The  interstitial cells of Cajal  are specialized pacemaker cells  [ 3 ]  located in the wall of the stomach, small intestine, and large intestine. [ 1 ]   These cells are connected to the smooth muscle via  gap junctions  and the  myenteric plexus .  The cell membranes of the pacemaker cells undergo a rhythmic  depolarization  and repolarization from -65 mV  to -45mV. [ citation needed ]   This rhythm of depolarization-repolarization of the cell membrane creates a slow wave known as a BER, and it is transmitted to the smooth muscle cells.  The frequency of these depolarizations in a region of the GI tract determines the possible frequency of contractions.  In order for a contraction to occur, a  hormone  or  neurocrine  signal must induce the smooth muscle cell to have an action potential.  The basal electrical rhythm allows the smooth muscle cell to depolarize and contract rhythmically when exposed to hormonal signals.  This action potential is transmitted to other smooth muscle cells via gap junctions, creating a peristaltic wave.


The specific mechanism for the contraction of smooth muscle in the GI tract depends upon  IP3R calcium release  channels in the muscle. [ 4 ]   Calcium  release from IP3 sensitive calcium stores activates calcium dependent  chloride channels . [ 4 ]  These chloride channels trigger spontaneous transient inward current which couples the calcium oscillations to electrical activity. [ 4 ]


The number of action potentials during the plateau of a particular BER slow wave can vary.  This variation in action potential generation does not impact the frequency of waves through the GI tract, only the strength of those contractile waves. [ 2 ]


The cells that respond to and secrete these substances include  I cells  and  K cells  in the proximal small intestine, whose stimulation is dependent on nutrient exposure and entry into the duodenum, and  L cells  in the distal small intestine and colon which are stimulated by unabsorbed nutrients and gastric emptying. [ 5 ]


The frequency of the BER, and thus the contractions, changes throughout the GI tract.  The  frequency  in the stomach is 3 per minute, while the  duodenum  is 11 to 12 per minute and the  ileum  is 9 per minute. [ 1 ]   The colon can have a BER frequency between 2 and 13 per minute. The electrical activity is oscillatory, so that the BER has peaks and valleys when graphed over time.


B. a. animalis B. a. lactis


Bifidobacterium animalis  is a  gram-positive , anaerobic, rod-shaped bacterium of the  Bifidobacterium  genus which can be found in the  large intestines  of most  mammals , including humans.


Bifidobacterium animalis  and  Bifidobacterium lactis  were previously described as two distinct species. Presently, both are considered  B. animalis  with the subspecies  Bifidobacterium animalis  subsp.  animalis  and  Bifidobacterium animalis  subsp.  lactis . [ 1 ] [ 2 ] [ 3 ]


Both old names  B. animalis  and  B. lactis  are still used on product labels, as this species is frequently used as a  probiotic . In most cases, which subspecies is used in the product is not clear.


Several companies have attempted [ clarification needed ]  to trademark particular strains, and as a marketing technique, have invented scientific-sounding names for the strains.


Danone  (Dannon in the United States) markets the subspecies strain  DN 173 010  as Bifidus Digestivum (UK), Bifidus Regularis (US and Mexico), Bifidobacterium Lactis or B.L. Regularis (Canada), DanRegularis (Brazil), Bifidus Actiregularis (Argentina, Austria, Belgium, Bulgaria, Chile, Czech Republic, France, Germany, Greece, Hungary, Israel, Italy, Kazakhstan, Netherlands, Portugal, Romania, Russia, South Africa, Spain and the UK), and Bifidus Essensis in the Middle East (and formerly in Hungary, Bulgaria, Romania and The Netherlands) through  Activia  from Safi Danone KSA. [ citation needed ]


Chr. Hansen A/S  from Denmark has a similar claim on a strain of  Bifidobacterium animalis  subsp.  lactis , marketed under the trademark BB-12. [ 4 ]


Lidl  lists "Bifidobacterium BB-12" in its "Proviact" yogurt.


Bifidobacterium lactis  Bl-04 and Bi-07 are strains from  DuPont 's  Danisco  FloraFIT range. They are used in many dietary probiotic supplements.


Theralac contains the strains  Bifidobacterium lactis  BI-07 and  Bifidobacterium lactis  BL-34 [ 5 ]  (also called BI-04) in its probiotic capsule.


Bifidobacterium animalis lactis  HN019 (DR10) is a strain from  Fonterra  licensed to DuPont, which markets it as HOWARU Bifido. It is sold in a variety of commercial probiotics, among them  Tropicana Products  Essentials Probiotics, [ 6 ]  Attune Wellness Bars [ 7 ]  and NOW Foods Clinical GI Probiotic. [ 8 ]  Fonterra has a yogurt that is sold in New Zealand called Symbio Probalance, where the strain is labelled as DR10.


Bifidobacterium animalis  subspecies lactis BB-12 administered in combination with other probiotics has showed "a trend toward increased remission" in a study of 32 patients with  ulcerative colitis . [ 9 ]


Research on  Bifidobacterium animalis  supplementation in preterm infants, as detailed in the systematic review by Szajewska et al., a meta-analysis of four randomized controlled trials (RCTs) involving a total of 324 infants, has shown promising results. These include increased fecal bifidobacteria counts, reduced Enterobacteriaceae and Clostridium spp counts, as well as improvements in stool pH, fecal calprotectin concentrations, fecal immunoglobulin A levels, and short-chain fatty acid concentrations. However, the analysis did not find significant effects on the risk of necrotizing enterocolitis stage ≥2, risk of sepsis, or use of antibiotics compared to controls. [ 10 ]


B. animalis  is present in many food products and dietary supplements. The  probiotic  is mostly found in dairy products. [ 11 ]   Bifidobacterium animalis  subsp.  lactis  BB-12 is a bacterial subspecies within the  animalis  strain that exhibits rod-shaped structure and lacks catalase activity. The subspecies was initially identified as  Bifidobacterium bifidum , however advancements in molecular classification later reclassified it as  Bifidobacterium animalis , and subsequently as  Bifidobacterium animalis  subsp.  lactis.  It was first preserved in Chr. Hansen's cell culture bank in 1983 as part of the dairy culture collection. It exhibits suitability for producing probiotic dairy products and has found application in infant formula, dietary supplements, and fermented milk products. This is due to a variety of favorable technological characteristics such as its fermentation activity, high tolerance to air, stability, and resilience to acidic and bile environments, even in freeze-dried products. Moreover,  Bifidobacterium animalis  subsp.  lactis BB-12 does not alter the taste, appearance, or texture of food products and maintains viability in probiotic foods until consumption. [ 12 ]


The manipulation of the  gut flora  is complex and may cause bacteria-host interactions. [ 13 ]  Although  probiotics , in general, are considered safe, there are concerns about their use in certain cases. [ 13 ] [ 14 ]  Some people, such as those with  compromised immune systems ,  short bowel syndrome ,  central venous catheters ,  heart valve disease  and  premature infants , may be at higher risk for adverse events. [ 15 ]  Rarely, consumption of probiotics may cause  bacteremia , and  sepsis , potentially fatal infections in children with lowered immune systems or who are already critically ill. [ 16 ]


Bile  (from Latin  bilis ), or  gall , is a yellow-green/misty green fluid produced by the  liver  of most  vertebrates  that aids the  digestion  of  lipids  in the  small intestine . In humans, bile is primarily composed of  water , is produced continuously by the liver, and is stored and concentrated in the  gallbladder . After a human eats, this stored bile is discharged into  the first section of the small intestine . [ 1 ]


In the human  liver , bile is composed of 97–98%  water , 0.7%  bile salts , 0.2%  bilirubin , 0.51% fats ( cholesterol ,  fatty acids , and  lecithin ), and 200 meq/L inorganic salts. [ 2 ] [ 3 ]  The two main pigments of bile are  bilirubin , which is orange-yellow, and its oxidised form  biliverdin , which is green. When mixed, they are responsible for the brown color of  feces . [ 4 ]  About 400 to 800 milliliters (14 to 27 U.S. fluid ounces) of bile is produced per day in adult human beings. [ 5 ]


Bile or gall acts to some extent as a  surfactant , helping to  emulsify  the lipids in food. Bile salt  anions  are  hydrophilic  on one side and  hydrophobic  on the other side; consequently, they tend to aggregate around droplets of lipids ( triglycerides  and  phospholipids ) to form  micelles , with the hydrophobic sides towards the fat and hydrophilic sides facing outwards. [ 6 ]  The hydrophilic sides are negatively charged, and this charge prevents fat droplets coated with bile from re-aggregating into larger fat particles. Ordinarily, the micelles in the  duodenum  have a diameter around 1–50  μm  in humans. [ 7 ]


The dispersion of food fat into micelles provides a greatly increased surface area for the action of the enzyme  pancreatic lipase , which digests the triglycerides, and is able to reach the fatty core through gaps between the bile salts. [ 8 ]  A triglyceride is broken down into two fatty acids and a  monoglyceride , which are absorbed by the  villi  on the intestine walls. After being transferred across the intestinal membrane, the fatty acids reform into triglycerides ( re-esterified ), before being absorbed into the lymphatic system through  lacteals . Without bile salts, most of the lipids in food would be excreted in feces, undigested. [ 9 ]


Since bile increases the absorption of fats, it is an important part of the absorption of the fat-soluble substances, [ 10 ]  such as the  vitamins   A ,  D ,  E , and  K . [ 11 ]


Besides its digestive function, bile serves also as the route of excretion for bilirubin, a byproduct of  red blood cells  recycled by the liver. Bilirubin derives from  hemoglobin  by  glucuronidation .


