The gastrointestinal tract (GI tract, digestive tract, alimentary canal) is the tract or passageway of the

digestive system The human digestive system consists of the gastrointestinal tract plus the accessory organs of digestion (the tongue, salivary glands, pancreas, liver, and gallbladder). Digestion involves the breakdown of food into smaller and smaller compone ...

that leads from the

mouth In animal anatomy, the mouth, also known as the oral cavity, or in Latin cavum oris, is the opening through which many animals take in food and issue vocal sounds. It is also the cavity lying at the upper end of the alimentary canal, bounded on ...

to the

anus The anus (Latin, 'ring' or 'circle') is an opening at the opposite end of an animal's digestive tract from the mouth. Its function is to control the expulsion of feces, the residual semi-solid waste that remains after food digestion, which, d ...

. The GI tract contains all the major

organ Organ may refer to: Biology * Organ (biology), a part of an organism Musical instruments * Organ (music), a family of keyboard musical instruments characterized by sustained tone ** Electronic organ, an electronic keyboard instrument ** Hammond ...

s of the digestive system, in humans and other animals, including the esophagus, stomach, and intestines. Food taken in through the mouth is

digested Digestion is the breakdown of large insoluble food molecules into small water-soluble food molecules so that they can be absorbed into the watery blood plasma. In certain organisms, these smaller substances are absorbed through the small inte ...

to extract

nutrient A nutrient is a substance used by an organism to survive, grow, and reproduce. The requirement for dietary nutrient intake applies to animals, plants, fungi, and protists. Nutrients can be incorporated into cells for metabolic purposes or excret ...

s and absorb energy, and the waste expelled at the anus as

feces Feces ( or faeces), known colloquially and in slang as poo and poop, are the solid or semi-solid remains of food that was not digested in the small intestine, and has been broken down by bacteria in the large intestine. Feces contain a relati ...

. ''Gastrointestinal'' is an adjective meaning of or pertaining to the stomach and intestines. Most animals have a "through-gut" or complete digestive tract. Exceptions are more primitive ones: sponges have small pores (

ostia Ostia may refer to: Places *Ostia (Rome), a municipio (also called ''Ostia Lido'' or ''Lido di Ostia'') of Rome *Ostia Antica, a township and port of ancient Rome *Ostia Antica (district), a district of the commune of Rome Arts and entertainment ...

) throughout their body for digestion and a larger dorsal pore ( osculum) for excretion, comb jellies have both a ventral mouth and dorsal anal pores, while cnidarians and acoels have a single pore for both digestion and excretion. The human gastrointestinal tract consists of the esophagus, stomach, and intestines, and is divided into the upper and lower gastrointestinal tracts. The GI tract includes all structures between the

and the

, forming a continuous passageway that includes the main organs of digestion, namely, the stomach,

small intestine The small intestine or small bowel is an organ in the gastrointestinal tract where most of the absorption of nutrients from food takes place. It lies between the stomach and large intestine, and receives bile and pancreatic juice through the p ...

, and large intestine. The complete human digestive system is made up of the gastrointestinal tract plus the accessory organs of digestion (the tongue, salivary glands, pancreas, liver and gallbladder). The tract may also be divided into

foregut The foregut is the anterior part of the alimentary canal, from the mouth to the duodenum at the entrance of the bile duct. Beyond the stomach, the foregut is attached to the abdominal walls by mesentery. The foregut arises from the endoderm, deve ...

, midgut, and

hindgut The hindgut (or epigaster) is the posterior ( caudal) part of the alimentary canal. In mammals, it includes the distal one third of the transverse colon and the splenic flexure, the descending colon, sigmoid colon and up to the ano-rectal juncti ...

, reflecting the embryological origin of each segment. The whole human GI tract is about nine metres (30 feet) long at

autopsy An autopsy (post-mortem examination, obduction, necropsy, or autopsia cadaverum) is a surgical procedure that consists of a thorough examination of a corpse by dissection to determine the cause, mode, and manner of death or to evaluate any di ...

. It is considerably shorter in the living body because the intestines, which are tubes of smooth muscle tissue, maintain constant

muscle tone In physiology, medicine, and anatomy, muscle tone (residual muscle tension or tonus) is the continuous and passive partial muscle contraction, contraction of the muscles, or the muscle's resistance to passive stretch during resting state.O’Sull ...

in a halfway-tense state but can relax in spots to allow for local distention and peristalsis. The gastrointestinal tract contains the

gut microbiota Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut m ...

, with some 4,000 different strains of bacteria having diverse roles in maintenance of immune health and metabolism, and many other microorganisms. Cells of the GI tract release hormones to help regulate the digestive process. These

digestive hormones Digestive may refer to: Biology *Digestion, biological process of metabolism Food and drink * Digestif, small beverage at the end of a meal *Digestive biscuit A digestive biscuit, sometimes described as a sweet-meal biscuit, is a semi- sweet bi ...

, including

gastrin Gastrin is a peptide hormone that stimulates secretion of gastric acid (HCl) by the parietal cells of the stomach and aids in gastric motility. It is released by G cells in the pyloric antrum of the stomach, duodenum, and the pancreas. Gastrin ...

secretin Secretin is a hormone that regulates water homeostasis throughout the body and influences the environment of the duodenum by regulating secretions in the stomach, pancreas, and liver. It is a peptide hormone produced in the S cells of the duode ...

, cholecystokinin, and ghrelin, are mediated through either intracrine or autocrine mechanisms, indicating that the cells releasing these hormones are conserved structures throughout evolution.

Human gastrointestinal tract

Structure

The structure and function can be described both as gross anatomy and as

microscopic anatomy Histology, also known as microscopic anatomy or microanatomy, is the branch of biology which studies the microscopic anatomy of biological tissues. Histology is the microscopic counterpart to gross anatomy, which looks at larger structures vis ...

or histology. The tract itself is divided into upper and lower tracts, and the intestines

small Small may refer to: Science and technology * SMALL, an ALGOL-like programming language * Small (anatomy), the lumbar region of the back * ''Small'' (journal), a nano-science publication * <small>, an HTML element that defines smaller text ...

and large parts.

