Anatomy and Normal Microbiota of the Digestive System

The human digestive system, or the gastrointestinal (GI) tract, begins with the mouth and ends with the anus. The parts of the mouth include the teeth, the gums, the tongue, the oral vestibule (the space between the gums, lips, and teeth), and the oral cavity proper (the space behind the teeth and gums). Other parts of the GI tract are the pharynx, esophagus, stomach, small intestine, large intestine, rectum, and anus. Accessory digestive organs include the salivary glands, liver, gallbladder, spleen, and pancreas.

The digestive system contains normal microbiota, including archaea, bacteria, fungi, protists, and even viruses. Because this microbiota is important for normal functioning of the digestive system, alterations to the microbiota by antibiotics or diet can be harmful. Additionally, the introduction of pathogens to the GI tract can cause infections and diseases. In this section, we will review the microbiota found in a healthy digestive tract and the general signs and symptoms associated with oral and GI infections.

Extended description

Reading top to bottom, the figure labels: the mouth and tongue; the salivary glands (the parotid gland at the very back of the mouth, the sublingual gland under the tongue, the submandibular gland below the jaw); the pharynx, a tube leading from the mouth; the esophagus, running down the neck to the stomach. In the upper torso: the liver (large, on the viewer’s left), the gallbladder (a small sac under the liver), the stomach, the spleen (on the viewer’s right, beside the stomach), and the pancreas (behind and below the stomach). The small intestine’s three regions follow in order: the duodenum, the jejunum, and the ileum. The large intestine’s regions follow: the cecum (with the appendix projecting from it), the ascending colon, the transverse colon, the descending colon, and the sigmoid colon, ending at the rectum, the anal canal, and the anus.

Anatomy and Normal Microbiota of the Oral Cavity

Food enters the digestive tract through the mouth, where mechanical digestion (by chewing) and chemical digestion (by enzymes in saliva) begin. Within the mouth are the tongue, teeth, and salivary glands, including the parotid, sublingual, and submandibular glands. The salivary glands produce saliva, which lubricates food and contains digestive enzymes.

Extended description

Panel (a), front to back: lips, jaw, and the tongue in the oral cavity; the nasal cavity above; the uvula at the back of the mouth; the pharynx, continuing down as the esophagus; and the larynx, which also connects to the pharynx but leads to the respiratory system — no teeth are labeled in this panel. Panel (b) shows the same head with the teeth and three labeled salivary glands: the sublingual gland below the tongue, the submandibular gland at the back and bottom of the mouth, and the parotid gland, the largest of the three, at the very back of the mouth near the ear.

The structure of a tooth begins with the visible outer surface, called the crown, which has to be extremely hard to withstand the force of biting and chewing. The crown is covered with enamel, which is the hardest material in the body. Underneath the crown, a layer of relatively hard dentin extends into the root of the tooth around the innermost pulp cavity, which includes the pulp chamber at the top of the tooth and pulp canal, or root canal, located in the root. The pulp that fills the pulp cavity is rich in blood vessels, lymphatic vessels, connective tissue, and nerves. The root of the tooth and some of the crown are covered with cementum, which works with the periodontal ligament to anchor the tooth in place in the jaw bone. The soft tissues surrounding the teeth and bones are called gums, or gingiva. The gingival space or gingival crevice is located between the gums and teeth.

Extended description

A brace on the left marks the crown, above the gum line, and a second brace marks the root, below the gum line. Labels on the right, top to bottom: enamel, the outermost layer of the crown; dentin, the layer beneath the enamel, equally thick in the crown and root; pulp cavity and pulp; gingival crevice, a small gap where the tooth meets the gum; gingiva (gums); bone, surrounding the root; pulp canal (root canal), inside the root; nerves and blood vessels, running through the pulp canal; and cementum, covering the outside of the root.

