Editing Gastrointestinal tract (section)

==Human gastrointestinal tract==
===Structure===
[[File:Digestive system simplified.svg|thumb|Illustration of [[Human digestive system|digestive system]]]]
The structure and function of the GI tract can be described both by [[gross anatomy]] and [[microscopic anatomy]] (histology). The tract itself is divided into upper and lower tracts, and the intestines into [[small intestine|small]] and [[large intestine]]s.<ref>{{cite web|website=The Physics Factbook|url=http://hypertextbook.com/facts/2001/AnneMarieThomasino.shtml|title=Length of a Human Intestine|date=2001|first=Anne Marie|last=Thomasino}}</ref>

====Upper gastrointestinal tract====
{{Main|Mouth|Pharynx|Esophagus|Stomach|duodenum}}
The upper gastrointestinal tract consists of the [[Human mouth|mouth]], [[pharynx]], [[esophagus]], [[stomach]], and [[duodenum]].<ref>{{MeSH name|Upper+Gastrointestinal+Tract}}</ref>
The exact demarcation between the upper and lower tracts is the [[suspensory muscle of the duodenum]]. 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]], the duodenum may appear to be a unified organ, but it is divided into four segments based on function, location, and internal anatomy. The four segments of the duodenum are as follows (starting at the stomach, and moving toward the jejunum): [[duodenal bulb|bulb]], descending, horizontal, and ascending. 

The suspensory muscle of the duodenum suspends the superior border of the ascending duodenum from the [[thoracic diaphragm|diaphragm]], and serves as an important anatomical landmark showing the formal division between the duodenum and the jejunum, the first and second parts of the small intestine, respectively.<ref name="Warrell2005">{{cite book|author=David A. Warrell|title=Oxford textbook of medicine: Sections 18-33|url=https://books.google.com/books?id=hL1NKQJlY1IC&pg=PA511|access-date=1 July 2010|year=2005|publisher=Oxford University Press|isbn=978-0-19-856978-7|pages=511–}}</ref> This is a thin muscle which is derived from the [[embryo]]nic [[mesoderm]].

====Lower gastrointestinal tract====
{{Redirect|Guts|Gut (disambiguation)}}
The lower gastrointestinal tract includes most of the [[small intestine]] and all of the [[large intestine]].<ref>{{MeSH name|Lower+Gastrointestinal+Tract}}</ref> In [[human anatomy]], the '''intestine''' ('''bowel''' or '''gut'''; Greek: '''éntera''') is the segment of the gastrointestinal tract extending from the [[pyloric sphincter]] of the [[stomach]] to the [[Human anus|anus]] and as in other mammals, consists of two segments: the [[small intestine]] and the [[large intestine]]. In humans, the small intestine is further subdivided into the [[duodenum]], [[jejunum]], and [[ileum]]. The large intestine is subdivided into the [[cecum]], and [[Ascending colon|ascending]], [[Transverse colon|transverse]], [[Descending colon|descending]], and [[Sigmoid colon|sigmoid]] [[Colon (anatomy)|colon]]s, [[rectum]], and [[anal canal]].<ref name="Kapoor2011">{{cite web|url=http://emedicine.medscape.com/article/1948929-overview|title=Large Intestine Anatomy|publisher=WebMD LLC.|work=Medscape|date=13 Jul 2011|access-date=2013-08-20|author=Kapoor, Vinay Kumar|editor=Gest, Thomas R.}}</ref><ref name="GrayLargeIntestine">{{cite book|url=http://www.bartleby.com/107/|title=Gray's Anatomy|publisher=Lea & Febiger|author=Gray, Henry|author-link=Henry Gray|year=1918|location=Philadelphia}}</ref>