Upper gastrointestinal tract

The upper gastrointestinal tract consists of the

, pharynx, esophagus, stomach, and

duodenum The duodenum is the first section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine m ...

. The exact demarcation between the upper and lower tracts is the

suspensory muscle of the duodenum The suspensory muscle of duodenum is a thin muscle connecting the junction between the duodenum, jejunum, and duodenojejunal flexure to connective tissue surrounding the superior mesenteric artery and coeliac artery. It is also known as the ...

. This differentiates the embryonic borders between the foregut and midgut, and is also the division commonly used by clinicians to describe gastrointestinal bleeding as being of either "upper" or "lower" origin. Upon

dissection Dissection (from Latin ' "to cut to pieces"; also called anatomization) is the dismembering of the body of a deceased animal or plant to study its anatomical structure. Autopsy is used in pathology and forensic medicine to determine the cause o ...

, the duodenum may appear to be a unified organ, but it is divided into four segments based upon function, location, and internal anatomy. The four segments of the duodenum are as follows (starting at the stomach, and moving toward the jejunum):

bulb In botany, a bulb is structurally a short stem with fleshy leaves or leaf basesBell, A.D. 1997. ''Plant form: an illustrated guide to flowering plant morphology''. Oxford University Press, Oxford, U.K. that function as food storage organs duri ...

, descending, horizontal, and ascending. The suspensory muscle attaches the superior border of the ascending duodenum to the

diaphragm Diaphragm may refer to: Anatomy * Thoracic diaphragm, a thin sheet of muscle between the thorax and the abdomen * Pelvic diaphragm or pelvic floor, a pelvic structure * Urogenital diaphragm or triangular ligament, a pelvic structure Other * Diap ...

. The suspensory muscle is an important anatomical landmark which shows the formal division between the duodenum and the jejunum, the first and second parts of the small intestine, respectively. This is a thin muscle which is derived from the

embryo An embryo is an initial stage of development of a multicellular organism. In organisms that reproduce sexually, embryonic development is the part of the life cycle that begins just after fertilization of the female egg cell by the male spe ...

nic

mesoderm The mesoderm is the middle layer of the three germ layers that develops during gastrulation in the very early development of the embryo of most animals. The outer layer is the ectoderm, and the inner layer is the endoderm.Langman's Medical E ...

Lower gastrointestinal tract

The lower gastrointestinal tract includes most of the

and all of the large intestine. In

human anatomy The human body is the structure of a human being. It is composed of many different types of cells that together create tissues and subsequently organ systems. They ensure homeostasis and the viability of the human body. It comprises a he ...

, the intestine (bowel, or gut. Greek: éntera) is the segment of the gastrointestinal tract extending from the pyloric sphincter of the stomach to the

and as in other mammals, consists of two segments: the

and the large intestine. In humans, the small intestine is further subdivided into the

, jejunum, and ileum while the large intestine is subdivided into the cecum, ascending, transverse, descending and sigmoid colon,

rectum The rectum is the final straight portion of the large intestine in humans and some other mammals, and the Gastrointestinal tract, gut in others. The adult human rectum is about long, and begins at the rectosigmoid junction (the end of the s ...

, and anal canal.

=Small intestine

The

begins at the

and is a tubular structure, usually between 6 and 7 m long. Its mucosal area in an adult human is about . The combination of the

circular folds The circular folds (also known as valves of Kerckring, valves of Kerchkring, plicae circulares, ''plicae circulae, and'' ''valvulae conniventes'') are large valvular flaps projecting into the lumen of the small intestine. Structure The entire sm ...

, the villi, and the microvilli increases the absorptive area of the mucosa about 600-fold, making a total area of about for the entire small intestine. Its main function is to absorb the products of digestion (including carbohydrates, proteins, lipids, and vitamins) into the bloodstream. There are three major divisions: #

Duodenum The duodenum is the first section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine m ...

: A short structure (about 20–25 cm long) which receives

bile Bile (from Latin ''bilis''), or gall, is a dark-green-to-yellowish-brown fluid produced by the liver of most vertebrates that aids the digestion of lipids in the small intestine. In humans, bile is produced continuously by the liver (liver bile ...

from the gall bladder. The digestive enzymes break down proteins, and bile emulsifies fats into micelles. The

contains Brunner's glands which produce a mucus-rich alkaline secretion containing bicarbonate. These secretions, in combination with bicarbonate from the pancreas, neutralize the stomach acids contained in the chyme. # Jejunum: This is the midsection of the small intestine, connecting the duodenum to the ileum. It is about long and contains the

also known as plicae circulares and villi that increase its surface area. Products of digestion (sugars, amino acids, and fatty acids) are absorbed into the bloodstream here. # Ileum: The final section of the small intestine. It is about 3 m long, and contains villi similar to the jejunum. It absorbs mainly vitamin B12 and bile acids, as well as any other remaining nutrients.

=Large intestine

= The large intestine also called the colon, consists of the cecum,

, and anal canal. It also includes the

appendix Appendix, or its plural form appendices, may refer to: __NOTOC__ In documents * Addendum, an addition made to a document by its author after its initial printing or publication * Bibliography, a systematic list of books and other works * Index (pub ...

, which is attached to the cecum. The colon is further divided into: # Cecum (first portion of the colon) and

Ascending colon ''Ascending'' is a science fiction novel by the Canadian writer James Alan Gardner, published in 2001 by HarperCollins Publishers under its various imprints.HarperCollins, Avon, HarperCollins Canada, SFBC/Avon; paperback edition 2001, Eos Books. ...

(ascending in the back wall of the abdomen) #

Right colic flexure In the anatomy of the human digestive tract, there are two colic flexures, or curvatures in the transverse colon. The right colic flexure is also known as the hepatic flexure, and the left colic flexure is also known as the splenic flexure. Note ...

(flexed portion of the ascending and transverse colon apparent to the liver) # Transverse colon (passing below the diaphragm) # Left colic flexure (flexed portion of the transverse and descending colon apparent to the spleen) #

Descending colon In the anatomy of humans and homologous primates, the descending colon is the part of the colon extending from the left colic flexure to the level of the iliac crest (whereupon it transitions into the sigmoid colon). The function of the descendin ...