Microbes such as bacteria and archaea are abundant in the mouth and coat all of the surfaces of the oral cavity. However, different structures, such as the teeth or cheeks, host unique communities of both aerobic and anaerobic microbes. Some factors appear to work against making the mouth hospitable to certain microbes. For example, chewing allows microbes to mix better with saliva so they can be swallowed or spit out more easily. Saliva also contains enzymes, including lysozyme, which can damage microbial cells. Recall that lysozyme is part of the first line of defense in the innate immune system and cleaves the β-(1,4) glycosidic linkages between N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) in bacterial peptidoglycan (see Chemical Defenses). Additionally, fluids containing immunoglobulins and phagocytic cells are produced in the gingival spaces. Despite all of these chemical and mechanical activities, the mouth supports a large microbial community.

Check Your Understanding

Anatomy and Normal Microbiota of the GI Tract

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.

Extended description

Panel (a) has three parts. First, a segment of the intestinal tube lined with muscle layers, with a blood vessel entering from outside and the lumen labeled at the tube’s open center; a cutout shows circular folds bearing deeply lobed villi. Second, a magnified cutaway of two villus folds: the surface is covered with absorptive cells and goblet cells; capillaries, arteries, veins, and lymphatic vessels run inside each fold; the indentation between the folds is the intestinal crypt; darker patches beneath the folds are Peyer’s patches; and duodenal glands sit at the base of the tissue. Third, a close-up of one absorptive cell’s surface showing rows of finger-shaped microvilli, labeled the brush border. Panels (b), (c), and (d) are micrographs at increasing magnification — a light micrograph of whole villi (scale bar 1.5 mm), a closer light micrograph with a boxed region (scale bar 100 microns), and an electron micrograph of the microvilli from that boxed region (scale bar 100 nm).

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.

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General Signs and Symptoms of Oral and GI Disease

Despite numerous defense mechanisms that protect against infection, all parts of the digestive tract can become sites of infection or intoxication. The term food poisoning is sometimes used as a catch-all for GI infections and intoxications, but not all forms of GI disease originate with foodborne pathogens or toxins.

In the mouth, fermentation by anaerobic microbes produces acids that damage the teeth and gums. This can lead to tooth decay, cavities, and periodontal disease, a condition characterized by chronic inflammation and erosion of the gums. Additionally, some pathogens can cause infections of the mucosa, glands, and other structures in the mouth, resulting in inflammation, sores, cankers, and other lesions. An open sore in the mouth or GI tract is typically called an ulcer.

Infections and intoxications of the lower GI tract often produce symptoms such as nausea, vomiting, diarrhea, aches, and fever. In some cases, vomiting and diarrhea may cause severe dehydration and other complications that can become serious or fatal. Various clinical terms are used to describe gastrointestinal symptoms. For example, gastritis is an inflammation of the stomach lining that results in swelling and enteritis refers to inflammation of the intestinal mucosa. When the inflammation involves both the stomach lining and the intestinal lining, the condition is called gastroenteritis. Inflammation of the liver is called hepatitis. Inflammation of the colon, called colitis, commonly occurs in cases of food intoxication. Because an inflamed colon does not reabsorb water as effectively as it normally does, stools become watery, causing diarrhea. Damage to the epithelial cells of the colon can also cause bleeding and excess mucus to appear in watery stools, a condition called dysentery.

Check Your Understanding

Summary

• The digestive tract, consisting of the oral cavity, pharynx, esophagus, stomach, small intestine, and large intestine, has a normal microbiota that is important for health.
• The constant movement of materials through the gastrointestinal canal, the protective layer of mucus, the normal microbiota, and the harsh chemical environment in the stomach and small intestine help to prevent colonization by pathogens.
• Infections or microbial toxins in the oral cavity can cause tooth decay, periodontal disease, and various types of ulcers.
• Infections and intoxications of the gastrointestinal tract can cause general symptoms such as nausea, vomiting, diarrhea, and fever. Localized inflammation of the GI tract can result in gastritis, enteritis, gastroenteritis, hepatitis, or colitis, and damage to epithelial cells of the colon can lead to dysentery.
• Foodborne illness refers to infections or intoxications that originate with pathogens or toxins ingested in contaminated food or water.

