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The human gastrointestinal tract is colonized throughout its length by complex luminal and mucosal microbiotas. Owing to sampling restrictions, most of the studies done to date have concentrated on luminal material. Recently, however, there has been an upsurge in interest in the role of microbial communities that occur in biofilms on surfaces in the gut. In the human biota, biofilms have been shown to exist on artificial surfaces and devices implanted in the host, on particulate materials in the gut lumen, and on the colonic mucosa. Owing to their proximity to host tissues, mucosal bacteria interact more readily with the gut epithelium and immune system than their luminal counterparts, and recent research indicates that they play an important role in health and disease processes. Because bacteria growing in biofilms are more resistant to antibiotics than their luminal counterparts, there is increased interest in the use of alternative therapeutic strategies to target potential pathogens on the mucosal surface, especially with respect to applications involving probiotics, prebiotics, and synbiotics.