(descending down the left side of the abdomen) #

Sigmoid colon The sigmoid colon (or pelvic colon) is the part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about in length. The loop is typically shaped like a Greek letter sigma (ς) or Latin letter S (thus ''s ...

(a loop of the colon closest to the rectum) #

Rectum The rectum is the final straight portion of the large intestine in humans and some other mammals, and the Gastrointestinal tract, gut in others. The adult human rectum is about long, and begins at the rectosigmoid junction (the end of the s ...

# Anal canal The main function of the large intestine is to absorb water and salts. The area of the large intestinal mucosa of an adult human is about .

Development

The gut is an

endoderm Endoderm is the innermost of the three primary germ layers in the very early embryo. The other two layers are the ectoderm (outside layer) and mesoderm (middle layer). Cells migrating inward along the archenteron form the inner layer of the gast ...

-derived structure. At approximately the sixteenth day of human development, the

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 toward one another. The result is that a piece of the yolk sac, an

-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 is gradually patterned into three segments:

, midgut, and

. Although these terms are often used in reference to segments of the primitive gut, they are also used regularly to describe regions of the definitive gut as well. Each segment of the gut is further specified and gives rise to specific gut and gut-related structures in later development. Components derived from the gut proper, including the stomach and colon, develop as swellings or dilatations in the cells of the primitive gut. In contrast, gut-related derivatives — that is, those structures that derive from the primitive gut but are not part of the gut proper, in general, develop as out-pouchings of the primitive gut. The blood vessels supplying these structures remain constant throughout development.

Histology

The gastrointestinal tract has a form of general histology with some differences that reflect the specialization in functional anatomy. The GI tract can be divided into four concentric layers in the following order: *

Mucosa A mucous membrane or mucosa is a membrane that lines various cavities in the body of an organism and covers the surface of internal organs. It consists of one or more layers of epithelial cells overlying a layer of loose connective tissue. It is ...

Submucosa The submucosa (or tela submucosa) is a thin layer of tissue (biology), tissue in various organ (anatomy), organs of the gastrointestinal tract, gastrointestinal, respiratory tract, respiratory, and genitourinary system, genitourinary tracts. It i ...

* Muscular layer * Adventitia or serosa

=Mucosa

= The mucosa is the innermost layer of the gastrointestinal tract. The mucosa surrounds the lumen, or open space within the tube. This layer comes in direct contact with digested food (

chyme Chyme or chymus (; from Greek χυμός ''khymos'', "juice") is the semi-fluid mass of partly digested food that is expelled by a person's stomach, through the pyloric valve, into the duodenum Epithelium Epithelium or epithelial tissue is one of the four basic types of animal tissue, along with connective tissue, muscle tissue and nervous tissue. It is a thin, continuous, protective layer of compactly packed cells with a little intercellul ...

– innermost layer. Responsible for most digestive, absorptive and secretory processes. *

Lamina propria The lamina propria is a thin layer of connective tissue that forms part of the moist linings known as mucous membranes or mucosae, which line various tubes in the body, such as the respiratory tract, the gastrointestinal tract, and the urogenita ...

– a layer of connective tissue. Unusually cellular compared to most connective tissue *

Muscularis mucosae The lamina muscularis mucosae (or muscularis mucosae) is a thin layer (lamina) of muscle of the gastrointestinal tract, located outside the lamina propria, and separating it from the submucosa. It is present in a continuous fashion from the esopha ...

– a thin layer of smooth muscle that aids the passing of material and enhances the interaction between the epithelial layer and the contents of the lumen by agitation and peristalsis 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.

=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 externa. It contains the submucosal plexus, an enteric nervous plexus, situated on the inner surface of the ''muscularis externa''.

=Muscular layer

= The muscular layer consists of an inner circular layer and a

longitudinal Longitudinal is a geometric term of location which may refer to: * Longitude ** Line of longitude, also called a meridian * Longitudinal engine, an internal combustion engine in which the crankshaft is oriented along the long axis of the vehicle, ...

outer layer. The circular layer prevents food from traveling backward and the longitudinal layer shortens the tract. The layers are not truly longitudinal or circular, rather the layers of muscle are helical with different pitches. The inner circular is helical with a steep pitch and the outer longitudinal is helical with a much shallower pitch. Whilst the muscularis externa is similar throughout the entire gastrointestinal tract, an exception is the stomach which has an additional inner oblique muscular layer to aid with grinding and mixing of food. The muscularis externa of the stomach is composed of the inner oblique layer, middle circular layer, and outer longitudinal layer. Between the circular and longitudinal muscle layers is the

myenteric plexus The myenteric plexus (or Auerbach's plexus) provides motor innervation to both layers of the muscular layer of the gut, having both parasympathetic and sympathetic input (although present ganglion cell bodies belong to parasympathetic innervation ...

. This controls peristalsis. Activity is initiated by the pacemaker cells, (myenteric

interstitial cells of Cajal Interstitial cells of Cajal (ICC) are interstitial cells found in the gastrointestinal tract. There are different types of ICC with different functions. ICC and another type of interstitial cell, known as platelet-derived growth factor receptor ...

). The gut has intrinsic peristaltic activity (

basal electrical rhythm The basal or basic electrical rhythm (BER) or electrical control activity (ECA) is the spontaneous depolarization and repolarization of pacemaker cells known as interstitial cells of Cajal (ICCs) in the smooth muscle of the stomach, small intestine, ...

) due to its self-contained enteric nervous system. The rate can be modulated by the rest of the

autonomic nervous system The autonomic nervous system (ANS), formerly referred to as the vegetative nervous system, is a division of the peripheral nervous system that supplies viscera, internal organs, smooth muscle and glands. The autonomic nervous system is a control ...

. The coordinated contractions of these layers is called peristalsis and propels the food through the tract. Food in the GI tract is called a bolus (ball of food) from the mouth down to the stomach. After the stomach, the food is partially digested and semi-liquid, and is referred to as

=Adventitia and serosa

= The outermost layer of the gastrointestinal tract consists of several layers of

connective tissue Connective tissue is one of the four primary types of animal tissue, along with epithelial tissue, muscle tissue, and nervous tissue. It develops from the mesenchyme derived from the mesoderm the middle embryonic germ layer. Connective tiss ...