=====Small intestine=====
{{Main|Small intestine|Duodenum|Jejunum|Ileum}}
The [[small intestine]] is a tubular structure around 6 to 7 m long, that begins at the [[duodenum]], and ends at the [[ileum]].<ref name="GRAYS2005">{{cite book|title=Gray's anatomy for students|last=Drake|first=Richard L.|author2=Vogl, Wayne|author3=Tibbitts, Adam W.M. Mitchell|author4=illustrations by Richard|author5=Richardson, Paul|publisher=Elsevier/Churchill Livingstone|year=2015|isbn=978-0-8089-2306-0|edition=3rd|location=Philadelphia|page=312}}</ref> Its [[mucosal]] area in an adult human is about {{convert|30|m2|abbr=on}}.<ref name="ReferenceA">{{Cite journal|last1=Helander|first1=Herbert F.|last2= Fändriks|first2=Lars|date=2014-06-01|title=Surface area of the digestive tract - revisited|journal=Scandinavian Journal of Gastroenterology|volume=49|issue=6|pages=681–689|doi=10.3109/00365521.2014.898326|issn=1502-7708|pmid=24694282|s2cid=11094705}}</ref> The combination of the [[circular folds]], the villi, and the microvilli increases the absorptive area of the mucosa about 600-fold, making a total area of about {{convert|250|sqm|sqft|abbr=on}} for the entire small intestine.<ref name="Hall">{{cite book|last1=Hall|first1=John|title=Guyton and Hall textbook of medical physiology|date=2011|isbn=9781416045748|page=794|publisher=Saunders/Elsevier|edition=Twelfth}}</ref> 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]]: A short structure (about 20–25&nbsp;cm long<ref name=GRAYS2005/>) that receives [[chyme]] from the stomach, together with [[pancreatic juice]] containing [[digestive enzymes]] and [[bile]] from the [[gall bladder]]. The digestive enzymes break down proteins, and bile [[emulsion|emulsifies]] fats into [[micelles]]. The [[duodenum]] 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 {{convert|2.5|m|ft|abbr=on}} long and contains the [[circular folds]] also known as plicae circulares and [[intestinal villus|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 [[intestinal villus|villi]] similar to the jejunum. It absorbs mainly [[vitamin B12]] and [[bile acids]], as well as any other remaining nutrients.

=====Large intestine=====
{{Main|Large intestine}}

The [[large intestine]] forms an arch starting at the [[cecum]] and ending at the [[rectum]] and [[anal canal]]. It also includes the [[appendix (anatomy)|appendix]], which is attached to the [[cecum]]. Its length is about 1.5 m, and the area of the mucosa in an adult human is about {{convert|2|m2|abbr=on}}.<ref name="ReferenceA" /> The longest part of the large intestine is the [[Large intestine#Structure|colon]] whose main function is to absorb water and salts.<ref name="Terms">{{cite web|title=definition colon|url=https://www.cancer.gov/publications/dictionaries/cancer-terms/def/colon|website=www.cancer.gov|access-date=24 January 2025|language=en|date=2 February 2011}}</ref>

The large intestine begins at the cecum, where the [[Appendix (anatomy)|appendix]] is located. This is also the start of the colon as the [[ascending colon]] in the back wall of the abdomen. At the [[right colic flexure]] ([[Liver|hepatic]] flexure) (the flexed portion of the ascending and [[transverse colon]]) it runs across the abdomen in the transverse colon, passing below the diaphragm. At the [[left colic flexure]] ([[Spleen|splenic]] flexure) the flexed portion of the transverse and [[descending colon]], it descends down the left side of the abdomen.
It reaches the [[sigmoid colon]] which is a loop of the colon closest to the rectum and continues to the rectum and [[anal canal]].

====Development====
{{main|Development of the digestive system}}
The gut is an [[endoderm]]-derived structure. At approximately the sixteenth day of human development, the [[embryo]] begins to fold [[ventral]]ly (with the embryo's ventral surface becoming [[concave polygon|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 [[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 [[fetus|fetal]] life, the primitive gut is gradually patterned into three segments: [[foregut]], [[midgut]], and [[hindgut]]. 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 (anatomy)|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.<ref>{{cite book|author=Bruce M. Carlson|title=Human Embryology and Developmental Biology|publisher=Mosby|location=Saint Louis|edition=3rd|year=2004|isbn=978-0-323-03649-8}}</ref>

{| class="wikitable"
|-
! Part || Part in adult || Gives rise to || Arterial supply
 |-
 | [[Foregut]] || esophagus to first 2 sections of the duodenum || Esophagus, stomach, duodenum (1st and 2nd parts), liver, gallbladder, pancreas, superior portion of pancreas<br />(Though the spleen is supplied by the [[Celiac artery|celiac trunk]], it is derived from dorsal mesentery and therefore not a foregut derivative) || celiac trunk
 |-1
 | [[Midgut]] || lower duodenum, to the first two-thirds of the transverse colon || lower [[duodenum]], [[jejunum]], [[ileum]], [[cecum]], [[vermiform appendix|appendix]], [[ascending colon]], and first two-thirds of the [[transverse colon]] || branches of the [[superior mesenteric artery]]
 |-
 | [[Hindgut]] || last third of the transverse colon, to the upper part of the anal canal || last third of the [[transverse colon]], [[descending colon]], [[rectum]], and upper part of the [[anal canal]] || branches of the [[inferior mesenteric artery]]
|}