Bile tends to be  alkaline  on average. The  pH  of common duct bile (7.50 to 8.05) is higher than that of the corresponding gallbladder bile (6.80 to 7.65). Bile in the gallbladder becomes more  acidic  the longer a person goes without eating, though resting slows this fall in pH. [ 12 ]  As an alkali, it also has the function of neutralizing excess  stomach acid  before it enters the duodenum, the first section of the  small intestine .  Bile salts  also act as  bactericides , destroying many of the microbes that may be present in the food. [ 13 ]


In the absence of bile, fats become indigestible and are instead excreted in  feces , a condition called  steatorrhea . Feces lack their characteristic brown color and instead are white or gray, and greasy. [ 14 ]  Steatorrhea can lead to deficiencies in  essential fatty acids  and  fat-soluble vitamins . [ 15 ]  In addition, past the small intestine (which is normally responsible for absorbing fat from food) the  gastrointestinal tract  and  gut flora  are not adapted to processing fats, leading to problems in the large intestine. [ 16 ]


The  cholesterol  contained in bile will occasionally accrete into lumps in the gallbladder, forming  gallstones . Cholesterol gallstones are generally treated through surgical removal of the gallbladder. However, they can sometimes be dissolved by increasing the concentration of certain naturally occurring bile acids, such as  chenodeoxycholic acid  and  ursodeoxycholic acid . [ 17 ] [ 18 ]


On an empty stomach – after repeated  vomiting , for example – a person's vomit may be green or dark yellow, and very bitter. The bitter and greenish component may be bile or normal digestive juices originating in the stomach. [ 19 ]  Bile may be forced into the stomach secondary due to a weakened valve ( pylorus ), the presence of certain drugs including  alcohol , or powerful muscular contractions and duodenal spasms. This is known as  biliary reflux . [ 20 ]


Biliary obstruction refers to a condition when  bile ducts  which deliver bile from the gallbladder or liver to the duodenum become obstructed. The blockage of bile might cause a buildup of  bilirubin  in the  bloodstream  which can result in  jaundice . There are several potential causes for biliary obstruction including gallstones, cancer, [ 21 ]  trauma,  choledochal cysts , or other benign causes of bile duct narrowing. [ 22 ]  The most common cause of bile duct obstruction is when gallstone(s) are dislodged from the gallbladder into the cystic duct or common bile duct resulting in a blockage. A blockage of the gallbladder or  cystic duct  may cause  cholecystitis . If the blockage is beyond the confluence of the pancreatic duct, this may cause gallstone  pancreatitis . In some instances of biliary obstruction, the bile may become infected by bacteria resulting in  ascending cholangitis .


In medical theories prevalent in the West from  classical antiquity  to the  Middle Ages , the body's health depended on the equilibrium of  four "humors" , or vital fluids, two of which related to bile: blood,  phlegm , "yellow bile" (choler), and "black bile". These "humors" are believed to have their roots in the appearance of a blood sedimentation test made in open air, which exhibits a dark clot at the bottom ("black bile"), a layer of unclotted erythrocytes ("blood"), a layer of white blood cells ("phlegm") and a layer of clear yellow serum ("yellow bile"). [ 23 ]


Excesses of black bile and yellow bile were thought to produce depression and aggression, respectively, and the Greek names for them gave rise to the English words  cholera  (from Greek χολή  kholē , "bile") and  melancholia . In the former of those senses, the same theories explain the derivation of the English word bilious from  bile , the meaning of gall in English as "exasperation" or "impudence", and the Latin word  cholera , derived from the Greek  kholé , which was passed along into some Romance languages as words connoting anger, such as  colère  (French) and  cólera  (Spanish). [ 24 ]


Soap can be mixed with bile from mammals, such as  ox gall . This mixture, called bile soap [ 25 ]  or gall soap, can be applied to textiles a few hours before washing as a traditional and effective method for removing various kinds of tough stains. [ 26 ]


Pinapaitan  is a dish in  Philippine cuisine  that uses bile as flavoring. [ 27 ]  Other areas where bile is commonly used as a cooking ingredient include  Laos  and northern parts of  Thailand .


During the  Boshin War ,  Satsuma  soldiers of the early  Imperial Japanese Army  reportedly  ate human livers  boiled in bile. [ 28 ]  The practice of eating a slain enemy's liver, known as  hiemondori  ( 冷え物取り ) , was a tradition of the Satsuma people.


In regions where bile products are a popular ingredient in  traditional medicine , the  use of bears  in bile-farming has been widespread. This practice has been condemned by activists, and some pharmaceutical companies have developed synthetic (non-ursine) alternatives. [ 29 ]


A  bile duct  is any of a number of long tube-like structures that carry  bile , and is present in most  vertebrates . The bile duct is separated into three main parts: the fundus (superior), the body (middle), and the neck (inferior).


Bile is required for the  digestion  of food and is secreted by the  liver  into passages that carry bile toward the  hepatic duct . It joins the  cystic duct  (carrying bile to and from the  gallbladder ) to form the  common bile duct  which then opens into the  intestine .


The top half of the common bile duct is associated with the liver, while the bottom half of the common bile duct is associated with the  pancreas , through which it passes on its way to the intestine. It opens into the part of the intestine called the duodenum via the  ampulla of Vater .


The  biliary tree  (see below) is the whole network of various sized ducts branching through the liver.


The path is as follows:  bile canaliculi   →   canals of Hering   →   interlobular bile ducts   →   intrahepatic bile ducts   →  left and right  hepatic ducts   merge to form   →   common hepatic duct   exits liver and joins   →   cystic duct  (from  gall bladder )  forming   →   common bile duct   →   joins with   pancreatic duct   →   forming   ampulla of Vater   →   enters   duodenum .


Inflation of a balloon in the bile duct causes, through the  vagus nerve , activation of the  brain stem  and the  insular cortex ,  prefrontal cortex , and  somatosensory cortex . [ 2 ]


Blockage or obstruction of the bile duct by  gallstones , scarring from injury, or cancer prevents the bile from being transported to the intestine and the active ingredient in the bile ( bilirubin ) instead accumulates in the blood. This condition results in  jaundice , where the skin and eyes become yellow from the bilirubin in the blood. This condition also causes severe itchiness from the bilirubin deposited in the tissues. In certain types of  jaundice , the urine will be noticeably darker, and the stools will be much paler than usual. This is caused by the bilirubin all going to the bloodstream and being filtered into the urine by the kidneys, instead of some being lost in the stools through the  ampulla of Vater .


Jaundice is commonly caused by conditions such as  pancreatic cancer , which causes blockage of the bile duct passing through the cancerous portion of the pancreas;  cholangiocarcinoma , cancer of the bile ducts; blockage by a stone in patients with gallstones; and from scarring after injury to the bile duct during gallbladder removal.


Biliary drainage is performed with a tube or catheter (called a  biliary drain ,  biliary  stent  or  biliary catheter ) by a surgeon or, commonly, an  interventional radiologist . [ 3 ]  It can be used to relieve a blockage in the bile duct, either permanently or as a temporary solution before definite treatment such as surgery. The drain can be placed  percutaneously  through the liver, with the procedure then being called  percutaneous transhepatic biliary drainage  (PTBD). [ 4 ]  This can additionally be performed as part of a  percutaneous transhepatic cholangiography , then a form of interventional radiology. A biliary drain can also be used to take bile samples for diagnostic workup or disease monitoring, as well as providing a  route of administration  for medical substances.


A surgically created passage between the common bile duct and the  jejunum  in a procedure called a  choledochojejunostomy , can be carried out to relieve the symptoms of biliary obstruction as well as allows the bile duct to drain. [ 5 ]


In infants with  biliary atresia ,  hepatoportoenterostomy  is an alternative method of providing bile drainage.


Cholangiocarcinoma  or bile duct cancer is a form of cancer that is composed of mutated  epithelial  cells (or cells showing characteristics of epithelial differentiation) that originate in the bile ducts. Cholangiocarcinoma is considered to be an incurable and rapidly lethal cancer unless both the primary tumor and any  metastases  can be fully removed by surgery. No potentially curative treatment exists except surgery, but most people have advanced stage disease at presentation and are inoperable at the time of diagnosis.


