Gastrointestinal tract

# Overview
The digestive tract is the system of organs within multicellular animals that takes in food, digests it to extract energy and nutrients, and expels the remaining waste. The major functions of the GI tract are ingestion, digestion, absorption, and defecation.
The GI tract differs substantially from animal to animal. Some animals have multi-chambered stomachs, while some animals' stomachs contain a single chamber. In a normal human adult male, the GI tract is approximately 6.5 meters (20 feet) long and consists of the upper and lower GI tracts. The tract may also be divided into foregut, midgut, and hindgut, reflecting the embryological origin of each segment of the tract.

# Upper gastrointestinal tract
The upper GI tract consists of the mouth, pharynx, esophagus, and stomach.
- The mouth contains the buccal mucosa, which contains the openings of the salivary glands; the tongue; and the teeth.
- Behind the mouth lies the pharynx, which leads to a hollow muscular tube, the esophagus.
- Peristalsis takes place, which is the contraction of muscles to propel the food down the esophagus which extends through the chest and pierces the diaphragm to reach the stomach.

# Lower gastrointestinal tract
The lower GI tract comprises the intestines and anus.
- Bowel or intestine
Small intestine, which has three parts:
Duodenum
Jejunum
Ileum
Large intestine, which has three parts:
Cecum (the vermiform appendix is attached to the cecum).
Colon (ascending colon, transverse colon, descending colon and sigmoid flexure)
Rectum
- Small intestine, which has three parts:
Duodenum
Jejunum
Ileum
- Duodenum
- Jejunum
- Ileum
- Large intestine, which has three parts:
Cecum (the vermiform appendix is attached to the cecum).
Colon (ascending colon, transverse colon, descending colon and sigmoid flexure)
Rectum
- Cecum (the vermiform appendix is attached to the cecum).
- Colon (ascending colon, transverse colon, descending colon and sigmoid flexure)
- Rectum
- Anus

# Accessory organs
Accessory organs to the alimentary canal include the liver, gallbladder, and pancreas. The liver secretes bile into the small intestine via the biliary system, employing the gallbladder as a reservoir. Apart from storing and concentrating bile, the gallbladder has no other specific function. The pancreas secretes an isosmotic fluid containing bicarbonate and several enzymes, including trypsin, chymotrypsin, lipase, and pancreatic amylase, as well as nucleolytic enzymes (deoxyribonuclease and ribonuclease), into the small intestine. Both of these secretory organs aid in  digestion.

# Embryology
The gut is an endoderm-derived structure. At approximately the 16th day of human development, the embryo begins to fold ventrally (with the embryo's ventral surface becoming concave) in two directions: the sides of the embryo fold in on each other and the head and tail fold towards one another. The result is that a piece of the yolk sac, an endoderm-lined structure in contact with the ventral aspect of the embryo, begins to be pinched off to become the primitive gut. The yolk sac remains connected to the gut tube via the vitelline duct. Usually this structure regresses during development; in cases where it does not, it is known as Meckel's diverticulum.
During fetal life, the primitive gut can be divided into three segments: foregut, midgut, and hindgut. Although these terms are often used in reference to segments of the primitive gut, they are nevertheless used regularly to describe components of the definitive gut as well.
Each segment of the primitive gut gives rise to specific gut and gut-related structures in the adult. Components derived from the gut proper, including the stomach and colon, develop as swellings or dilatations of the primitive gut. In contrast, gut-related derivativesthat is, those structures that derive from the primitive gut but are not part of the gut properin general develop as outpouchings of the primitive gut. The blood vessels supplying these structures remain constant throughout development.

# Physiology

## Specialization of organs
Four organs are subject to specialization in the kingdom Animalia.
- The first organ is the tongue which is only present in the phylum Chordata.
- The second organ is the esophagus. The crop is an enlargement of the esophagus in birds, insects and other invertebrates that is used to store food temporarily.
- The third organ is the stomach. In addition to a glandular stomach (proventriculus), birds have a muscular "stomach" called the ventriculus or "gizzard." The gizzard is used to mechanically grind up food.
- The fourth organ is the large intestine. An outpouching of the large intestine called the cecum is present in non-ruminant herbivores such as rabbits. It aids in digestion of plant material such as cellulose

# The "Brain-Gut Connection"
Several studies have linked the human brain and the gastrointestinal system. Emotional state is strongly linked to gastrointestinal symptoms; many people experience altered bowel habits as a result of stress, anxiety, and depression. Many researchers consider the gastrointestinal system to be a "second brain".
For example, Irritable Bowel Syndrome is strongly linked to emotional state, and the symptoms of a number of gastrointestinal disorders, including IBS and inflammatory bowel disease, are exacerbated, but not caused by, stress and axiety.

