Site-specific programming of the host epithelial transcriptome by the gut microbiota

Research output: Contribution to journalJournal articleResearchpeer-review

Felix Sommer, Intawat Nookaew, Nina Sommer, Per Fogelstrand, Gert Fredrik Bäckhed

BACKGROUND: The intestinal epithelium separates us from the microbiota but also interacts with it and thus affects host immune status and physiology. Previous studies investigated microbiota-induced responses in the gut using intact tissues or unfractionated epithelial cells, thereby limiting conclusions about regional differences in the epithelium. Here, we sought to investigate microbiota-induced transcriptional responses in specific fractions of intestinal epithelial cells. To this end, we used microarray analysis of laser capture microdissection (LCM)-harvested ileal and colonic tip and crypt epithelial fractions from germ-free and conventionally raised mice and from mice during the time course of colonization.

RESULTS: We found that about 10% of the host's transcriptome was microbially regulated, mainly including genes annotated with functions in immunity, cell proliferation, and metabolism. The microbial impact on host gene expression was highly site specific, as epithelial responses to the microbiota differed between cell fractions. Specific transcriptional regulators were enriched in each fraction. In general, the gut microbiota induced a more rapid response in the colon than in the ileum.

CONCLUSIONS: Our study indicates that the microbiota engage different regulatory networks to alter host gene expression in a particular niche. Understanding host-microbiota interactions on a cellular level may facilitate signaling pathways that contribute to health and disease and thus provide new therapeutic strategies.

Original languageEnglish
Article number62
JournalGenome Biology (Online Edition)
Pages (from-to)1-15
Number of pages15
Publication statusPublished - 2015

    Research areas

  • Animals, Epithelial Cells, Gastrointestinal Microbiome, Gastrointestinal Tract, Gene Expression Regulation, Immune System, Mice, Microarray Analysis, Microbiota, Signal Transduction, Transcriptome

ID: 156087693