. Intraperitoneal parts of the GI tract are covered with serosa. These include most of the stomach, first part of the

, all of the

, caecum and

, transverse colon,

sigmoid colon The sigmoid colon (or pelvic colon) is the part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about in length. The loop is typically shaped like a Greek letter sigma (ς) or Latin letter S (thus ''s ...

and

. In these sections of the gut, there is a clear boundary between the gut and the surrounding tissue. These parts of the tract have a

mesentery The mesentery is an organ that attaches the intestines to the posterior abdominal wall in humans and is formed by the double fold of peritoneum. It helps in storing fat and allowing blood vessels, lymphatics, and nerves to supply the intestines ...

. Retroperitoneal parts are covered with adventitia. They blend into the surrounding tissue and are fixed in position. For example, the retroperitoneal section of the duodenum usually passes through the transpyloric plane. These include the esophagus, pylorus of the stomach, distal

ascending colon ''Ascending'' is a science fiction novel by the Canadian writer James Alan Gardner, published in 2001 by HarperCollins Publishers under its various imprints.HarperCollins, Avon, HarperCollins Canada, SFBC/Avon; paperback edition 2001, Eos Books. ...

descending colon In the anatomy of humans and homologous primates, the descending colon is the part of the colon extending from the left colic flexure to the level of the iliac crest (whereupon it transitions into the sigmoid colon). The function of the descendin ...

and anal canal. In addition, the oral cavity has adventitia.

Gene and protein expression

Approximately 20,000 protein coding genes are expressed in human cells and 75% of these genes are expressed in at least one of the different parts of the digestive organ system. Over 600 of these genes are more specifically expressed in one or more parts of the GI tract and the corresponding proteins have functions related to digestion of food and uptake of nutrients. Examples of specific proteins with such functions are pepsinogen PGC and the lipase LIPF, expressed in

chief cells In human anatomy, there are three types of chief cells, the gastric chief cell, the parathyroid chief cell, and the type 1 chief cells found in the carotid body. Cell types The gastric chief cell (also known as a zymogenic cell or peptic cell) is a ...

, and gastric ATPase ATP4A and gastric intrinsic factor GIF, expressed in parietal cells of the stomach mucosa. Specific proteins expressed in the stomach and duodenum involved in defence include mucin proteins, such as

mucin 6 Mucin 6, oligomeric mucus/gel-forming, also known as MUC6, is a human gene In biology, the word gene (from , ; "...Wilhelm Johannsen coined the word gene to describe the Mendelian units of heredity..." meaning ''generation'' or ''birth'' o ...

and

intelectin-1 Intelectin-1, also known as omentin or intestinal lactoferrin receptor, is an intelectin encoded in humans by the ''ITLN1'' gene. Intelectin-1 functions both as a receptor for bacterial arabinogalactans and for lactoferrin. Having conserved ligan ...

Transit time

The time taken for food to transit through the gastrointestinal tract varies on multiple factors, including age, ethnicity, and gender. Several techniques have been used to measure transit time, including radiography following a

barium Barium is a chemical element with the symbol Ba and atomic number 56. It is the fifth element in group 2 and is a soft, silvery alkaline earth metal. Because of its high chemical reactivity, barium is never found in nature as a free element. Th ...

-labeled meal, breath hydrogen analysis,

scintigraphic Nuclear medicine or nucleology is a medical specialty involving the application of radioactive substances in the diagnosis and treatment of disease. Nuclear imaging, in a sense, is "radiology done inside out" because it records radiation emittin ...

analysis following a radiolabeled meal, and simple ingestion and spotting of corn kernels. It takes 2.5 to 3 hours for 50% of the contents to leave the stomach. The rate of digestion is also dependent of the material being digested, as food composition from the same meal may leave the stomach at different rates. Total emptying of the stomach takes around 4–5 hours, and transit through the colon takes 30 to 50 hours.

Immune function

The gastrointestinal tract forms an important part of the immune system.

=Immune barrier

= The surface area of the digestive tract is estimated to be about 32 square meters, or about half a badminton court. With such a large exposure (more than three times larger than the exposed surface of the skin), these immune components function to prevent pathogens from entering the blood and lymph circulatory systems. Fundamental components of this protection are provided by the intestinal mucosal barrier, which is composed of physical, biochemical, and immune elements elaborated by the intestinal mucosa. Microorganisms also are kept at bay by an extensive immune system comprising the

gut-associated lymphoid tissue Gut-associated lymphoid tissue (GALT) is a component of the mucosa-associated lymphoid tissue (MALT) which works in the immune system to protect the body from invasion in the gut. Owing to its physiological function in food absorption, the mucosa ...

(GALT) There are additional factors contributing to protection from pathogen invasion. For example, low pH (ranging from 1 to 4) of the stomach is fatal for many microorganisms that enter it. Similarly, mucus (containing

IgA Iga may refer to: Arts and entertainment * Ambush at Iga Pass, a 1958 Japanese film * Iga no Kagemaru, Japanese manga series * Iga, a set of characters from the Japanese novel '' The Kouga Ninja Scrolls'' Biology * ''Iga'' (beetle), a gen ...

antibodies An antibody (Ab), also known as an immunoglobulin (Ig), is a large, Y-shaped protein used by the immune system to identify and neutralize foreign objects such as pathogenic bacteria and viruses. The antibody recognizes a unique molecule of the ...