====Histology====
{{Main|Gastrointestinal wall}}
[[File:Layers of the GI Tract english.svg|thumb|300px|General structure of the gut wall]]

The gastrointestinal tract has a form of general histology with some differences that reflect the specialization in functional anatomy.<ref>{{cite book|author=Abraham L. Kierszenbaum|title=Histology and cell biology: an introduction to pathology|publisher=Mosby|location=St. Louis|year=2002|isbn=978-0-323-01639-1}}</ref> The GI tract can be divided into four concentric layers in the following order:
* [[Mucous membrane|Mucosa]]
* [[Submucosa]]
* [[Muscular layer]]
* [[Adventitia]] or [[Serous membrane|serosa]]

=====Mucosa=====
{{See also|Oral mucosa|Gastric mucosa}}
The mucosa is the innermost layer of the gastrointestinal tract. The mucosa surrounds the [[lumen (anatomy)|lumen]], or open space within the tube. This layer comes in direct contact with digested food ([[chyme]]). The mucosa is made up of:
* [[Intestinal epithelium|Epithelium]] – innermost layer. Responsible for most digestive, absorptive and secretory processes.
* [[Lamina propria]] – a layer of connective tissue. Unusually cellular compared to most connective tissue
* [[Muscularis mucosae]] – 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=====
{{Main|Submucosa}}
The submucosa consists of a dense irregular layer of connective tissue with large blood vessels, lymphatics, and nerves branching into the mucosa and [[Muscular layer|muscularis externa]]. It contains the [[submucosal plexus]], an [[enteric nervous system|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 [[Anatomical terms of location|longitudinal]] 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.<ref name="Sarna">{{Cite book|title=Colonic Motility: From Bench Side to Bedside|last=Sarna|first=S.K.|publisher=Morgan & Claypool Life Sciences|year=2010|isbn=9781615041503|location=San Rafael, California|chapter=Introduction}}</ref> 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 the outer longitudinal layer.

Between the circular and longitudinal muscle layers is the [[myenteric plexus]]. This controls peristalsis. Activity is initiated by the pacemaker cells, (myenteric [[interstitial cells of Cajal]]). The gut has intrinsic peristaltic activity ([[basal electrical rhythm]]) due to its self-contained enteric nervous system. The rate can be modulated by the rest of the [[autonomic nervous system]].<ref name="Sarna"/>

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 [[chyme]]. In the large intestine, the remaining semi-solid substance is referred to as [[Human feces|faeces]].<ref name="Sarna"/>

=====Adventitia and serosa=====
{{Main|Serous membrane|Adventitia}}
The outermost layer of the gastrointestinal tract consists of several layers of [[connective tissue]].

[[Peritoneum#Classification of abdominal structures|Intraperitoneal]] parts of the GI tract are covered with [[serosa]]. These include most of the [[stomach]], first part of the [[duodenum]], all of the [[small intestine]], [[caecum]] and [[Vermiform appendix|appendix]], [[transverse colon]], [[sigmoid colon]] and [[rectum]]. 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]].

[[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 [[duodenum]], [[ascending colon]], [[descending colon]] and [[anal canal]]. In addition, the [[human mouth|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.<ref>{{Cite web|url=https://www.proteinatlas.org/humanproteome/gastrointestinal+tract|title=The human proteome in gastrointestinal tract - The Human Protein Atlas|website=www.proteinatlas.org|access-date=2017-09-21}}</ref><ref>{{Cite journal|last1=Uhlén|first1=Mathias|last2=Fagerberg|first2=Linn|last3=Hallström|first3=Björn M.|last4=Lindskog|first4=Cecilia|last5=Oksvold|first5=Per|last6=Mardinoglu|first6=Adil|last7=Sivertsson|first7=Åsa|last8=Kampf|first8=Caroline|last9=Sjöstedt|first9=Evelina|date=2015-01-23|title=Tissue-based map of the human proteome|journal=Science|language=en|volume=347|issue=6220|pages=1260419|doi=10.1126/science.1260419|issn=0036-8075|pmid=25613900|s2cid=802377}}</ref> 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 [[Pepsin|pepsinogen PGC]] and the [[Lipase|lipase LIPF]], expressed in [[Gastric chief cell|chief cells]], and gastric [[ATPase|ATPase ATP4A]] and [[Gastric intrinsic factor|gastric intrinsic factor GIF]], expressed in [[parietal cell]]s of the stomach mucosa. Specific proteins expressed in the stomach and duodenum involved in defence include [[mucin]] proteins, such as [[mucin 6]] and [[intelectin-1]].<ref>{{Cite journal|last1=Gremel|first1=Gabriela|last2=Wanders|first2=Alkwin|last3=Cedernaes|first3=Jonathan|last4=Fagerberg|first4=Linn|last5=Hallström|first5=Björn|last6=Edlund|first6=Karolina|last7=Sjöstedt|first7=Evelina|last8=Uhlén|first8=Mathias|last9=Pontén|first9=Fredrik|date=2015-01-01|title=The human gastrointestinal tract-specific transcriptome and proteome as defined by RNA sequencing and antibody-based profiling|journal=Journal of Gastroenterology|language=en|volume=50|issue=1|pages=46–57|doi=10.1007/s00535-014-0958-7|pmid=24789573|s2cid=21302849|issn=0944-1174}}</ref>