In  cholecystectomy  there is a slight risk (0.3–0.5%) of injury of the bile ducts, most commonly of the  common bile duct . [ 6 ]  This complication can range from mild forms, which are easy to address during the operation, to more severe forms. [ 6 ]  If not addressed such injury can be debilitating and lead to considerable morbidity. [ 6 ]  Such injury can be prevented by routinely using X-ray investigation of the bile ducts (intraoperative  cholangiography ). [ 6 ]


BioGaia  is a Swedish biotechnology company that develops, markets and sells a range of   probiotic  products. [ 1 ] [ 2 ] [ 3 ]  It has patented the use of several  Lactobacillus reuteri  strains and offers gut and immune health products containing  L. reuteri  Protectis ( DSM  17938). Their oral health products contain  L. reuteri  Prodentis,  a blend of the  L. reuteri  strains DSM 17938 and  ATCC  PTA 5289. [ citation needed ]  Products containing  L. reuteri  have been proven to be both effective and safe in several applications: [ dubious  –  discuss ]  infant colic, [ 4 ] [ 5 ]  diarrhea prevention and mitigation in children, [ 6 ] [ 7 ]  eradication of  H. pylori  infection and reduction of side effects from standard  H. pylori  treatment, [ 8 ] [ 9 ] [ 10 ]  amelioration of  gingivitis , [ 11 ] [ 12 ]  and general illness prevention in children [ 13 ]  and adults. [ 14 ]  BioGaia was ranked 9th in the Top 30 Global Probiotic Food Ingredient Companies list by FoodTalks in 2021. [ 15 ]  The BioGaia -B share is listed on the  NASDAQ OMX Nordic Exchange . [ citation needed ]


BioGaia was founded in 1990 to develop and commercialize a new strain of  L. reuteri . The company's research director Dr. Ivan Casas believed that newborn chickens consumed their mothers' feces, allowing the transfer of beneficial microorganisms from the mother to the sterile newborn bird. He believed that the same was true for humans. [ 16 ]  It is generally accepted that newborn babies are sterile at birth and are very sensitive to pathogenic bacteria before they establish a microbial flora of their own. [ 17 ]


This flora should preferably come from their mother. Ivan believed that  Lactobacillus reuteri  is one of the bacteria that a mother should transfer to her offspring, whether a chicken, a human baby or any other mammal. He wanted to create probiotic products that would confirm this "Circle of Life”. [ citation needed ]


The first step involved analysis of breast milk from mothers in the United States,  Sweden ,  Israel ,  South Africa ,  Denmark ,  Japan , Peru and South Korea. Approximately 14-15% of the samples contained  L. reuteri . [ 18 ]  In a separate study, Casas found that samples of breast milk collected from women in Andean villages in Peru also contained numerous strains of  L. reuteri , which were subsequently isolated. [ 19 ]


One of these strains is still used in BioGaia’s probiotic products. [ 20 ] [ citation needed ]


In  digestion , a  bolus  (from  Latin   bolus , "ball") is a ball-like mixture of food and  saliva  that forms in the mouth during the process of  chewing  (which is largely an adaptation for  plant-eating   mammals ). [ 1 ]  It has the same color as the food being eaten, and the saliva gives it an  alkaline   pH .


Under normal circumstances, the bolus is  swallowed , and travels down the  esophagus  to the  stomach  for digestion. [ 2 ]


Brunner's glands  (or  duodenal glands ) are compound tubuloalveolar  submucosal   glands  found in that portion of the  duodenum  proximal to the  hepatopancreatic sphincter  (i.e  sphincter of Oddi ). [ citation needed ]


For decades, it was believed that the main function of the glands is to  secrete alkaline ( bicarbonate -containing) mucus in order to: [ citation needed ]


However, more recent studies have demonstrated that Brunner’s glands actually act as major modulators of the gut microbiome and systemic immunity.


They are the distinguishing feature of the duodenum, and are named for the  Swiss  physician who first described them,  Johann Conrad Brunner . [ citation needed ]


Duodenal glands are situated within the mucosa and submucosa of the duodenum. They are most abundant near the pylorus, growing shorter and more sparse distally towards the terminal portion of the duodenum. [ 1 ]


The duodenum can be distinguished from the  jejunum  and  ileum  by the presence of Brunner's glands in the submucosa. [ citation needed ]


Their excretory cannals are tortuous, opening at the bases of the villi. [ 1 ]


Two forms of duodenal glands are distinguished: the external group (which are more voluminous and extend into the duodenal submucosa), and the internal group (which are smaller and are situated within the duodenal mucosa). [ 1 ]


They also secrete  epidermal growth factor , which inhibits  parietal  and  chief cells  of the stomach from secreting acid and their digestive enzymes. [ 2 ] [ citation needed ]  This is another form of protection for the duodenum. [ citation needed ]


The Brunner glands, which empty into the  intestinal glands , secrete an alkaline fluid composed of  mucin , which exerts a physiologic anti-acid function by coating the duodenal epithelium, therefore protecting it from the acid chyme of the stomach. Furthermore, in response to the presence of acid in the duodenum, these glands secrete  pepsinogen  and  urogastrone , which inhibit gastric acid secretion. [ citation needed ]


More recent studies have demonstrated that Brunner’s glands are major modulators of the gut microbiome and systemic immunity. Studies conducted by  Ivan De Araujo ’s laboratory revealed that Brunner’s gland secretions promote the proliferation of probiotics and protect the host against foreign pathogens. [ 3 ]


Hyperplasia of Brunner glands with a lesion greater than 1 cm was initially described as a Brunner gland adenoma. Several features of these lesions favor their designation as  hamartomas , including the lack of encapsulation; the mixture of acini, smooth muscles, adipose tissue, Paneth cells, and mucosal glands; and the lack of any cell atypia. These hamartomas are rare, with approximately 150 cases described in the literature. It is estimated that they represent approximately 5–10% of benign duodenal tumors. They are variable in size, typically 1–3 cm, with only a few reported cases of lesions larger than 5 cm. [ citation needed ]


Most patients with Brunner gland hamartomas are asymptomatic or have nonspecific complaints such as nausea, bloating, or vague abdominal pain. [ citation needed ]


Most reports in the literature describe local surgical resection of Brunner gland hamartoma via duodenotomy. Increasingly, successful endoscopic resection has been reported and is primarily used for  pedunculated  Brunner gland hamartomas. The endoscopic approach in selective cases appears to be safe, less invasive, and less costly. [ citation needed ]


Consistent with the more recent idea that Brunner’s glands influence systemic immunity via the microbiome, patients who had the duodenal bulb removed (where the glands are mostly located) showed greater alterations in immune factors compared to patients having  more distal parts of the duodenum removed. [ 3 ]


Catastalsis  is the rhythmic contraction and relaxation of the  muscle  of the  intestines . It resembles ordinary  peristalsis  but is not preceded by a  wave of inhibition . [ 1 ] [ 2 ] [ 3 ]


The  cecum  or  caecum  is a pouch within the  peritoneum  that is considered to be the beginning of the  large intestine . [ 1 ]  It is typically located on the right side of the body (the same side of the body as the  appendix , to which it is joined). The word cecum ( / ˈ s iː k əm / , plural  ceca   / ˈ s iː k ə / ) stems from the  Latin   caecus  meaning  blind .


It receives  chyme  from the  ileum , and connects to the  ascending colon  of the  large intestine . It is separated from the ileum by the  ileocecal valve  (ICV), also called Bauhin's valve. It is also separated from the  colon  by the cecocolic junction. While the cecum is usually intraperitoneal, the ascending colon is  retroperitoneal . [ 2 ]


In  herbivores , the cecum stores food material where bacteria are able to break down the  cellulose . In humans, the cecum is involved in absorption of  salts  and  electrolytes  and lubricates the solid waste that passes into the large intestine. [ 3 ]


The cecum and appendix are derived from the bud of cecum that forms during week six in the midgut next to the apex of the umbilical herniation. [ 5 ]  Specifically, the cecum and appendix are formed by the enlargement of the postarterial segment of the midgut loop.  The proximal part of the bud grows rapidly to form the cecum. The lateral wall of the cecum grows much more rapidly than the medial wall, with the result that the point of attachment of the  appendix  comes to lie on the medial side. [ citation needed ]  The cecum's position changes after the midgut rotates and the ascending colon elongates, and the accumulation of meconium inside the cecum may result in the latter's increased diameter. [ 5 ]


The term  cecum  comes from Latin  (intestinum) caecum , literally 'blind intestine', in the sense 'blind gut' or ' cul de sac '. [ 6 ]  It is a direct translation from Ancient Greek  τυφλὸν  ( ἔντερον )  typhlòn  ( énteron ). Thus the inflammation of the cecum is called typhlitis.


In  dissections  by the  Greek   philosophers , the connection between the  ileum  of the  small intestine  and the cecum was not fully understood. Most of the studies of the  digestive tract  were done on animals and the results were compared to human  structures . [ 7 ]


The junction between the small intestine and the colon, called the  ileocecal valve , is so small in some animals that it was not considered to be a connection between the small and large intestines. During a dissection, the colon could be traced from the  rectum , to the  sigmoid colon , through the  descending ,  transverse , and  ascending  sections. The cecum is an end point for the colon with a dead-end portion terminating with the  appendix . [ 8 ]


The connection between the end of the small intestine (ileum) and the start (as viewed from the perspective of food being processed) of the colon (cecum) is now clearly understood, and is called the ileocecal orifice. The connection between the end of the cecum and the beginning of the ascending colon is called the cecocolic orifice.


A cecal carcinoid tumor is a  carcinoid tumor  of the cecum. An  appendiceal carcinoid tumor  (a carcinoid tumor of the appendix) is sometimes found next to a cecal carcinoid. [ 9 ]


Neutropenic enterocolitis  (typhlitis) is the condition of inflammation of the cecum, primarily caused by bacterial infections.


Over 99% of the bacteria in the gut are  anaerobes , [ 10 ] [ 11 ] [ 12 ] [ 13 ] [ 14 ]  but in the cecum,  aerobic bacteria  reach high densities. [ 15 ]


A cecum is present in most  amniote  species, and also in  lungfish , but not in any living species of  amphibian . In  reptiles , it is usually a single median structure, arising from the dorsal side of the large intestine.  Birds  typically have two paired ceca, as do, unlike other mammals,  hyraxes . [ 16 ]  Parrots do not have ceca. [ 17 ]


Most mammalian  herbivores  have a relatively large cecum.  In many species, it is considerably wider than the colon. For some herbivores such as  lagomorphs  (rabbits, hares, pikas), easily digestible food is processed in the gastrointestinal tract and expelled as regular feces.  But in order to get nutrients out of hard to digest fiber, lagomorphs ferment fiber in the cecum and then expel the contents as  cecotropes , which are reingested (cecotrophy).  The cecotropes are then absorbed in the small intestine to utilize the nutrients.