) neutralizes many pathogenic microorganisms. Other factors in the GI tract contribution to immune function include enzymes secreted in the

saliva Saliva (commonly referred to as spit) is an extracellular fluid produced and secreted by salivary glands in the mouth. In humans, saliva is around 99% water, plus electrolytes, mucus, white blood cells, epithelial cells (from which DNA can be ...

and

=Immune system homeostasis

= Beneficial bacteria also can contribute to the homeostasis of the gastrointestinal immune system. For example, Clostridia, one of the most predominant bacterial groups in the GI tract, play an important role in influencing the dynamics of the gut's immune system. It has been demonstrated that the intake of a high fiber diet could be responsible for the induction of

T-regulatory cell The regulatory T cells (Tregs or Treg cells), formerly known as suppressor T cells, are a subpopulation of T cells that modulate the immune system, maintain tolerance to self-antigens, and prevent autoimmune disease. Treg cells are immunosu ...

s (Tregs). This is due to the production of short-chain fatty acids during the fermentation of plant-derived nutrients such as

butyrate The conjugate acids are in :Carboxylic acids. {{Commons category, Carboxylate ions, Carboxylate anions Carbon compounds Oxyanions ...

and propionate. Basically, the butyrate induces the differentiation of Treg cells by enhancing

histone H3 Histone H3 is one of the five main histones involved in the structure of chromatin in eukaryotic cells. Featuring a main globular domain and a long N-terminal tail, H3 is involved with the structure of the nucleosomes of the 'beads on a stri ...

acetylation : In organic chemistry, acetylation is an organic esterification reaction with acetic acid. It introduces an acetyl group into a chemical compound. Such compounds are termed ''acetate esters'' or simply '' acetates''. Deacetylation is the oppo ...

in the promoter and conserved non-coding sequence regions of the FOXP3 locus, thus regulating the T cells, resulting in the reduction of the inflammatory response and allergies.

Intestinal microbiota

The large intestine hosts several kinds of bacteria that can deal with molecules that the human body cannot otherwise break down. This is an example of

symbiosis Symbiosis (from Greek , , "living together", from , , "together", and , bíōsis, "living") is any type of a close and long-term biological interaction between two different biological organisms, be it mutualistic, commensalistic, or parasit ...

. These bacteria also account for the production of gases at host-pathogen interface inside the intestine (this gas is released as ''

flatulence Flatulence, in humans, is the expulsion of gas from the intestines via the anus, commonly referred to as farting. "Flatus" is the medical word for gas generated in the stomach or bowels. A proportion of intestinal gas may be swallowed environm ...

'' when eliminated through the anus). However the large intestine is mainly concerned with the absorption of water from digested material (which is regulated by the hypothalamus) and the reabsorption of sodium, as well as any nutrients that may have escaped primary digestion in the ileum. Health-enhancing

intestinal bacteria Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut mic ...

of the

gut flora Gut microbiota, gut microbiome, or gut flora, are the microorganisms, including bacteria, archaea, fungi, and viruses that live in the digestive tracts of animals. The gastrointestinal metagenome is the aggregate of all the genomes of the gut mi ...

serve to prevent the overgrowth of potentially harmful bacteria in the gut. These two types of bacteria compete for space and "food", as there are limited resources within the intestinal tract. A ratio of 80-85% beneficial to 15–20% potentially harmful bacteria generally is considered normal within the intestines, and maintains homeostasis. A bad ratio of potentially harmful bacteria may disrupt this balance and cause

dysbiosis Dysbiosis (also called dysbacteriosis) is characterized by a disruption to the microbiome resulting in an imbalance in the microbiota, changes in their functional composition and metabolic activities, or a shift in their local distribution. For ex ...

Detoxification and drug metabolism

Enzymes such as

CYP3A4 Cytochrome P450 3A4 (abbreviated CYP3A4) () is an important enzyme in the body, mainly found in the liver and in the intestine. It oxidizes small foreign organic molecules (xenobiotics), such as toxins or drugs, so that they can be removed from t ...

, along with the

antiporter An antiporter (also called exchanger or counter-transporter) is a cotransporter and integral membrane protein involved in secondary active transport of two or more different molecules or ions across a phospholipid membrane such as the plasma memb ...

activities, are also instrumental in the intestine's role of drug metabolism in the detoxification of antigens and

xenobiotic A xenobiotic is a chemical substance found within an organism that is not naturally produced or expected to be present within the organism. It can also cover substances that are present in much higher concentrations than are usual. Natural compo ...

Clinical significance

Diseases

There are many diseases and conditions that can affect the gastrointestinal system, including infections, inflammation and cancer. Various pathogens, such as bacteria that cause foodborne illnesses, can induce

gastroenteritis Gastroenteritis, also known as infectious diarrhea and gastro, is an inflammation of the gastrointestinal tract including the stomach and intestine. Symptoms may include diarrhea, vomiting, and abdominal pain. Fever, lack of energy, and dehydra ...

which results from inflammation of the stomach and small intestine.

Antibiotic An antibiotic is a type of antimicrobial substance active against bacteria. It is the most important type of antibacterial agent for fighting bacterial infections, and antibiotic medications are widely used in the treatment and prevention of ...

s to treat such bacterial infections can decrease the microbiome diversity of the gastrointestinal tract, and further enable inflammatory mediators. Gastroenteritis is the most common disease of the GI tract. *

Gastrointestinal cancer Gastrointestinal cancer refers to malignant conditions of the gastrointestinal tract (GI tract) and accessory organs of digestion, including the esophagus, stomach, biliary system, pancreas, small intestine, large intestine, rectum and anus. The ...

may occur at any point in the gastrointestinal tract, and includes mouth cancer,

tongue cancer Oral cancer, also known as mouth cancer, is cancer of the lining of the lips, mouth, or upper throat. In the mouth, it most commonly starts as a painless white patch, that thickens, develops red patches, an ulcer, and continues to grow. When on ...

, oesophageal cancer,

stomach cancer Stomach cancer, also known as gastric cancer, is a cancer that develops from the lining of the stomach. Most cases of stomach cancers are gastric carcinomas, which can be divided into a number of subtypes, including gastric adenocarcinomas. Lymph ...

, and

colorectal cancer Colorectal cancer (CRC), also known as bowel cancer, colon cancer, or rectal cancer, is the development of cancer from the colon or rectum (parts of the large intestine). Signs and symptoms may include blood in the stool, a change in bowel m ...

. * Inflammatory conditions. Ileitis is an inflammation of the ileum, colitis is an inflammation of the large intestine. * Appendicitis is inflammation of the

located at the caecum. This is a potentially fatal condition if left untreated; most cases of appendicitis require surgical intervention.

