Transcriptional response of colon or small-intestinal tissues to bacterial colonization ex-vivo

We analyzed the transcriptional profile of colon and small-intestinal (SI) tissues in response to ex-vivo colonization with members of the gut microbiota. Tissues were dissected from SPF or GF mice, and connected to the ex-vivo gut organ culture system. Then, microbial cultures or fecal samples were infused into the lumen, and tissues were processed in different time points, as indicated below. A small 3-5 mm segment of the proximal colon or SI terminal ileum of mice was placed directly into TRIzol.