====Transit time====
The time taken for food to transit through the gastrointestinal tract varies on multiple factors, including age, ethnicity, and gender.<ref>{{Citation|last1=Degen|first1=L.P.|last2=Phillips|first2=S.F.|title=Variability of gastrointestinal transit in healthy women and men|journal=Gut|volume=39|pages=299–305|date=August 1996|issue=2|doi=10.1136/gut.39.2.299|pmid=8977347|pmc=1383315}}</ref><ref>{{Citation|last=Madsen, MD|first=Jan Lysgard|title=Effects of gender, age, and body mass index on gastrointestinal transit times|journal=Digestive Diseases and Sciences|volume=37|pages=1548–1553|date=1992|issue=10|doi=10.1007/BF01296501|pmid=1396002}}</ref> Several techniques have been used to measure transit time, including radiography following a [[barium]]-labeled meal, breath [[hydrogen]] analysis, [[scintigraphic]] analysis following a [[radionuclide|radiolabeled]] meal,<ref name=Bowen>{{cite web|last=Bowen|first=Richard|title=Gastrointestinal Transit: How Long Does It Take?|publisher= Colorado State University|url=http://www.vivo.colostate.edu/hbooks/pathphys/digestion/basics/transit.html}}</ref> and simple ingestion and spotting of [[maize|corn kernel]]s.<ref>{{cite journal|last1=Keendjele|first1=Tuwilika P. T.|last2=Eelu|first2=Hilja H.|last3=Nashihanga|first3=Tunelago E.|last4=Rennie|first4=Timothy W.|last5=Hunter|first5=Christian John|title=Corn? When did I eat corn? Gastrointestinal transit time in health science students|journal=Advances in Physiology Education|date=1 March 2021|volume=45|issue=1|pages=103–108|doi=10.1152/advan.00192.2020|pmid=33544037|s2cid=231817664|doi-access=free}}</ref> It takes 2.5 to 3 hours for 50% of the contents to leave the stomach.{{medical citation needed|date=July 2020}} 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.<ref>{{Citation|last1=Wilson|first1=Malcom J.|last2=Dickson|first2=W.H.|last3=Singleton|first3=A.C.|title=Rate of evacuation of various foods from the normal stomach: a preliminary communication|journal=Arch Intern Med|volume=44|pages=787–796|date=1929|doi=10.1001/archinte.1929.00140060002001}}</ref> Total emptying of the stomach takes around 4–5 hours, and transit through the colon takes 30 to 50 hours.<ref name=Bowen/><ref>{{cite journal|last1=Kim|first1=SK|year=1968|title=Small intestine transit time in the normal small bowel study|journal=American Journal of Roentgenology|volume=104|issue=3|pages=522–524|doi=10.2214/ajr.104.3.522|pmid=5687899|doi-access=free}}</ref><ref>{{Cite journal|pmc=3325313|year=2012|last1=Ghoshal|first1=U. C.|title=Colonic Transit Study Technique and Interpretation: Can These be Uniform Globally in Different Populations with Non-uniform Colon Transit Time?|journal=Journal of Neurogastroenterology and Motility|volume=18|issue=2|pages=227–228|last2=Sengar|first2=V.|last3=Srivastava|first3=D.|pmid=22523737|doi=10.5056/jnm.2012.18.2.227}}</ref>