Diverticular disease Diverticular disease is when problems occur due to diverticulosis, a condition defined by the presence of pouches in the wall of the large intestine (diverticula). This includes diverticula becoming inflamed ( diverticulitis) or bleeding. Colonic ...

is a condition that is very common in older people in industrialized countries. It usually affects the large intestine but has been known to affect the small intestine as well.

Diverticulosis Diverticulosis is the condition of having multiple pouches (diverticulum, diverticula) in the colon (anatomy), colon that are not inflamed. These are outpockets of the colonic mucosa and submucosa through weaknesses of muscle layers in the col ...

occurs when pouches form on the intestinal wall. Once the pouches become inflamed it is known as

diverticulitis Diverticulitis, specifically colonic diverticulitis, is a gastrointestinal disease characterized by inflammation of abnormal pouches—diverticula—which can develop in the wall of the large intestine. Symptoms typically include lower abdominal ...

Inflammatory bowel disease Inflammatory bowel disease (IBD) is a group of inflammation, inflammatory conditions of the colon (anatomy), colon and small intestine, Crohn's disease and ulcerative colitis being the principal types. Crohn's disease affects the small intestine a ...

is an inflammatory condition affecting the bowel walls, and includes the subtypes

Crohn's disease Crohn's disease is a type of inflammatory bowel disease (IBD) that may affect any segment of the gastrointestinal tract. Symptoms often include abdominal pain, diarrhea (which may be bloody if inflammation is severe), fever, abdominal distension ...

and ulcerative colitis. While Crohn's can affect the entire gastrointestinal tract, ulcerative colitis is limited to the large intestine. Crohn's disease is widely regarded as an

autoimmune disease An autoimmune disease is a condition arising from an abnormal immune response to a functioning body part. At least 80 types of autoimmune diseases have been identified, with some evidence suggesting that there may be more than 100 types. Nearly a ...

. Although ulcerative colitis is often treated as though it were an autoimmune disease, there is no consensus that it actually is such.

Functional gastrointestinal disorder Functional gastrointestinal disorders (FGID), also known as disorders of gut–brain interaction, include a number of separate idiopathic disorders which affect different parts of the gastrointestinal tract and involve visceral hypersensitivity ...

s the most common of which is irritable bowel syndrome. Functional constipation and

chronic functional abdominal pain Chronic functional abdominal pain (CFAP) or functional abdominal pain syndrome (FAPS) is the ongoing presence of abdominal pain for which there is no known medical explanation, and has the potential to interfere with all aspects of daily functioni ...

are other functional disorders of the intestine that have physiological causes but do not have identifiable structural, chemical, or infectious pathologies.

Symptoms

Several symptoms are used to indicate problems with the gastrointestinal tract: * Vomiting, which may include regurgitation of food or the vomiting of blood * Diarrhea, or the passage of liquid or more frequent stools * Constipation, which refers to the passage of fewer and hardened stools *

Blood in stool Blood in stool looks different depending on how early it enters the digestive tract—and thus how much digestive action it has been exposed to—and how much there is. The term can refer either to melena, with a black appearance, typically orig ...

, which includes fresh red blood, maroon-coloured blood, and tarry-coloured blood

Treatment

Gastrointestinal surgery can often be performed in the outpatient setting. In the United States in 2012, operations on the digestive system accounted for 3 of the 25 most common ambulatory surgery procedures and constituted 9.1 percent of all outpatient ambulatory surgeries.

Imaging

Various methods of imaging the gastrointestinal tract include the

upper Upper may refer to: * Shoe upper or ''vamp'', the part of a shoe on the top of the foot * Stimulant, drugs which induce temporary improvements in either mental or physical function or both * ''Upper'', the original film title for the 2013 found fo ...

and lower gastrointestinal series: *

Radioopaque Radiodensity (or radiopacity) is opacity to the radio wave and X-ray portion of the electromagnetic spectrum: that is, the relative inability of those kinds of electromagnetic radiation to pass through a particular material. Radiolucency or hypod ...

dyes may be swallowed to produce a

barium swallow An upper gastrointestinal series, also called a barium swallow, barium study, or barium meal, is a series of radiographs used to examine the gastrointestinal tract for abnormalities. A contrast medium, usually a radiocontrast agent such as barium ...

* Parts of the tract may be visualised by camera. This is known as endoscopy if examining the upper gastrointestinal tract and

colonoscopy Colonoscopy () or coloscopy () is the endoscopic examination of the large bowel and the distal part of the small bowel with a CCD camera or a fiber optic camera on a flexible tube passed through the anus. It can provide a visual diagnosis (''e. ...

or sigmoidoscopy if examining the lower gastrointestinal tract.

Capsule endoscopy Capsule endoscopy is a medical procedure used to record internal images of the gastrointestinal tract for use in disease diagnosis. Newer developments are also able to take biopsies and release medication at specific locations of the entire ...

is where a capsule containing a camera is swallowed in order to examine the tract.

Biopsies A biopsy is a medical test commonly performed by a surgeon, interventional radiologist, or an interventional cardiologist. The process involves extraction of sample cells or tissues for examination to determine the presence or extent of a diseas ...

may also be taken when examined. * An abdominal x-ray may be used to examine the lower gastrointestinal tract.

Other related diseases

Cholera Cholera is an infection of the small intestine by some strains of the bacterium ''Vibrio cholerae''. Symptoms may range from none, to mild, to severe. The classic symptom is large amounts of watery diarrhea that lasts a few days. Vomiting and ...

Enteric duplication cyst Enteric duplication cysts, sometimes simply called duplication cysts, are rare congenital malformations of the gastrointestinal tract. They most frequently occur in the small intestine, particularly the ileum, but can occur anywhere along the gastro ...

Giardiasis Giardiasis is a parasitic disease caused by ''Giardia duodenalis'' (also known as ''G. lamblia'' and ''G. intestinalis''). Infected individuals who experience symptoms (about 10% have no symptoms) may have diarrhea, abdominal pain, and weight los ...

