The gastrointestinal tract (GIT) and the accessory digestive organs (teeth, tongue, salivary glands, liver, gallbladder, and pancreas) together constitute the digestive system whose function is to break down dietary constituents into small molecules and then to absorb these molecules for subsequent distribution throughout the body. The GIT is, basically, a continuous tube extending from the mouth to the anus (Figure 7.1). The main regions of the GIT include the oral cavity, the oropharynx, and laryngopharynx (which are also part of the respiratory tract), oesophagus, stomach, small intestine (duodenum, jejunum, and ileum), and the large intestine (caecum, colon, and rectum). Because of differences in their anatomy, physiology, organisation, and location, each of these regions provides a different set of environmental conditions for potential microbial colonisers and has, therefore, a distinctive microbiota. Although each of these regions is distinctly different, the oral cavity has some unique features (e.g., a complex anatomy leading to a great variety of habitats, the presence of non–shedding surfaces; i.e., teeth, which enable biofilm formation and a high oxygen content), which render it very different from the rest of the GIT. In contrast, the other regions of the GIT have a far simpler structure (basically, tubular in nature), which results in a lower habitat diversity within a particular region, non–shedding surfaces are absent, most regions (below the stomach) are anaerobic, and many regions (within the large intestine) have a lumen which is usually filled with material.