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and the microbes living in the mucus layer of theProvidence, RI, USA Full list of author information is available at the end of the articleBackground In recent years, clinical research has highlighted the im-portant role of commensal gut microbes in human health. The gut microbiota not only plays a major role in health, but also in the etiopathogenesis of complex immune disor-ders such as inflammatory bowel diseases, type I diabetes, metabolic disorders, irritable bowel syndrome, and cancer [1-8]. Most studies of human gut microbial communities rely on the non-invasive collection of stool samples. While this has proven informative, analyses of the fecal microbiota may miss opportunities to understand the role of the mucosa-associated microbes, which live in close proximity to the intestinal epithelium and may not be adequately rep-resented in the luminal (fecal) samples. The mucosa-associated microbes may also play a more important role in diseases such as inflammatory bowel disease (IBD), where direct interactions likely occur between the host immun