# Pathology
There are a number of diseases and conditions affecting the gastrointestinal system, including:
- Irritable Bowel Syndrome
- Inflammatory Bowel Disease (Crohn's Diseae and ulcerative colitis)
- Giardiasis
- Colorectal cancer
- Gastroenteritis, also known as "stomach flu";an inflammation of the stomach and intestines
- Diverticulitis
- Pancreatitis

# Immune function
The gastrointestinal tract is also a prominent part of the immune system. The low pH (ranging from 1 to 4) of the stomach is fatal for many microorganisms that enter it. Similarly, mucus (containing IgA antibodies) neutralizes many of these microorganisms. Other factors in the GI tract help with immune function as well, including enzymes in the saliva and bile. Enzymes such as Cyp3A4, along with the antiporter activities, are also instrumental in the intestine's role of detoxification of antigens and xenobiotics, such as drugs, involved in first pass metabolism.  Health-enhancing intestinal bacteria serve to prevent the overgrowth of potentially harmful bacteria in the gut. Microorganisms are also kept at bay by an extensive immune system comprising the gut-associated lymphoid tissue (GALT).

# Histology
The gastrointestinal tract has a uniform general histology with some differences which reflect the specialization in functional anatomy. The GI tract can be divided into 4 concentric layers:
- Mucosa
- Submucosa
- Muscularis externa (the external muscle layer)
- Adventitia or serosa

## Mucosa
The mucosa is the innermost layer of the gastrointestinal tract, surrounding the lumen, or space within the tube. This layer comes in direct contact with the food (or bolus), and is responsible for absorption and secretion, important processes in digestion.
The mucosa can be divided into:
- Epithelium
- Lamina propria
- Muscularis mucosae
The mucosae are highly specialized in each organ of the gastrointestinal tract, facing a low pH in the stomach, absorbing a multitude of different substances in the small intestine, and also absorbing specific quantities of water in the large intestine. Reflecting the varying needs of these organs, the structure of the mucosa can consist of invaginations of secretory glands (e.g., gastric pits), or it can be folded in order to increase surface area (examples include villi and plicae circulares).

## Submucosa
The submucosa consists of a dense irregular layer of connective tissue with large blood vessels, lymphatics and nerves branching into the mucosa and muscularis. It contains Meissner's plexus, an enteric nervous plexus, situated on the inner surface of the muscularis externa.

## Muscularis externa
The muscularis externa consists of an inner circular layer and a longitudinal outer muscular layer. The circular muscle layer prevents the food from going backwards and the longitudinal layer shortens the tract. The coordinated contractions of these layers is called peristalsis and propels the bolus, or balled-up food, through the GI tract. 
Between the two muscle layers are the myenteric or Auerbach's plexus.

## Adventitia
The adventitia consists of several layers of epithelia.
When the adventitia is facing the mesentery or peritoneal fold, the adventitia is covered by a mesothelium supported by a thin connective tissue layer, together forming a serosa, or serous membrane.

# Uses of animal gut by humans
- The stomachs of calves have commonly been used as a source of rennet for making cheese.
- The use of animal gut strings by musicians can be traced back to the third dynasty of Egypt.  In the recent past, strings were made out of lamb gut.  With the advent of the modern era, musicians have tended to use strings made of silk, or synthetic materials such as nylon or steel.  Some instrumentalists, however, still use gut strings in order to evoke the older tone quality.  Although such strings were commonly referred to as "catgut" strings, cats were never used as a source for gut strings.
- Sheep gut was the original source for natural gut string used in racquets, such as for tennis.  Today, synthetic strings are much more common, but the best strings are now made out of cow gut.
- Gut cord has also been used to produce strings for the snares which provide the snare drum's characteristic buzzing timbre.  While the snare drum currently almost always uses metal wire rather than gut cord, the North African bendir frame drum still uses gut for this purpose.
- "Natural" sausage hulls (or casings) are made of animal gut, especially hog, beef, and lamb.
- Animal gut was used to make the cord lines in longcase clocks and for fusee movements in bracket clocks, but may be replaced by metal wire.
- The oldest known condoms, from 1640, were made from animal intestine.