Anatomy and Normal Microbiota of the GI Tract


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The small intestines with increasing magnification. A) is a diagram and b), c), and d) are micrographs of each magnification. The micrograph of the larges magnification shows a pink region on the bottom with a deeply waved darker pink region at the surface; the top of the image is clear. There are some darker patches in the bottom layer labeled Peyer’s patches. The diagram sows a tube lined with three layers of muscle; blood vessels connected to the outside of the tube. A cutout of the tube shows circular folds along the diameter of the tube. These folds contain deeply lobed villi. The empty space in the tube is labeled lumen. The next layer of magnification is one of the vili. The micrograph is filled with pink layers folding back and forth. The diagram shows two folds. The surface of the fold is covered with absorptive cells and some goblet cells. Between the folds is further indent labeled intestinal crypt. Inside the folds are capillaries, arteries, and lymphatic vesicles. At the very bottom of the structure (below the blood and lymph vessels, are a few duodenal glands. The final close-up shows finger-shapes in a row on the surface of a cell. These are labeled microvilli (brush border) on the diagram.
(a) The structure of the wall of the small intestine allows for the majority of nutrient absorption in the body. (b) Villi are folds in the surface of the small intestine. Microvilli are cytoplasmic extensions on individual cells that increase the surface area for absorption. (c) A light micrograph shows the shape of the villi. (d) An electron micrograph shows the shape of the microvilli. (credit b, c, d: Modification of micrographs provided by the Regents of University of Michigan Medical School © 2012)

OpenStax Microbiology

As food leaves the oral cavity, it travels through the pharynx, or the back of the throat, and moves into the esophagus, which carries the food from the pharynx to the stomach without adding any additional digestive enzymes. The stomach produces mucus to protect its lining, as well as digestive enzymes and acid to break down food. Partially digested food then leaves the stomach through the pyloric sphincter, reaching the first part of the small intestine called the duodenum. Pancreatic juice, which includes enzymes and bicarbonate ions, is released into the small intestine to neutralize the acidic material from the stomach and to assist in digestion. Bile, produced by the liver but stored in the gallbladder, is also released into the small intestine to emulsify fats so that they can travel in the watery environment of the small intestine. Digestion continues in the small intestine, where the majority of nutrients contained in the food are absorbed. Simple columnar epithelial cells called enterocytes line the lumen surface of the small intestinal folds called villi. Each enterocyte has smaller microvilli (cytoplasmic membrane extensions) on the cellular apical surface that increase the surface area to allow more absorption of nutrients to occur.

Digested food leaves the small intestine and moves into the large intestine, or colon, where there is a more diverse microbiota. Near this junction, there is a small pouch in the large intestine called the cecum, which attaches to the appendix. Further digestion occurs throughout the colon and water is reabsorbed, then waste is excreted through the rectum, the last section of the colon, and out of the body through the anus.

The environment of most of the GI tract is harsh, which serves two purposes: digestion and immunity. The stomach is an extremely acidic environment (pH 1.5–3.5) due to the gastric juices that break down food and kill many ingested microbes; this helps prevent infection from pathogens. The environment in the small intestine is less harsh and is able to support microbial communities. Microorganisms present in the small intestine can include lactobacilli, diptherioids and the fungus Candida. On the other hand, the large intestine (colon) contains a diverse and abundant microbiota that is important for normal function. These microbes include Bacteriodetes (especially the genera  Bacteroides  and  Prevotella) and Firmicutes (especially members of the genus Clostridium). Methanogenic archaea and some fungi are also present, among many other species of bacteria. These microbes all aid in digestion and contribute to the production of feces, the waste excreted from the digestive tract, and flatus, the gas produced from microbial fermentation of undigested food. They can also produce valuable nutrients. For example, lactic acid bacteria such as bifidobacteria can synthesize vitamins, such as vitamin B12, folate, and riboflavin, that humans cannot synthesize themselves. E. coli found in the intestine can also break down food and help the body produce vitamin K, which is important for blood coagulation.

The GI tract has several other methods of reducing the risk of infection by pathogens. Small aggregates of underlying lymphoid tissue in the ileum, called Peyer’s patches, detect pathogens in the intestines via microfold (M) cells, which transfer antigens from the lumen of the intestine to the lymphocytes on Peyer’s patches to induce an immune response. The Peyer’s patches then secrete IgA and other pathogen-specific antibodies into the intestinal lumen to help keep intestinal microbes at safe levels. Goblet cells, which are modified simple columnar epithelial cells, also line the GI tract. Goblet cells secrete a gel-forming mucin, which is the major component of mucus. The production of a protective layer of mucus helps reduce the risk of pathogens reaching deeper tissues.

The constant movement of materials through the gastrointestinal tract also helps to move transient pathogens out of the body. In fact, feces are composed of approximately 25% microbes, 25% sloughed epithelial cells, 25% mucus, and 25% digested or undigested food. Finally, the normal microbiota provides an additional barrier to infection via a variety of mechanisms. For example, these organisms outcompete potential pathogens for space and nutrients within the intestine. This is known as competitive exclusion. Members of the microbiota may also secrete protein toxins known as bacteriocins that are able to bind to specific receptors on the surface of susceptible bacteria.

Micrograph of intestinal villi which are 2 pink regions separated by a clear space. The surface of each pink band is darker pink than the center and the surface contains lighter pink oval cells labeled goblet cells.
A magnified image of intestinal villi in the GI tract shows goblet cells. These cells are important in producing a protective layer of mucus.

Source: OpenStax Microbiology


Parker, N., Schneegurt, M., Thi Tu, A.-H., Forster, B. M., & Lister, P. (n.d.). Microbiology. Houston, Texas: OpenStax. Access for free at: