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The GI tract is composed of four layers. Each layer has different tissues and functions. From the inside out they are called: mucosa, submucosa, muscularis, and serosa and . The mucosa is the absorptive and secretory layer. It is composed of simple epithelium cells and a thin connective tissue. There are specialized goblet cells that secrete mucus throughout the GI tract located within the mucosa. On the mucosa layer there are villi and microvilli.
The mucosa is the innermost layer of the gastrointestinal tract that is surrounding the lumen, or open space within the tube. This layer comes in direct contact with digested food (chyme). The mucosa is made up of three layers: epithelium, lamina propria, and muscularis mucosae. The epithelium is the innermost layer and it is responsible for most digestive, absorptive, and secretory processes. The lamina propria is a layer of connective tissue that is unusually cellular compared to most connective tissue. The muscularis mucosae is a thin layer of smooth muscle and its function is still under debate.
The mucosae are highly specialized in each organ of the gastrointestinal tract to deal with the different conditions. The most variation is seen in the epithelium. In the oesophagus, the epithelium is stratified, squamous, and non-keratinizing, for protective purposes. In the stomach it is simple columnar and is organized into gastric pits and glands to deal with secretion. The gastro-oesophageal junction is extremely abrupt. The small intestine epithelium (particularly the ileum) is specialized for absorption; it is organized into plicae circulares and villi, and the enterocytes have microvilli. This creates a brush border which greatly increases the surface area for absorption. The epithelium is simple columnar with microvilli. In the ileum there are occasionally Peyer's patches in the lamina propria. The colon has simple columnar epithelium with no villi. There are goblet cells. The appendix has a mucosa resembling the colon but is heavily infiltrated with lymphocytes. The ano-rectal junction (at the pectinate line) is again very abrupt; there is a transition from simple columnar to stratified squamous non-keratinizing epithelium (as in the oesophagus) for protective purposes.