====Immune function====
The gastrointestinal tract forms an important part of the [[immune system]].<ref>{{Cite journal|last1=Mowat|first1=Allan M.|last2=Agace|first2=William W.|date=2014-10-01|title=Regional specialization within the intestinal immune system|journal=Nature Reviews. Immunology|volume=14|issue=10|pages=667–685|doi=10.1038/nri3738|issn=1474-1741|pmid=25234148|s2cid=31460146}}</ref>

=====Immune barrier=====
The surface area of the digestive tract is estimated to be about 32 square meters, or about half a badminton court.<ref name="ReferenceA" /> With such a large exposure (more than three times larger than the [[Human skin|exposed surface of the skin]]), these immune components function to prevent pathogens from entering the blood and lymph circulatory systems.<ref>{{Cite journal|last1= Flannigan|first1=Kyle L.|last2=Geem|first2=Duke|last3=Harusato|first3=Akihito|last4=Denning|first4=Timothy L.|date=2015-07-01|title=Intestinal Antigen-Presenting Cells: Key Regulators of Immune Homeostasis and Inflammation|journal=The American Journal of Pathology|volume=185|issue=7|pages=1809–1819|doi= 10.1016/j.ajpath.2015.02.024|issn=1525-2191|pmc=4483458|pmid=25976247}}</ref> 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.<ref>{{Cite journal|last1=Sánchez de Medina|first1=Fermín|last2=Romero-Calvo|first2=Isabel|last3=Mascaraque|first3=Cristina|last4=Martínez-Augustin|first4=Olga|date=2014-12-01|title= Intestinal inflammation and mucosal barrier function|journal=Inflammatory Bowel Diseases|volume=20|issue=12|pages= 2394–2404|doi=10.1097/MIB.0000000000000204|issn=1536-4844|pmid=25222662|s2cid=11434730|doi-access=free}}</ref> Microorganisms also are kept at bay by an extensive immune system comprising the [[gut-associated lymphoid tissue]] (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 [[microorganism]]s that enter it.<ref>{{Cite journal|last=Schubert|first=Mitchell L.|date=2014-11-01|title=Gastric secretion|journal=Current Opinion in Gastroenterology|volume=30|issue=6|pages=578–582|doi=10.1097/MOG.0000000000000125|issn=1531-7056|pmid=25211241|s2cid=8267813}}</ref> Similarly, [[mucus]] (containing [[IgA]] [[antibody|antibodies]]) neutralizes many pathogenic microorganisms.<ref>{{Cite journal|last1=Márquez|first1=Mercedes|last2=Fernández Gutiérrez Del Álamo|first2=Clotilde|last3=Girón-González|first3=José Antonio|date=2016-01-28|title=Gut epithelial barrier dysfunction in human immunodeficiency virus-hepatitis C virus coinfected patients: Influence on innate and acquired immunity|journal=World Journal of Gastroenterology|volume=22|issue=4|pages=1433–1448|doi=10.3748/wjg.v22.i4.1433|issn=2219-2840|pmc=4721978|pmid=26819512|doi-access=free}}</ref> Other factors in the GI tract contribution to immune function include [[enzyme]]s secreted in the [[saliva]] and [[bile]].

=====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.<ref>{{Cite journal|title=Commensal microbe-derived butyrate induces the differentiation of colonic regulatory T cells|journal=Nature|volume=504|issue=7480|pages=446–450|doi=10.1038/nature12721|pmid=24226770|year=2013|last1=Furusawa|first1=Yukihiro|last2=Obata|first2=Yuuki|last3=Fukuda|first3=Shinji|last4=Endo|first4=Takaho A.|last5=Nakato|first5=Gaku|last6=Takahashi|first6=Daisuke|last7=Nakanishi|first7=Yumiko|last8=Uetake|first8=Chikako|last9=Kato|first9=Keiko|last10=Kato|first10=Tamotsu|last11=Takahashi|first11=Masumi|last12=Fukuda|first12=Noriko N.|last13=Murakami|first13=Shinnosuke|last14=Miyauchi|first14=Eiji|last15=Hino|first15=Shingo|last16=Atarashi|first16=Koji|last17=Onawa|first17=Satoshi|last18=Fujimura|first18=Yumiko|last19=Lockett|first19=Trevor|last20=Clarke|first20=Julie M.|last21=Topping|first21=David L.|last22=Tomita|first22=Masaru|last23=Hori|first23=Shohei|last24=Ohara|first24=Osamu|last25=Morita|first25=Tatsuya|last26=Koseki|first26=Haruhiko|last27=Kikuchi|first27=Jun|last28=Honda|first28=Kenya|last29=Hase|first29=Koji|last30=Ohno|first30=Hiroshi|bibcode=2013Natur.504..446F|s2cid=4408815}}</ref> It has been demonstrated that the intake of a high fiber diet could be responsible for the induction of [[T-regulatory cell]]s (Tregs). This is due to the production of [[short-chain fatty acid]]s during the fermentation of plant-derived nutrients such as [[butyrate]] and [[propionate]]. Basically, the butyrate induces the differentiation of Treg cells by enhancing [[histone H3]] [[Acetylation#Protein acetylation|acetylation]] 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.