In contrast, obligate  carnivores , whose diets contain little or no plant matter, have a reduced cecum, which is often partially or wholly replaced by the  appendix . [ 16 ]  Mammalian species which do not develop a cecum include  raccoons , [ 18 ]   bears , [ 19 ]  and the  red panda . [ 20 ]


Many fish have a number of small outpockets, called  pyloric ceca , along their intestine; despite the name, they are not  homologous  with the cecum of amniotes – their purpose is to increase the overall area of the digestive epithelium. [ 16 ]  Some invertebrates, such as squid, [ 21 ]  may also have structures with the same name, but these have no relationship with those of vertebrates.


Centroacinar cells  are spindle-shaped cells in the exocrine  pancreas . They are small and have  microvilli  on the  apical  surface. They work with organs such as the kidney, lungs, stomach, brain, intestine.


The exocrine pancreas is one of two compartments that include digestive-acting acinar cells and duct cells.They represent an extension of the  intercalated duct  into each pancreatic  acinus . [ 1 ]  These cells are commonly known as  duct cells , and secrete an aqueous  bicarbonate  solution under stimulation by the hormone  secretin . They also secrete  mucin . As well as direct the pathway of the enzyme into the gut, which helps the endocrine pancreas in secreting the hormone into the circulation. This is important in glucose metabolism, insulin-producing B cells, glucagon-producing A cells and somatostatin producing δ cells


The intercalated ducts take the bicarbonate to  intralobular ducts  which become lobular ducts. These lobular ducts finally converge to form the main pancreatic duct. [ 2 ]  These intercalated ducts take the bicarbonate to intralobular ducts which become lobular ducts. These lobular ducts finally converge to form the main pancreatic duct. [ 1 ]  These pancreatic ducts can act as a response mechanism when injury occurs and to avoid disruptions in the pancreatic lumen. [ 3 ]  This keeps the ionic content in check while keeping it open for flow to occur. Mutations that can occur because of blockage/ accumulation in the pancreatic duct are disorders such as cystic fibrosis.


This article incorporates text in the  public domain  from  page 1204  of the 20th edition of   Gray's Anatomy   (1918)


This  cell biology  article is a  stub . You can help Wikipedia by  expanding it .


Chewing  or  mastication  is the process by which  food  is  crushed and ground  by the  teeth . It is the first step in the process of  digestion , allowing a greater surface area for  digestive enzymes  to break down the foods.


During the mastication process, the food is positioned by the  cheek  and  tongue  between the teeth for grinding. The  muscles of mastication  move the  jaws  to bring the teeth into intermittent contact, repeatedly  occluding  and opening. As chewing continues, the food is made softer and warmer, and the enzymes in saliva begin to break down  carbohydrates  in the food. After chewing, the food (now called a  bolus ) is swallowed. It enters the  esophagus  and via  peristalsis  continues on to the stomach, where the next step of digestion occurs. [ 1 ]  Increasing the number of chews per bite increases relevant gut hormones. [ 2 ]  Studies suggest that chewing may decrease self-reported hunger and food intake. [ 2 ]   Chewing gum  has been around for many centuries; there is evidence that northern Europeans chewed  birch bark tar  9,000 years ago.


Chewing, needing specialized teeth, is mostly a mammalian adaptation that appeared in early  Synapsids , though some later herbivorous dinosaurs, since extinct, had developed chewing too. Nowadays, only mammals chew in the strict sense of the word, though some fishes have a somewhat similar behavior. Neither birds, nor amphibians or any living reptiles chew.


Premastication  is sometimes performed by human parents for infants who are unable to do so for themselves. The food is masticated in the mouth of the parent into a bolus and then transferred to the infant for consumption [ 3 ]  (some other animals also premasticate).


Cattle  and some other animals, called  ruminants , chew food more than once to extract more nutrients. After the first round of chewing, this food is called  cud .


Chewing is primarily an unconscious ( semi-autonomic ) act, but can be mediated by higher conscious input. The motor program for mastication is a hypothesized central nervous system function by which the complex patterns governing mastication are created and controlled.


It is thought that feedback from  proprioceptive  nerves in teeth and the  temporomandibular  joints govern the creation of neural pathways, which in turn determine duration and force of individual muscle activation (and in some cases muscle fiber groups as in the masseter and temporalis).


This motor program continuously adapts to changes in food type or occlusion. [ 4 ]  This adaptation is a learned skill that may sometimes require relearning to adapt to loss of teeth or to dental appliances such as  dentures .


It is thought that conscious mediation is important in the limitation of  parafunctional habits  as most commonly, the motor program can be excessively engaged during periods of sleep and times of stress. It is also theorized that excessive input to the motor program from myofascial pain or occlusal imbalance can contribute to  parafunctional habits .


Chewing stimulates  saliva  production and increases sensory perception of the food being eaten, controlling when the food is swallowed. [ 5 ]  Evidence from one study suggests that chewing almonds 25-40 times kept people fuller while also allowing them to get more nutrients out of the almonds. The researchers also suggest that this is likely to be the case in other foods. [ 6 ]  A 2015  systemic review  found evidence that chewing can decrease self-reported hunger and therefore food intake. [ 7 ]  Eating food which does not require chewing, by choice or for medical reasons as  tooth loss , is known as a  soft diet . Such a diet may lead to inadequate nutrition due to a reduction in fruit and vegetable intake. [ 8 ]


Chewing also stimulates the  hippocampus  and is necessary to maintain its normal function. [ 9 ]  Chewing stimulates hippocampal  neurogenesis  in both humans and mice. [ 10 ]


Chewing is largely an adaptation for  mammalian   herbivory .  Carnivores  generally chew very little or swallow their food whole or in chunks. [ 11 ]  This act of gulping food (or medicine pills) without chewing has inspired the English  idiom  "wolfing it down". [ 12 ]


Other animals such as cows chew their food for long periods to allow for proper digestion in a process known as rumination. Rumination in cows has been shown by researchers to intensify during the night. They concluded that cows chewed more intently in the night time compared to the morning. [ 13 ]


Ornithopods , a group of  dinosaurs  including the  Hadrosaurids  ("duck-bills"), developed teeth analogous to mammalian  molars  and  incisors  during the  Cretaceous  period; this advanced, cow-like dentition allowed the creatures to obtain more nutrients from the tough plant life. This may have given them the advantage needed to compete with the formidable  sauropods , who depended on their massive gastrointestinal tracts to digest food without grinding it. [ 14 ]


The process of chewing has, by analogy, been applied to machinery. The  U.S. Forest Service  uses a machine called a  masticator  (also called a  forestry mulching machine ) to "chew" through brush and timber in order to clear  firelines  in advance of a wildfire. [ 15 ]


Cholangiocytes  are the  epithelial cells  of the  bile duct . [ 1 ]  They are  cuboidal epithelium  in the small interlobular bile ducts, but become  columnar  and  carbonate -secreting in larger bile ducts approaching the  porta hepatis  and the extrahepatic ducts. They contribute to  hepatocyte  survival by transporting  bile acids .


In the healthy liver, cholangiocytes contribute to  bile  secretion via release of  bicarbonate  and water. Several hormones and locally acting mediators are known to contribute to cholangiocyte fluid/electrolyte secretion. These include  secretin ,  acetylcholine ,  ATP , and  bombesin .


Cholangiocytes act through bile-acid independent bile flow, which is driven by the active transport of electrolytes. In contrast,  hepatocytes  secrete bile through bile-acid dependent bile flow, which is coupled to canalicular secretion of bile acids via ATP-driven transporters. This results in passive transcellular and paracellular secretion of fluid and electrolytes through an osmotic effect.


Disordered functioning of cholangiocytes is at the center of a variety of pathological conditions known as "cholangiopathies." These diseases include  primary biliary cirrhosis ,  primary sclerosing cholangitis , AIDS cholangiopathy, disappearing bile duct syndromes,  Alagille's syndrome ,  cystic fibrosis , and  biliary atresia . Often either the best or the only curative treatment option for cholangiopathies is  liver transplantation , and as a group, cholangiopathies account for a substantial percentage of both adult and pediatric liver transplants. [ 2 ]


Active scientific investigation of cholangiocytes focuses on such diverse processes as mechanisms of fluid/electrolyte secretion, regulation of cholangiocyte proliferation, roles of cholangiocytes in the pathogenesis of liver fibrosis and cirrhosis, and cholangiocyte apoptosis. Specific investigation of individual cholangiopathies is also pursued actively. [ 1 ]


Chyle  (from  Greek     χυλός  (chylos)  'juice' [ 1 ] ) is a milky  bodily fluid  consisting of  lymph  and emulsified  fats , or free  fatty acids  (FFAs). It is formed in the  small intestine  during digestion of fatty foods, and taken up by  lymph vessels  specifically known as  lacteals . The lipids in the chyle are  colloidally  suspended in  chylomicrons .


A chyle  fistula  occurs when defect(s) of lymphatic vessel(s) result in leakage of lymphatic fluid, typically accumulating in the thoracic (pleural) or abdominal (peritoneal) cavities, [ 2 ]  leading to a chylous pleural effusion ( chylothorax ) or  chylous ascites , respectively.