* Pancreatitis * Peptic ulcer disease * Yellow fever * '' Helicobacter pylori'' is a gram-negative spiral bacterium. Over half the world's population is infected with it, mainly during childhood; it is not certain how the disease is transmitted. It colonizes the gastrointestinal system, predominantly the stomach. The bacterium has specific survival conditions that are specific to the human gastric microenvironment: it is both capnophilic and microaerophilic. ''Helicobacter'' also exhibits a tropism for gastric epithelial lining and the gastric mucosal layer about it. Gastric colonization of this bacterium triggers a robust immune response leading to moderate to severe inflammation, known as gastritis. Signs and symptoms of infection are gastritis, burning abdominal pain, weight loss, loss of appetite, bloating, burping, nausea, bloody vomit, and black tarry stools. Infection can be detected in a number of ways: GI X-rays, endoscopy, blood tests for anti-''Helicobacter'' antibodies, a stool test, and a urease breath test (which is a by-product of the bacteria). If caught soon enough, it can be treated with three doses of different proton pump inhibitors as well as two antibiotics, taking about a week to cure. If not caught soon enough, surgery may be required. *

Intestinal pseudo-obstruction Intestinal pseudo-obstruction (IPO) is a clinical syndrome caused by severe impairment in the ability of the intestines to push food through. It is characterized by the signs and symptoms of Bowel obstruction, intestinal obstruction without any les ...

is a syndrome caused by a malformation of the digestive system, characterized by a severe impairment in the ability of the intestines to push and assimilate. Symptoms include daily abdominal and stomach pain, nausea, severe distension, vomiting, heartburn, dysphagia, diarrhea, constipation, dehydration and malnutrition. There is no cure for intestinal pseudo-obstruction. Different types of surgery and treatment managing life-threatening complications such as ileus and volvulus, intestinal stasis which lead to bacterial overgrowth, and resection of affected or dead parts of the gut may be needed. Many patients require parenteral nutrition. * Ileus is a blockage of the intestines. * Coeliac disease is a common form of malabsorption, affecting up to 1% of people of northern European descent. An autoimmune response is triggered in intestinal cells by digestion of gluten proteins. Ingestion of proteins found in wheat, barley and rye, causes villous atrophy in the small intestine. Lifelong dietary avoidance of these foodstuffs in a gluten-free diet is the only treatment. * Enteroviruses are named by their transmission-route through the intestine (''enteric'' meaning intestinal), but their symptoms aren't mainly associated with the intestine. *

Endometriosis Endometriosis is a disease of the female reproductive system in which cells similar to those in the endometrium, the layer of tissue that normally covers the inside of the uterus, grow outside the uterus. Most often this is on the ovaries, f ...

can affect the intestines, with similar symptoms to IBS. *

Bowel twist A volvulus is when a loop of intestine twists around itself and the mesentery that supports it, resulting in a bowel obstruction. Symptoms include abdominal pain, bloating, abdominal bloating, vomiting, constipation, and bloody stool. Onset of sy ...

(or similarly, bowel strangulation) is a comparatively rare event (usually developing sometime after major bowel surgery). It is, however, hard to diagnose correctly, and if left uncorrected can lead to bowel infarction and death. (The singer Maurice Gibb is understood to have died from this.) *

Angiodysplasia In medicine (gastroenterology), angiodysplasia is a small vascular malformation of the gut. It is a common cause of otherwise unexplained gastrointestinal bleeding and anemia. Lesions are often multiple, and frequently involve the cecum or asce ...

of the colon * Constipation * Diarrhea * Hirschsprung's disease (aganglionosis) *

Intussusception Intussusception may refer to: * Intussusception (medical disorder) Intussusception is a medical condition in which a part of the intestine folds into the section immediately ahead of it. It typically involves the small bowel and less commonly t ...

Polyp (medicine) In anatomy, a polyp is an abnormal growth of tissue projecting from a mucous membrane. If it is attached to the surface by a narrow elongated stalk, it is said to be ''pedunculated''; if it is attached without a stalk, it is said to be ''sess ...

(see also

colorectal polyp A colorectal polyp is a polyp (fleshy growth) occurring on the lining of the colon or rectum. Untreated colorectal polyps can develop into colorectal cancer. Colorectal polyps are often classified by their behaviour (i.e. benign vs. malignant) ...

) *

Pseudomembranous colitis Colitis is swelling or inflammation of the large intestine ( colon). Colitis may be acute and self-limited or long-term. It broadly fits into the category of digestive diseases. In a medical context, the label ''colitis'' (without qualification) ...

* Toxic megacolon usually a complication of ulcerative colitis

Uses of animal guts

Intestines from animals other than humans are used in a number of ways. From each species of livestock that is a source of milk, a corresponding

rennet Rennet () is a complex set of enzymes produced in the stomachs of ruminant mammals. Chymosin, its key component, is a protease enzyme that curdles the casein in milk. In addition to chymosin, rennet contains other enzymes, such as pepsin and a ...

is obtained from the intestines of milk-fed . Pig and

calf Calf most often refers to: * Calf (animal), the young of domestic cattle. * Calf (leg), in humans (and other primates), the back portion of the lower leg Calf or calves may also refer to: Biology and animal byproducts * Veal, meat from calves * ...

intestines are eaten, and pig intestines are used as sausage casings. Calf intestines supply

calf-intestinal alkaline phosphatase Calf-intestinal alkaline phosphatase (CIAP/CIP) is a type of alkaline phosphatase that catalyzes the removal of phosphate groups from the 5' end of DNA strands and phosphomonoesters from RNA. This enzyme is frequently used in DNA sub-cloning, a ...

(CIP), and are used to make goldbeater's skin. Other uses are: * The use of animal gut

strings String or strings may refer to: *String (structure), a long flexible structure made from threads twisted together, which is used to tie, bind, or hang other objects Arts, entertainment, and media Films * ''Strings'' (1991 film), a Canadian anim ...

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 Steel is an alloy made up of iron with added carbon to improve its strength and fracture resistance compared to other forms of iron. Many other elements may be present or added. Stainless steels that are corrosion- and oxidation-resistant ty ...