====Gastrointestinal microbiota====
{{Main article|Gut microbiota}}
[[File:Microbiome.jpg|thumb|upright=1.6|Diagram of human [[microbiota]] depicted in various regions of the gastrointestinal tract]]
The large intestine contains multiple types of [[bacteria]], and other [[microorganism]]s that can break down molecules the human body cannot process alone,<ref name="Knight2002">{{Cite book|url=https://books.google.com/books?id=G0sCAAAACAAJ|title=Science of Everyday Things: Real-life biology|isbn=9780787656348|volume=4|last1=Knight|first1=Judson|year=2002|publisher=Gale}}</ref><ref>{{cite journal|last1=Hillman|first1=Ethan T|last2=Lu|first2=Hang|last3=Yao|first3=Tianmang|last4=Nakatsu|first4=Cindy H|title=Minireview: Microbial Ecology along the Gastrointestinal Tract|journal=Microbes Environ|date=2017|volume=32|issue=4|pages=300–313|doi=10.1264/jsme2.ME17017|pmid=29129876 |pmc=5745014 |url=https://www.jstage.jst.go.jp/article/jsme2/32/4/32_ME17017/_html/-char/en|access-date=30 March 2025}}</ref> demonstrating a [[symbiosis|symbiotic]] relationship. These microbes are responsible for gas production at [[host–pathogen interface]], which is released as [[flatulence]]. Intestinal bacteria can also participate in biosynthesis reactions. For example, certain strains in the large intestine produce vitamin B<sub>12</sub>;<ref>{{Cite journal|last=Martens, H. Barg, M. Warren, D. Jah|first=J.-H.|date=2002-03-01|title=Microbial production of vitamin B 12|url=http://link.springer.com/10.1007/s00253-001-0902-7|journal=Applied Microbiology and Biotechnology|volume=58|issue=3|pages=275–285|doi=10.1007/s00253-001-0902-7|pmid=11935176|issn=0175-7598}}</ref> an essential compound in humans for things like DNA synthesis and red blood cell production.<ref>{{Cite web|title=Are You Getting Enough Vitamin B12? What You Need to Know|url=https://www.yalemedicine.org/news/are-you-getting-enough-vitamin-b12#:~:text=Vitamin%20B12,%20also%20called%20cobalamin,meaning%20it%20dissolves%20in%20water.|access-date=2024-11-23|website=Yale Medicine|language=en}}</ref> However, the primary function of the large intestine is water absorption from digested material (regulated by the [[hypothalamus]]) and the reabsorption of [[sodium]] and nutrients.<ref>{{cite journal|url=https://www.ncbi.nlm.nih.gov/books/NBK507857/#:~:text=The%20large%20intestine%20has%203,toward%20the%20rectum%20for%20elimination.|title=Physiology, Large Intestine|last1=Azzouz|first1=Laura L.|last2=Sharma|first2=Sandeep|publisher=StatPearls Publishing|date=31 July 2023|website=National Library of Medicine|pmid=29939634|access-date=24 March 2024}}</ref>

Beneficial [[Gut flora|intestinal bacteria]] compete with potentially harmful [[bacteria]] for space and "food", as the intestinal tract has limited resources. A ratio of 80–85% beneficial to 15–20% potentially harmful bacteria is proposed for maintaining [[homeostasis]].{{citation needed|date=May 2016}} An imbalanced ratio results in [[dysbiosis]].

====Detoxification and drug metabolism====
[[Enzyme]]s such as [[CYP3A4]], along with the [[antiporter]] activities, are also instrumental in the intestine's role of [[drug metabolism]] in the detoxification of [[antigen]]s and [[xenobiotic]]s.<ref>{{cite journal|last2=Ziegler|first2=DM|date=5 December 1990|title=The enzymes of detoxication.|journal=The Journal of Biological Chemistry|volume=265|issue=34|pages=20715–8|pmid=2249981|last1=Jakoby|first1=WB|doi=10.1016/S0021-9258(17)45272-0|doi-access=free}}</ref>