Diagnosis of a chyle fistula may be accomplished by analysis of pleural/peritoneal fluid. Identifying the source (localizing the lymphatic defect) is often challenging, but may be accomplished with lymphangiography, which is occasionally associated with a serendipitous therapeutic effect (resolution of the leak), thought to be secondary to a sclerosant effect of the lymphangiography contrast.


Due to the extreme  friability  of the lymphatic vessels, direct repair of defects is impractical. Therefore, treatment of chyle fistulae relies upon either decreased production of lymphatic fluid to allow for healing of lymphatic defect(s) or permanent diversion of lymphatic fluid away from lymphatic defect(s). Decreased production of lymphatic fluid may be accomplished by dietary restriction (or complete replacement of oral intake with  total parenteral nutrition ), as well as by the medications  octreotide  (a synthetic analogue of the hormone  somatostatin ) [ 3 ]  and  orlistat  (a lipase inhibitor that decreases absorption of dietary fats). Permanent diversion of lymphatic fluid may be accomplished by   thoracic duct  embolization (a needle-based procedure to occlude the duct by depositing glue/embolic material into it) or by thoracic duct ligation (an open surgical procedure to occlude the duct by suturing tightly around it).


Chyme  or  chymus  ( / k aɪ m / ; from  Greek  χυμός  khymos , "juice" [ 1 ] [ 2 ] ) is the semi-fluid mass of partly digested food that is expelled by the  stomach , through the  pyloric valve , into the  duodenum [ 3 ]  (the beginning of the  small intestine ).


Chyme results from the mechanical and chemical breakdown of a  bolus  and consists of partially digested food, water,  hydrochloric acid , and various  digestive enzymes . Chyme slowly passes through the pyloric  sphincter  and into the duodenum, where the extraction of  nutrients  begins. Depending on the quantity and contents of the meal, the stomach will digest the food into chyme in some time from 40 minutes to 3 hours. [ 4 ]
With a  pH  of approximately 2, chyme emerging from the stomach is very acidic. The duodenum secretes a  hormone ,  cholecystokinin  (CCK), which causes the  gall bladder  to contract, releasing alkaline  bile  into the duodenum. CCK also causes the release of digestive enzymes from the  pancreas . The duodenum is a short section of the small intestine located between the stomach and the rest of the small intestine. The duodenum also produces the hormone  secretin  to stimulate the pancreatic secretion of large amounts of  sodium bicarbonate , which then raises pH of the chyme to 7. The chyme moves through the  jejunum  and the  ileum , where digestion progresses, and the non-useful portion continues onward into the  large intestine . The duodenum is protected by a thick layer of  mucus  and the neutralizing actions of the sodium bicarbonate and bile.


At a pH of 7, the enzymes that were present from the stomach are no longer active. The breakdown of any nutrients still present is by  anaerobic bacteria , which at the same time help to package the remains. These bacteria also help synthesize  vitamin B  and  vitamin K , which will be absorbed along with other nutrients.


Chyme has a low pH that is countered by the production of  bile , which helps the further digestion of food. Chyme is part liquid and part solid: a thick semifluid mass of partially digested food and digestive secretions that is formed in the  stomach  and small intestine during digestion. Chyme also contains cells from the mouth and esophagus that slough off from the mechanical action of chewing and swallowing.


After hours of mechanical and chemical digestion, food has been reduced into chyme. As particles of food become small enough, they are passed out of the stomach at regular intervals into the small intestine, which stimulates the  pancreas  to release fluid containing a high concentration of  bicarbonate . This fluid neutralizes the gastric juices, which can damage the lining of the intestine and result in  duodenal ulcer . Other secretions from the pancreas,  gallbladder ,  liver , and  glands  in the intestinal wall help in digestion, as these secretions contain a variety of  digestive enzymes  and chemicals that assist in the breakdown of complex compounds into those that can be absorbed and used by the body.


When food particles are sufficiently reduced in size and composition, they are absorbed by the intestinal wall and transported to the bloodstream. Some food material is passed from the small intestine to the  large intestine . In the large intestine, bacteria break down any proteins and starches in chyme that were not digested fully in the small intestine.


When all of the nutrients have been absorbed from chyme, the remaining waste material changes into semisolids that are called  feces . The feces pass to the  rectum , to be stored until ready to be discharged from the body during  defecation .


The chyme of an  unweaned  calf is the defining ingredient of  pajata , a traditional  Roman recipe .


Chyme is sometimes used in  Pinapaitan , a bitter  Ilocano  stew.


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 .


The entire  small intestine  has circular folds of  mucous membrane . [ 1 ]  The majority extend transversely around the  cylinder  of the small intestine, [ 2 ]  for about one-half or two-thirds of its  circumference . Some form complete  circles . Others have a spiral direction. The latter usually extend a little more than once around the bowel, but occasionally two or three times. While the larger folds are about 1 cm in depth at their broadest part, most folds are smaller. There tends to be an alternating pattern between larger and smaller folds. [ 1 ]


They are not found at the commencement of the  duodenum , but begin to appear about 2.5 or 5 cm beyond the  pylorus .


In the lower part of the descending portion, below the point where the  bile  and  pancreatic ducts  enter the small intestine, they are very large and closely approximated.


In the horizontal and ascending portions of the duodenum and upper half of the  jejunum , they are large and numerous. [ 3 ]  From this point, down to the middle of the ileum, they diminish considerably in size.


In the lower part of the  ileum , they almost entirely disappear; [ 4 ]  hence the comparative thinness of this portion of the intestine, as compared with the duodenum and jejunum. [ citation needed ]


Unlike the  gastric folds  in the  stomach , they are permanent, and are not obliterated when the  intestine  is distended.


The spaces between circular folds are smaller than the  haustra  of the  colon , and, in contrast to haustra, circular folds reach around the whole circumference of the intestine. These differences can assist in distinguishing the small intestine from the colon on an  abdominal x-ray .


The circular folds slow the passage of the partly digested  food  along the intestines, and afford an increased surface for  absorption . [ 5 ]  They are covered with small finger-like projections called  villi  (singular, villus). Each villus, in turn, is covered with  microvilli . The microvilli absorb fats and nutrients from the  chyme .


The circular folds are also called the valves of Kerckring, [ 3 ]  valves of Kerchkring, [ 6 ]  plicae circulares, [ 3 ] [ 5 ]   plicae circulae , [ 6 ]  and  valvulae conniventes . [ 3 ]


This article incorporates text in the  public domain  from  page 1173  of the 20th edition of   Gray's Anatomy   (1918)


A  cloaca  ( / k l oʊ ˈ eɪ k ə /   ⓘ   kloh- AY -kə ),  pl. :  cloacae  ( / k l oʊ ˈ eɪ s i /   kloh- AY -see  or  / k l oʊ ˈ eɪ k i /   kloh- AY -kee ), or  vent , is the rear  orifice  that serves as the only opening for the  digestive  ( rectum ),  reproductive , and  urinary tracts  (if present) of many  vertebrate  animals. All  amphibians ,  reptiles ,  birds , and a few mammals ( monotremes ,  afrosoricids , and  marsupial moles , etc.) have this orifice, from which they excrete both  urine  and  feces ; this is in contrast to most  placental mammals , which have separate orifices for evacuation and reproduction.  Excretory  openings with analogous purpose in some  invertebrates  are also sometimes called cloacae. Mating through the cloaca is called cloacal  copulation  and cloacal kissing.


The cloacal region is also often associated with a secretory organ, the cloacal gland, which has been implicated in the scent-marking behavior of some reptiles, [ 1 ]  marsupials, [ 2 ]  amphibians, and  monotremes . [ 3 ]


The word is from the  Latin  verb  cluo , "(I) cleanse", thus the noun  cloaca , " sewer , drain". [ 4 ] [ 5 ] [ 6 ]


Birds reproduce using their cloaca; this occurs during a cloacal kiss in most birds. [ 7 ]  Birds that mate using this method touch their cloacae together, in some species for only a few seconds, sufficient time for  sperm  to be transferred from the male to the female. [ 8 ]  For  palaeognaths  and  waterfowl , the males do not use the cloaca for reproduction, but have a  phallus . [ 9 ]


One study [ 10 ]  has looked into birds that use their cloaca for cooling. [ 11 ]


Among  falconers , the word vent is also a verb meaning "to defecate".


Among fish, a true cloaca is present only in  elasmobranchs  (sharks and rays) and  lobe-finned fishes . In  lampreys  and in some  ray-finned fishes , part of the cloaca remains in the adult to receive the urinary and reproductive ducts, although the anus always opens separately. In  chimaeras  and most  teleosts , however, all three openings are entirely separated. [ 12 ]


With a few exceptions noted below, mammals have no cloaca. Even in the marsupials that have one, the cloaca is partially subdivided into separate regions for the  anus  and  urethra .


The  monotremes  (egg-laying mammals) possess a true cloaca. [ 14 ]


In  marsupials , the genital tract is separate from the anus, but a trace of the original cloaca does remain externally. [ 12 ]  This is one of the features of marsupials (and monotremes) that suggest their basal nature, as the  amniotes  from which mammals evolved had a cloaca, and probably so did the earliest  mammals .


