Prokaryote Diversity of Epithelial Mucosal Biofilms in the Human Digestive Tract

The gastrointestinal epithelium is covered by a "natural biofilm" or protective mucus gel composed predominantly of mucin glycoproteins that are synthesized and secreted by host goblet cells. Thus, the gut mucosal biofilm is dynamic and interactive with contributions from both the host and resident bacterial community. This arrangement ensures that the indigenous intestinal microbiota are in continuous and intimate contact with host tissues where they outnumber the surrounding host cells by at least an order of magnitude. The protective functions of mucus can be considered as a dynamic defensive barrier rather than a static and constitutive structure. In this chapter we define the chemical composition, distribution, and functional properties of the gut mucosal biofilm. Enzymatic digestion of the mucus coat (mucolysis) by resident microbes provides access to readily available sources of carbon and energy. At present, mucus resident bacterial populations are poorly described for all animal species but our understanding of mucosal and luminal populations has been greatly enhanced by the application of molecular microbial ecology techniques which are cultivation independent. Research using these techniques to study bacterial populations in the intestinal tract according to age, location, and compartment is also compiled and compared in this contribution.