Intestinal microbiota have become the subject of intense investigation in inflammatory bowel disease (IBD) over the past years after some groups demonstrated that significant alterations of the composition of enteric bacteria might be related to the underlying inflammatory process (Gut 2006;55:205–11).^1–4 However, the complexity of the intestinal microbiota and the availability of a variety of different experimental approaches generated sometimes conflicting and inconsistent data. Manichanh et al (Gut 2006;55:205–11) recently published an extensive study using metagenomic libraries, a novel molecular technique allowing the recruitment of …