Unlike other marsupials,  marsupial moles  have a true cloaca. [ 15 ]  This fact has been used to argue that they are not marsupials. [ 16 ] [ 17 ] [ unreliable source? ]


Most adult  placentals  have no cloaca. In the embryo, the  embryonic cloaca  divides into a posterior region that becomes part of the  anus , and an anterior region that develops depending on sex: in males, it forms the  penile urethra , while in females, it develops into the  vestibule  or  urogenital sinus  that receives the urethra and vagina. [ 12 ] [ 18 ]  However, some placentals retain a cloaca as adults: those are members of the order   Afrosoricida  (small mammals native to Africa) as well as  pikas ,  beavers , and some  shrews . [ 19 ] [ 20 ] [ 21 ] [ 22 ]


Being placental animals, humans have an embryonic cloaca which divides into separate tracts during the  development of the urinary and reproductive organs . However, a few human  congenital disorders  result in persons being born with a cloaca, including  persistent cloaca  and  sirenomelia  (mermaid syndrome).


In reptiles, the cloaca consists of the  urodeum ,  proctodeum , and  coprodeum . [ 23 ] [ 24 ]  Some species have modified cloacae for increased gas exchange (see  reptile respiration  and  reptile reproduction ). This is where reproductive activity occurs. [ 25 ]


Some  turtles , especially those specialized in diving, are highly reliant on cloacal  respiration  during dives. [ 26 ]  They accomplish this by having a pair of accessory air bladders connected to the cloaca, which can absorb oxygen from the water. [ 27 ]


Sea cucumbers  use cloacal respiration. The constant flow of water through it has allowed various  fish ,  polychaete  worms and even  crabs  to specialize to take advantage of it while living protected inside the cucumber. At night, many of these species emerge through the anus of the sea cucumber in search of food. [ 28 ]


Colonization resistance  is the mechanism whereby the  microbiome  protects itself against incursion by new and often harmful  microorganisms . [ 1 ] [ 2 ] [ 3 ]


Colonization resistance was first identified in 1967, and it was initially referred to as  antibiotic -associated susceptibility. It was observed that animals being treated with the antibiotic  streptomycin  were susceptible to  Salmonella enterica  at doses 10,000 fold lower than the standard minimal infectious dose. [ 4 ]  This led to investigations about the mechanisms utilized by endogenous microbial populations that conferred protection against exogenous pathogens attempting to  colonize  the  gut flora .


It has been observed that colonization resistance can occur within the host in a 'direct' or 'indirect' manner. [ 5 ]  The former refers to particular components of the microbiota directly competing with exogenous pathogens for nutritional niches (e.g.  E. coli  directly competes with  Citrobacter rodentium  for  carbohydrates  in the  intestinal lumen [ 6 ] ) or by producing growth inhibitors (e.g.  Bacteroides thuringiensis  can secrete  bacteriocin  that directly targets spore-forming  Clostridioides difficile , thus inhibiting its growth through an unknown mechanism), [ 7 ]  that directly inhibit the colonizing pathogen. Indirect colonization resistance is thought to be mediated through the induction of  immune  responses in the host that concomitantly inhibit the colonizing pathogen. An example of this has been observed with  B. thetaiotaomicron , which can induce the host to produce antimicrobial C-type lectins  REGIIIγ  and  REGIIIβ , both anti-microbial peptides that target  gram-positive  bacteria. [ 8 ]


Scientists found that gut infections increase its microbiota's resistance to subsequent infections, that  taurine  is used in as a nutrient to nourish and train the microbiota for this by potentiating its production of sulfide and that the exogenous supply of taurine can induce this microbiota alteration. [ 9 ] [ 10 ]


The  bile duct [ 1 ] [ 4 ]  (formerly known as the  common bile duct [ 4 ] ) is a part of the  biliary tract . [ 4 ]  It is formed by the union of the  common hepatic duct  and  cystic duct . It ends by uniting with the  pancreatic duct  to form the  hepatopancreatic ampulla . It possesses its  sphincter  to enable the regulation of bile flow.


The bile duct is some 6–8 cm long, and normally up to 8 mm in diameter. [ 4 ]


Its proximal supraduodenal part is situated within the free edge of the  lesser omentum . Its middle retroduodenal part is oriented inferiorly and right-ward, and is situated posterior to the first part of the duodenum, and anterior to the inferior vena cava. Its distal paraduodenal part is oriented still more right-ward, is accommodated by a groove upon (sometimes a channel within) the posterior aspect of the head of the pancreas, and is situated anterior to the right  renal vein . [ 4 ]


The bile duct terminates by uniting with the  pancreatic duct  (at an angle of about 60°) to form the  hepatopancreatic ampulla . [ 4 ]


The distal extremity of the bile duct invariably features its own  sphincteric muscle  (the pancreatic duct and the hepatopancreatic ampulla usually possess sphincters of their own to allow the flow of pancreatic juice to be regulated independently, however, these two can be absent). [ 4 ]


Several problems can arise within the common bile duct, usually related to its obstruction. Opinions vary slightly on the maximum calibre of a normal CBD, but 6 mm is one accepted upper limit of normal  [ 5 ]  with a further 1mm diameter allowed for each decade over 60 years.


It normally gets slightly dilated after  cholecystectomy , with upper limit (95%  prediction interval ) being about 10 mm after a few months. [ 6 ]


On  abdominal ultrasonography , the common bile duct is most readily seen in the  porta hepatis  (where the CBD lies anterior to the  portal vein  and  hepatic artery ). The absence of  Doppler  signal distinguishes it from the  portal vein  and  hepatic artery .


Tumours in the head of the pancreas  may come to  obstruct the distal bile duct. [ 4 ]


If obstructed by a  gallstone , a condition called  choledocholithiasis  can result. [ 7 ]  In this obstructed state, the duct is especially vulnerable to an infection called  ascending cholangitis . One form of treatment is a  cholecystenterostomy . Rare deformities of the common bile duct are cystic dilations (4 cm), choledochoceles (cystic dilation of the ampula of Vater (3–8 cm)), and  biliary atresia .


Obstruction of the common bile duct and related  jaundice  has been documented since at least since the time of  Erasistratus . [ 8 ]


The  common hepatic duct  is the first part of the  biliary tract . It joins the  cystic duct  coming from the  gallbladder  to form the  common bile duct .


The common hepatic duct is the first part of the biliary tract. [ 2 ]  It is formed by the union of the right hepatic duct (which drains bile from the right functional lobe of the liver) and the left hepatic duct (which drains bile from the left functional lobe of the liver). [ 3 ]


The duct is about 3 cm long. [ 4 ]  The common hepatic duct is about 6 mm in diameter in adults, with some variation. [ 5 ]


The common hepatic duct typically unites with the cystic duct some 1–2 cm superior to the duodenum and anterior to the right hepatic artery, with the cystic duct approaching the common hepatic duct from the right. [ 4 ]


The right branch of the  hepatic artery proper  usually passes posterior to the duct, but may rarely pass anterior to it instead. [ 4 ]


The inner surface is covered in a  simple columnar epithelium . [ 3 ]


Accessory hepatic ducts


Around 1.7% [ 6 ]  of people have additional accessory hepatic ducts that opens into the common hepatic duct. [ 6 ]  Accessory hepatic ducts may also instead open into the cystic duct or gallbladder. [ 4 ]


Termination


Occasionally, the cystic duct may first run along the right side of the common bile duct for some distance before joining it, or may pass posteriorly around to the common hepatic duct to unite with it from the left side. [ 4 ]


Rarely, the common hepatic duct and gallbladder join directly (with the cystic duct being absent), [ 6 ] [ 4 ]  leading to illness. [ 6 ]


The hepatic duct is part of the  biliary tract  that transports secretions from the liver into the  intestines .


The common hepatic ducts carries a higher volume of bile in people who have had their gallbladder removed. [ citation needed ]


The common hepatic duct is an important anatomic landmark during surgeries such as  cholecystectomy . It forms one edge of  Calot's triangle , along with the cystic duct and the  cystic artery . All constituents of this triangle must be identified to avoid cutting or clipping the wrong structure.


A diameter of more than 8 mm is regarded as abnormal dilatation, and is a sign of  cholestasis . [ 7 ]


Mirizzi's syndrome  occurs when the common hepatic duct is blocked by  gallstones . [ 8 ]


Cud  is a portion of food that returns from a  ruminant 's stomach to the mouth to be chewed for the second time. More precisely, it is a  bolus  of semi-degraded food  regurgitated  from the  reticulorumen  of a  ruminant . Cud is produced during the physical digestive process of rumination. [ 1 ]


The  alimentary canal  of ruminants, such as  cattle ,  giraffes ,  goats ,  sheep ,  alpacas , and  antelope , are unable to produce the  enzymes  required to break down the  cellulose  and  hemicellulose  of plant matter. [ 2 ]  Accordingly, these animals rely on a  symbiotic  relationship with a wide range of  microbes , which largely reside in the  reticulorumen , and which are able to synthesize the requisite enzymes. The reticulorumen thus hosts a microbial fermentation which yields products (mainly  volatile fatty acids  and microbial protein), which the ruminant is able to digest and absorb. This allows the animals to extract nutritional value from cellulose which is usually undigested.


The process of rumination is stimulated by the presence of  roughage  in the upper part of the  reticulorumen . The chest cavity is stretched, forming a vacuum in the gullet that sucks the semi-liquid stomach content into the  esophagus . From the esophagus it is taken back to the mouth with retro  peristaltic  movements. When the stomach content, or the cud, arrives in the mouth of the ruminant, it is pushed against the palate with the tongue to remove excess liquid, the latter is swallowed and the solid material is chewed thoroughly so the cattle can extract the minerals present in the cud brought to the surface during rumination. The function of rumination is that food is physically refined to expose more surface area for bacteria working in the reticulorumen, as well as stimulation of  saliva  secretion to  buffer  the rumen  pH .


