NK) T cells in the small intestine showed higher scores than those in the large intestine, while the pattern-recognition receptor signaling pathway-related genes are highly expressed in the large intestine. In terms of microbial composition, Proteobacteria and Actinobacteria are abundant in the small intestine, while Firmicutes and Spirochaete are abundant in large intestine. The correlation analysis showed a high correlation between intestinal microorganisms and gene modules related to digestion and absorption. In addition, cross-species analysis showed the SCFA metabolism gene expression trends in human and rodent intestine were different. In conclusion, we analyzed the changes in substance transport, immune and microbial composition between different intestinal segments of guinea pigs, and explored the relationship between intestinal transcriptome and microorganisms, our research will provides a reference for subsequent intestinal-related research.