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RNA sequencing analysis of commensal microbial regulation of host intestinal transcriptome
Author(s) -
Fu Zidong Donna,
Selwyn Felcy Pavithra,
Cui Julia Yue
Publication year - 2017
Publication title -
the faseb journal
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.709
H-Index - 277
eISSN - 1530-6860
pISSN - 0892-6638
DOI - 10.1096/fasebj.31.1_supplement.668.5
Subject(s) - duodenum , ileum , jejunum , biology , transcriptome , biochemistry , small intestine , gene , gene expression , medicine
Commensal microbiota can regulate intestinal physiology by modifying host genes. To identify host responses induced by commensal microbiota along the intestine, transcriptomes of duodenum, jejunum, ileum, and large intestine (LI) were compared between germ‐free (GF) mice and conventional (CV) controls using RNA sequencing. Cuffdiff (FDR‐BH<0.05) revealed that jejunum had the highest number of differentially expressed genes (2137) between CV and GF mice, followed by LI (781), duodenum (392), and ileum (329). Pathway analysis (GSAA, FDR<0.05) identified that protein digestion and absorption was the most up‐regulated pathway in duodenum and LI, whereas ribosome (duodenum) and protein processing in endoplasmic reticulum (LI) ranked among the top most down‐regulated pathways in GF mice. Notably, caboxypeptidase a1 (Cpa1) and chymotrypsin‐like elastase family member 3b (Cela3b), which were previously thought to be pancreatic‐specific enzymes, ranked among the top 10 most up‐regulated genes within the entire transcriptomes in duodenum and LI of GF mice. Whereas Cpa1 is involved in cleaving C‐terminal branched‐chain and aromatic amino acid from dietary proteins, Cela3b preferably cleaves proteins after alanine residues and may also function in the intestinal transport and cholesterol metabolism. Xenobiotic metabolism by cytochrome P450s (Cyp) was down‐regulated in duodenum and ileum of GF mice. Notably, Cyp1a1 ranked among the top 10 most down‐regulated genes in duodenum and ileum of GF mice. Cyp3a cluster was down‐regulated in duodenum of GF mice. Conversely, enzymes involved in alcohol and aldehyde oxidation were up‐regulated in jejunum of GF mice. Although drug‐metabolizing enzymes were generally thought to be more important in small intestine, there was a consistent up‐regulation in Cyp2d and aldo‐keto reductase 1c (Akr1c) isoforms in LI of GF mice, suggesting the importance of LI in xenobiotic metabolism in absence of intestinal microbiota. For carbohydrate metabolism, glycolysis/gluconeogenesis was down‐regulated in ileum, whereas starch and sucrose metabolism was up‐regulated in LI of GF mice. For lipid metabolism, the cholesterol synthesis and triglyceride synthesis were up‐regulated in ileum and jejunum of GF mice, respectively. Fatty acid binding protein 6 (Fabp6/Ibabp) was the most down‐regulated gene in jejunum of GF mice. The lack of intestinal microbiota also alter the mRNA expression of genes involved in the absorption of water and ion, mineral, vitamin, nucleotides, and bile acids, immune response, and cell junction. Taken together, we have identified that segment‐specific host gene alterations were induced in GF conditions, and the intestinal microbiota may impact a lot more key metabolic pathways than previously anticipated.