When food has been degraded sufficiently it passes from the reticulorumen through the reticulomasal orifice to the  omasum  followed by the  abomasum  to continue the digestion process in the lower parts of the alimentary canal. No enzymes are secreted in the rumen. Enzymes and  hydrochloric acid  are only secreted from the  abomasum  (fourth stomach) onwards, and ruminants function from that point onwards much like monogastric animals, such as  pigs  and humans.


The reticulorumen has an optimum pH of 6.5 for the microbe population to thrive. Consumption by ruminants of an insufficiently fibrous diet leads to little cud formation and therefore lowered amounts of saliva production. This in turn is associated with rumen  acidosis , where the rumen pH can fall to 5 or lower. Rumen acidosis is associated with a lowered appetite which leads to still lower rates of saliva secretion. Eventually, a collapse of the microbial  ecosystem  in the rumen will occur because of the low pH. Acute rumen acidosis can lead to death of the animal, and will occur if the animal is allowed to eat a diet with no roughage but high levels of highly  digestible  starchy concentrate. Some dairy cows in intensive systems of milk production may have sub-acute acidosis because of the high rates of cereals in their diets relative to an insufficient amount of forage. However, most producers provide adequate  fodder  in the form of  hay  to prevent this. [ 3 ] [ additional citation(s) needed ]


Jewish dietary laws  state that an animal that chews the cud and has a  cloven hoof  is acceptable for consumption. Any animal that doesn't chew the cud and have a  cloven hoof  is unclean.


Goat cud is sometimes an ingredient in  Pinapaitan .


The  cystic duct  is the  duct  that (typically) joins the  gallbladder  and the  common hepatic duct ; the union of the cystic duct and common hepatic duct forms  the bile duct  (formerly known as the common bile duct). Its length varies.


The cystic duct typically [ 2 ]  measures (sources differ) 2–4 cm [ 3 ] [ 4 ] /2–3 cm [ 2 ]  in length (though its length has been known to range from 0.5 cm to 9 cm [ 3 ] ), and 2–3 mm in diameter. [ 2 ] [ 4 ]  It is often tortuous. [ 3 ] [ 4 ]


It is the distal continuation of the neck of the gallbladder, from where it is directed inferoposteriorly and to the left [ 2 ] /medially [ 4 ]  (this occurs in half of individuals [ 3 ] ). It typically [ 2 ]  terminates by uniting with the  common hepatic duct  to form the  bile duct  (usually anterior to the right hepatic artery). [ 2 ]  It usually joins the common bile duct from the right lateral side (forming an oblique angle between the two), [ 4 ]  and at such a distance that the bile duct is twice as long as the common hepatic duct. [ 3 ] [ 4 ]  It often fuses with the common hepatic duct before actually opening into it after a variable distance [ 4 ] [ 3 ]  (this arrangement may have the purpose of directing bile flow distally instead of back towards the liver [ 3 ] ).


The inner surface of the cystic duct features spiral, crescentic mucosal folds - the  spiral folds of cystic duct . [ 4 ] [ 3 ]


The inner surface of the proximal cystic duct exhibits a network of submicroscopic convoluted folds (rugae), whereas that of the distal cystic duct exhibits submicroscopic parallel longitudinal folds. [ 3 ]


The epithelial lining of the inner surface of the duct is similar to that of the gallbladder and consists mostly of  columnar epithelial cells  with short  microvilli  upon their apical surfaces. [ 3 ]


The subepithelial layer consists of  elastic connective tissue  and is highly vascular; vessels that are adjacent to the epithelial  basement membrane  are  fenestrated , possibly to facilitate ion and fluid exchange with the bile as is the case in the gallbladder itself. [ 3 ]


The outer fibromuscular layer contains  smooth muscle  continuous with that of the gallbladder; some of the smooth muscle extends into the spiral valves. [ 3 ]


It usually lies next to the  cystic artery . [ citation needed ]


The cystic duct may rarely be doubled. [ 2 ] [ 3 ]


An accessory hepatic duct may join the cystic duct. [ 2 ] [ 4 ]


A pathological diverticulum known as the  Hartmann’s pouch  may be present at the junction of the neck of bladder and the cystic duct. [ 2 ]


Length


The duct may sometimes be extremely short (making cholecystectomy risky) [ 2 ]  or may rarely be altogether absent (so that the gallbladder is directly attached to the bile duct). [ 2 ] [ 4 ] [ 3 ]


Shape


While most often tortuous, it may occasionally be curved, straight, or S-shaped. [ 3 ]


The cystic duct may unite with the common hepatic duct so that the common hepatic duct is either very short or very long (and the bile duct in turn very long or very short, respectively), [ 4 ]  or it may instead unite with the a hepatic duct. [ 3 ]


Occasionally, the cystic duct may first run alongside the common hepatic duct for some distance [ 2 ] [ 4 ]  within the  hepatoduodenal ligament [ 4 ]  before joining it. [ 2 ] [ 4 ]  It sometimes join the common hepatic duct at its anterior, posterior, or medial side [ 4 ] [ 3 ]  (in the latter case by passing posteriorly around the common bile duct to join it from the other side). [ 2 ]   It may spiral around the common hepatic duct before joining it. [ 4 ]


Very rarely, the cystic duct opens into the  duodenum . [ 3 ]


Bile can flow in either direction between the gallbladder, and the common bile duct and  hepatic duct . [ 3 ]  In this way, bile is stored in the gallbladder in between meal times. The hormone  cholecystokinin , when stimulated by a fatty meal, promotes bile secretion by increased production of hepatic bile, contraction of the gall bladder, and relaxation of the  Sphincter of Oddi .


The bile duct was once thought to possess a  sphincteric  function, however, it is now known that bile flow through the cystic duct proceeds unimpeded and is instead regulated by other mechanisms at other points of the biliary system. [ 3 ]


Gallstones  can enter and obstruct the cystic duct, preventing the flow of bile. The increased pressure in the gallbladder leads to swelling and pain. This pain, known as  biliary colic , is sometimes referred to as a gallbladder "attack" because of its sudden onset.


During a  cholecystectomy , the cystic duct is clipped two or three times and a cut is made between the clips, freeing the gallbladder to be taken out.


Defecation  (or  defaecation ) follows  digestion , and is a necessary process by which organisms eliminate a solid, semisolid, or liquid  waste  material known as  feces  from the  digestive tract  via the  anus  or  cloaca . The act has a variety of names ranging from the common, like  pooping  or  crapping , to the technical, e.g.  bowel movement , to the obscene ( shitting ), to the  euphemistic  ("doing a number two", "dropping a deuce" or "taking a dump"), to the juvenile ("making doo-doo"). The topic, usually avoided in polite company, can become the basis for some  potty humor .


Humans  expel  feces  with a frequency varying from a few times daily to a few times weekly. [ 1 ]  Waves of  muscular contraction  (known as  peristalsis ) in the walls of the  colon  move fecal matter through the digestive tract towards the  rectum . Undigested food may also be expelled within the feces, in a process called  egestion . When  birds  defecate, they also expel  urine  and  urates  in the same mass, whereas other animals may also  urinate  at the same time, but spatially separated. Defecation may also accompany  childbirth  and  death . Babies defecate a unique substance called  meconium  prior to eating external foods.


There are a number of medical conditions associated with defecation, such as  diarrhea  and  constipation , some of which can be serious. The feces expelled can carry diseases, most often through the contamination of food.  E. coli  is a particular concern.


Before  toilet training , human feces are most often collected into a  diaper . Thereafter, in many societies people commonly defecate into a  toilet . However,  open defecation , the practice of defecating outside without using a toilet of any kind, is still widespread in some  developing countries . [ 2 ]  Some people defecate into  the ocean . First world countries use  sewage treatment plants  and/or  on-site treatment .


The  rectum ampulla  stores fecal waste (also called stool) before it is excreted. As the waste fills the rectum and expands the rectal walls, stretch receptors in the rectal walls stimulate the desire to defecate. This urge to defecate arises from the reflex contraction of rectal muscles, relaxation of the  internal anal sphincter , and an initial contraction of the skeletal muscle of the  external anal sphincter . If the urge is not acted upon, the material in the rectum is often returned to the colon by  reverse peristalsis , where more water is absorbed and the feces are stored until the next mass peristaltic movement of the transverse and descending colon.


When the rectum is full, an increase in pressure within the rectum forces apart the walls of the  anal canal , allowing the fecal matter to enter the canal. The rectum shortens as material is forced into the anal canal and peristaltic waves push the feces out of the rectum. The internal and external anal sphincters along with the  puborectalis muscle  allow the feces to be passed by muscles pulling the anus up over the exiting feces. [ 3 ]


The  external anal sphincter  is under voluntary control whereas the  internal anal sphincter  is involuntary. In  infants , the defecation occurs by  reflex action  without the voluntary control of the external anal sphincter. Defecation is voluntary in adults. Young children learn voluntary control through the process of  toilet training . Once trained, loss of control, called  fecal incontinence , may be caused by physical injury, nerve injury, prior surgeries (such as an  episiotomy ),  constipation ,  diarrhea , loss of storage capacity in the  rectum , intense fright,  inflammatory bowel disease ,  psychological  or  neurological  factors,  childbirth , or  death . [ 4 ]


Sometimes, due to the inability to control one's bowel movement or due to excessive fear, defecation (usually accompanied by urination) occurs involuntarily, soiling a person's undergarments. This may cause significant embarrassment to the person if this occurs in the presence of other people or a public place.


