Until recently, it’s been difficult to study the mucus layers in the GI tract because upon exposure to air, the mucus loses all of its liquid content and adheres in a thin sheen to human epithelial cells[i]. Most of the actual knowledge of the mucus layers comes from studies on the colon. We do know that the small intestinal wall contains goblet cells to secret mucus, so we can infer that the mucus layer serves as a protective physical barrier and selective force in the stomach, small intestine, and lower intestine[ii]. The two layers of mucus are divided into the sterile dense layer that adheres to the epithelial cells (imaginatively called the adherent layer) and the more loosely organized free-flowing upper layer. Think of it like the silty bottom of a river with the moving water up top. In the small intestine this moving water quickly zips through. In the lower intestine, the movement slows down to a lazy river pace, allowing many microbial communities to form.
The lower intestine (colon) is truly an urban space. Every available piece of real estate is developed into microbial homes. These structures—called biofilms—functionally resemble skyscrapers that reach into the hollow space outside the mucus layer, waving in the flowing river of nutrients and mucus and housing millions of microbes from a single colony.
By the time the our internal river that began in our mouths gets to the colon (the most studied geography of all the gut ecosystems) all the easy stuff to digest has been mostly absorbed into the blood by epithelial cells which are not very efficient, rejecting perfectly good sources of energy like cellulose. These indigestible compounds make their way from the small intestine into the colon. At this point, our human cells have pretty much finished doing the direct work of gleaning energy, so the microbial rabble takes over. The topology of the lower gut consists of the valleys and peaks of the mucus membrane minus the villi and crypts of the small intestine, potentially making interactions between human, microbial, and viral entities more prevalent here (though comparative studies haven’t been done). The epithelial lining of the lower intestine contains far more goblet cells than that of the upper. Thus, the lower intestine secretes more mucus which serves simultaneously as a barrier, a site for microbes to establish their niche, and a hideout for viral predators, waiting for just the right victim.