. 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 gut strings are now made out of cow gut. * Gut cord has also been used to produce strings for the snares that provide a

snare drum The snare (or side drum) is a percussion instrument that produces a sharp staccato sound when the head is struck with a drum stick, due to the use of a series of stiff wires held under tension against the lower skin. Snare drums are often used ...

's characteristic buzzing timbre. While the modern snare drum almost always uses metal wire rather than gut cord, the North African

bendir The ''bendir'' ( ar, بندير, plural ''banadir'', ) is a wooden-framed frame drum of North Africa and Southwest Asia. The bendir is a traditional instrument that is played throughout North Africa, as well as in Sufi ceremonies; it was played ...

frame drum still uses gut for this purpose. * "Natural" sausage hulls, or casings, are made of animal gut, especially hog, beef, and lamb. * The wrapping of kokoretsi,

gardoubakia Kokoretsi or kokoreç is a dish of the Balkans and Anatolia (Asia Minor), consisting of lamb or goat intestines wrapped around seasoned offal, including sweetbreads, hearts, lungs, or kidneys, and typically grilled; a variant consists of choppe ...

, and

torcinello Torcinello (turcenélle in the Apulian and Molise dialects, mboti, turcinieddi, or turcinieddhri in the Salento dialect) is an Italian dish from Apulia and Molise consisting of lamb intestines wrapped around lamb liver or offal, typically testicle ...

is made of lamb (or goat) gut. * Haggis is traditionally boiled in, and served in, a sheep stomach. *

Chitterlings Chitterlings (), sometimes spelled chitlins or chittlins, are the small intestines of domestic animals. They are usually made from pigs' intestines. They may also be filled with a forcemeat to make sausage.''Oxford English Dictionary'', 1st editi ...

, a kind of food, consist of thoroughly washed pig's gut. * Animal gut was used to make the cord lines in

longcase clock A grandfather clock (also a longcase clock, tall-case clock, grandfather's clock, or floor clock) is a tall, freestanding, weight-driven pendulum clock with the pendulum held inside the tower or waist of the case. Clocks of this style are common ...

s and for

fusee Fusee or fusée may refer to: * Fusee (horology), a component of a clock * Flare, a pyrotechnic device sometimes called a Fusee * Fusee, an old word for "flintlock Flintlock is a general term for any firearm that uses a flint-striking lock (fi ...

movements in bracket clocks, but may be replaced by metal wire. * The oldest known

condom A condom is a sheath-shaped barrier device used during sexual intercourse to reduce the probability of pregnancy or a sexually transmitted infection (STI). There are both male and female condoms. With proper use—and use at every act of in ...

s, from 1640 AD, were made from animal intestine.

Other animals

Many birds and other animals have a specialised stomach in the digestive tract called a gizzard used for grinding up food. Another feature not found in the human but found in a range of other animals is the crop. In birds this is found as a pouch alongside the esophagus. Most vertebrates including fishes,

amphibian Amphibians are tetrapod, four-limbed and ectothermic vertebrates of the Class (biology), class Amphibia. All living amphibians belong to the group Lissamphibia. They inhabit a wide variety of habitats, with most species living within terres ...

s, birds,

reptile Reptiles, as most commonly defined are the animals in the class Reptilia ( ), a paraphyletic grouping comprising all sauropsids except birds. Living reptiles comprise turtles, crocodilians, squamates (lizards and snakes) and rhynchocephalians ( ...

s, and egg-laying mammals have a major difference in their GI tract in that it ends in a

cloaca In animal anatomy, a cloaca ( ), plural cloacae ( or ), is the posterior orifice that serves as the only opening for the digestive, reproductive, and urinary tracts (if present) of many vertebrate animals. All amphibians, reptiles and birds, a ...

and not an

, having merged the urinary system with the genito-anal pore. Therians (most/other mammals, including humans) separated their anus from their uro-genital opening for both sexes, with subgroup

placentalia Placental mammals (infraclass Placentalia ) are one of the three extant subdivisions of the class Mammalia, the other two being Monotremata and Marsupialia. Placentalia contains the vast majority of extant mammals, which are partly distinguished ...

ns later separating their urinary and genital openings by a little distance, this time only in females. In 2020, the oldest known fossil digestive tract, of an extinct wormlike organism in the

Cloudinidae The cloudinids, an early metazoan family containing the genera ''Acuticocloudina'', ''Cloudina'' and ''Conotubus'', lived in the late Ediacaran period about 550 million years ago. and became extinct at the base of the Cambrian. They formed mil ...

was discovered; it lived during the late

Ediacaran The Ediacaran Period ( ) is a geological period that spans 96 million years from the end of the Cryogenian Period 635 million years ago (Mya), to the beginning of the Cambrian Period 538.8 Mya. It marks the end of the Proterozoic Eon, and th ...

period about 550 million years ago. A through-gut (one with both mouth and anus) is thought to have evolved within the nephrozoan clade of

Bilateria The Bilateria or bilaterians are animals with bilateral symmetry as an embryo, i.e. having a left and a right side that are mirror images of each other. This also means they have a head and a tail (anterior-posterior axis) as well as a belly and ...

, after their ancestral ventral orifice (single, as in cnidarians and acoels; re-evolved in nephrozoans like flatworms) stretched antero-posteriorly, before the middle part of the stretch would get narrower and closed fully, leaving an anterior orifice (mouth) and a posterior orifice (anus plus genital opening). A stretched gut without the middle part closed is present in another branch of bilaterians, the extinct proarticulates. This and the amphistomic development (when both mouth and anus develop from the gut stretch in the embryo) present in some nephrozoans (e.g. roundworms) are considered to support this hypothesis.De Robertis, E. M., & Tejeda-Muñoz, N. (2022). Evo-Devo of urbilateria and its larval forms. ''Developmental Biology'', 487, 10–20. https://doi.org/10.1016/j.ydbio.2022.04.003

References

External links

The gastro intestinal tract in the Human Protein Atlas

Your Digestive System and How It Works at National Institutes of Health
{{DEFAULTSORT:Gastrointestinal Abdomen Digestive system Endocrine system Routes of administration