Key terms

• Peyer’s patches — lymphoid tissue in the ileum that monitors and fights infections.
• periodontal disease — a condition in which the gums are inflamed and may erode.
• ulcer — open sore.
• gastritis — inflammation of the lining of the stomach.
• enteritis — inflammation of the lining of the intestine.
• gastroenteritis — inflammation of the lining of the stomach and intestine.
• hepatitis — inflammation of the liver.
• colitis — inflammation of the large intestine.
• dysentery — intestinal inflammation that causes diarrhea with blood and mucus.

Practice

Describe the major anatomical features of the human digestive system

Describe the normal microbiota of various regions in the human digestive system

Explain how microorganisms overcome the defenses of the digestive tract to cause infection or intoxication

Describe general signs and symptoms associated with infections of the digestive system

This section is adapted from Microbiology, Section 24.1: Anatomy and Normal Microbiota of the Digestive System by Nina Parker, Mark Schneegurt, Anh-Hue Thi Tu, Philip Lister, Brian M. Forster, and OpenStax, © OpenStax, licensed under CC BY-NC-SA 4.0. Access the original for free at openstax.org. Changes: all five figures re-encoded as WebP and rendered as mediafigures, kind="diagram" for the four labeled line-art figures (GITract, OralCavity, Tooth, Villi) and kind="photo" for the goblet-cell micrograph, after each image was inspected; GITract carries eager="true" as the page’s first figure; the GITract, OralCavity, Tooth, and Villi alts are rewritten as plain descriptions from the images (the source alts ran 552–1,224 characters and read as full label transcripts rather than accessible descriptions), with the full label walk-through moved into a longdesc for each; the GobletCell alt is likewise rewritten from the image; the Clinical Focus box’s “Jump to the next Clinical Focus box” link is replaced with a plain sentence naming that the case continues in Section 24.3 (authored this run); the two internal cross-references to figures already shown in the body (the GI-tract diagram, referenced a second time at the anus mention; the villi diagram, referenced a second time at the Peyer’s-patches mention) are dropped rather than repeated, since Hugo does not number figures and the sentences read cleanly without them; the cross-reference to Chemical Defenses (m58878) is rendered as a link to Section 17.2; the two source Multiple Choice items and the one Fill in the Blank item are adapted into Practice unchanged with their source keys (the Fill in the Blank’s four-word key “Large intestine or colon” becomes a textin keyed “large intestine” with “colon” in accept, per this book’s rule for a key printed as the module’s own “A or B” synonym pair); the section’s one unkeyed Short Answer question (“How does the diarrhea caused by dysentery differ from other types of diarrhea?”) is graded as a multiplechoice, since one sentence of the module fixes the whole answer, keyed to that sentence with distractors drawn from the module’s own sibling symptom sentences; none of the section’s three body Check Your Understanding bullets is fixed by a single module sentence, so all three remain self-checks with model answers assembled from this module’s own text; seven textin items fill out the four objective groups: three from ## Key terms (periodontal disease, ulcer, hepatitis) and four built from the module’s own body sentences for terms the source never bolds (cementum, Candida, competitive exclusion, bacteriocins); objective group 1 (“Describe the major anatomical features…”) has no source exercise of its own, so it is filled with two author-built multiplechoice fillers, each keyed to one module sentence (“Which layer of a tooth is the hardest material in the body?”, keyed Enamel, from “The crown is covered with enamel, which is the hardest material in the body”; “Which structure carries food from the pharynx to the stomach without adding any digestive enzymes?”, keyed The esophagus, from the esophagus sentence); key terms compiled from the module’s nine <term> elements (no repeats), all with a Glossary appendix entry; no source exercise, table, or Check Your Understanding bullet is omitted.