The positions and modalities of defecation are  culture-dependent .  Squat toilets  are used by the vast majority of the world, including most of Africa, Asia, and the Middle East. [ 5 ]  The use of sit-down  toilets  in the  Western world  is a relatively recent development, beginning in the 19th century with the advent of indoor plumbing. [ 6 ]


Regular bowel movements determine the functionality and the health of the alimentary tracts in human body. Defecation is the most common regular bowel movement which eliminates waste from the human body. The frequency of defecation is hard to identify, which can vary from daily to weekly depending on individual bowel habits, the impact from the environment and genetic. [ 7 ]  If defecation is delayed for a prolonged period the fecal matter may harden, resulting in  constipation . If defecation occurs too fast, before excess liquid is absorbed,  diarrhea  may occur. [ 8 ]  Other associated symptoms can include abdominal bloating, abdominal pain, and abdominal distention. [ 9 ]  Disorders of the bowel can seriously impact quality of life and daily activities. The causes of functional bowel disorder are multifactorial, and dietary habits such as food intolerance and low fiber diet are considered to be the primary factors. [ 10 ]


Constipation, also known as defecatory dysfunction, is difficulty experienced when passing stools. It is one of the most notable alimentary disorders that affects different age groups in the population. Common constipation is associated with abdominal distention, pain or bloating. [ 11 ]  Research has revealed that chronic constipation complied with higher risk of cardiovascular events such as coronary heart disease and ischemic stroke, while associating with an increasing risk of mortality. [ 12 ]  Besides dietary factors, psychological traumas and 'pelvic floor disorders' can also cause chronic constipation and defecatory disorder respectively. [ 11 ]  Multiple interventions, including physical activities, 'high-fibre diet', probiotics [ 13 ]  and drug therapies can be widely and efficiently used to treat constipation and defecatory disorder.


Inflammatory disease is characterized as long-lasting, chronic inflammation throughout the gastrointestinal tract.  Crohn's disease  (CD) and  ulcerative colitis  (UC) are two universal types of inflammatory bowel disease that have been studied over a century. They are closely related to different environmental risk factors, family genetics, and lifestyle choices such as smoking. [ 14 ]  Crohn's disease has been found to be related to immune disorders particularly. [ 15 ]  Different levels of cumulative intestinal injuries can cause different complications, such as fistulae, damage of bowel function, symptom recurrence, disability, etc. [ 16 ]  Patients can be children or adults. Recent research shows that immunodeficiency and monogenic disorders are the causes in young patients with inflammatory bowel diseases. [ 17 ]


Common symptoms of inflammatory bowel diseases differ by the infection level, but may include severe abdominal pain, diarrhea, fatigue, and unexpected weight loss.  Crohn's disease  can lead to infection of any part of the digestive tract, including ileum to anus. [ 18 ]  Internal manifestations include diarrhea, abdomen pain, fever, chronic anaemia, etc. External manifestations include impact on skin, joints, eyes, and liver. Significantly reduced microbiota diversity inside the gastrointestinal tract can also be observed. Ulcerative colitis mainly affects the function of the large bowel, and its incidence rate is three times greater than that of Crohn's disease. [ 19 ]  In terms of clinical features, over 90 percent of patients exhibit constant diarrhea, rectal bleeding, softer stool, mucus in the stool, tenesmus, and abdominal pain. [ 19 ]  The symptoms may continue for around 6 weeks or even longer.


The inflammatory bowel diseases could be effectively treated by 'pharmacotherapies' to relieve and maintain the symptoms, which showed in 'mucosal healing' and symptoms elimination. [ 20 ]  However, an optimal therapy for curing both inflammatory diseases are still under research due to the heterogeneity in clinical feature. [ 20 ]  Although both UC and CD are sharing similar symptoms, the medical treatment of them are distinctively different. [ 20 ]  Dietary treatment can benefit for curing CD by increase the dietary zinc and fish intake, which is related to mucosal healing of the bowel. [ 15 ]  Treatments vary from drug treatment to surgery based on the active level of the CD. UC can also be relieved by using immunosuppressive therapy for mild to moderate disease level and application of biological agents for severe cases. [ 19 ]


Irritable bowel syndrome is diagnosed as an intestinal disorder with chronic abdominal pain and inconsistency in form of stool, and is a common bowel disease that can be easily diagnosed in modern society. [ 21 ]  The variation in incident rate can be explained by different diagnostic criteria in different countries, with the 18–34 age group being recognized as the high frequency incident group. [ 21 ]  The definite cause of irritable bowel syndrome remains a mystery; however, it has been found to relate to multiple factors, such as 'alternation of mood and pressure, sleep disorders, food triggers, changing of dysbiosis and even sexual dysfunction'. [ 21 ]  One third of irritable bowel syndrome patients has family history with the disease suggesting that genetic predisposition could be a significant cause for irritable bowel syndrome. [ 22 ]


Patients with irritable bowel syndrome commonly experience abdominal pain, changes to stool form, recurrent abdominal bloating and gas, [ 22 ]  co-morbid disorders and alternation in bowel habits that caused diarrhea or constipation. [ 21 ]  However, anxiety and tension can also be detected, although patients with irritable bowel disease seem healthy. Apart from these typical symptoms, rectal bleeding, unexpected weight loss and increased inflammatory markers require further medical examination and investigation. [ 21 ]


Treatment for irritable bowel disease is multimodal. Dietary intervention and pharmacotherapies can both relieve the symptoms to a certain degree. Avoiding allergic food groups can be beneficial by reducing fermentation in the digestive tract and gas production, hence effectively alleviating abdominal pain and bloating. [ 21 ]  Drug interventions, such as laxatives, loperamide, [ 21 ]  and lubiprostone [ 22 ]  are applied to relieve intense symptoms including diarrhea, abdominal pain and constipation. Psychological treatment, dietary supplements [ 21 ]  and gut-focused hypnotherapy [ 22 ]  are recommended for targeting depression, mood disorders and sleep disturbance.


Bowel obstruction is a bowel condition which is a blockage that can be found in both the small intestines and large intestines. Increase of contractions can relieve blockages; however, continuous contractions with decreasing functionality may lead to terminated mobility of the small intestines, which then forms the obstruction. At the same time, the lack of contractility encourages liquid and gas accumulation. [ 23 ]  and "electrolyte disturbances". [ 24 ]  Small bowel obstruction can result in severe renal damage and hypovolemia. [ 24 ]  while evolving into "mucosal ischemia and perforation". [ 23 ]  Patients with small bowel obstruction were found to experience constipation, strangulation and abdominal pain and vomiting. [ 23 ]  Surgical intervention is primarily used to cure severe small bowel obstruction condition. Nonoperative therapy included nasogastric tube decompression, water-soluble-contrast medium process or symptomatic management can be applied to treat less severe symptoms [ 23 ]


According to research, large bowel obstruction is less common than small bowel obstruction, but is still associated with a high mortality rate. [ 25 ]  Large bowel obstruction, also known as colonic obstruction, includes acute colonic obstruction, where a blockage is formed in the colon. Colonic obstructions frequently occur within the elder population, often accompanied by significant 'comorbidities'. [ 26 ]  Although colonic malignancy is revealed as the major cause of the colonic obstruction, volvulus has also been founded as a secondary common cause around the world. [ 25 ]  In addition, lower mobility, unhealthy mentality and restricted living environment are also listed as risk factors. Surgery and colonic stent placements are widely applied for curing colonic obstructions. [ 27 ]


Attempting forced expiration of breath against a closed airway (the  Valsalva maneuver ) is sometimes practiced to induce defecation while on a  toilet . This contraction of expiratory  chest  muscles,  diaphragm , abdominal wall muscles, and  pelvic  diaphragm exerts pressure on the digestive tract.  Ventilation  at this point temporarily ceases as the lungs push the chest diaphragm down to exert the pressure.  Cardiac arrest [ 28 ]  and other cardiovascular complications [ 29 ]  can in rare cases occur due to attempting to defecate using the Valsalva maneuver.  Valsalva retinopathy  is another pathological syndrome associated with the Valsalva maneuver. [ 30 ] [ 31 ]  Thoracic  blood pressure  rises and as a reflex response the amount of blood pumped by the heart decreases. Death has been known to occur in cases where defecation causes the blood pressure to rise enough to cause the rupture of an  aneurysm  or to dislodge blood clots (see  thrombosis ). Also, in releasing the Valsalva maneuver blood pressure falls; this, coupled with standing up quickly to leave the toilet, can result in a blackout. [ citation needed ]


Open defecation  is the human practice of defecating outside (in the open environment) rather than into a  toilet . People may choose fields, bushes, forests, ditches, streets, canals or other open space for defecation. They do so because either they do not have a toilet readily accessible or due to traditional cultural practices. [ 32 ]  The practice is common where  sanitation  infrastructure and services are not available. Even if toilets are available,  behavior change  efforts may still be needed to promote the use of toilets.


Open defecation can pollute the environment and cause health problems. High levels of open defecation are linked to high  child mortality , poor  nutrition ,  poverty , and large disparities between rich and poor. [ 33 ] : 11


Ending open defecation is an indicator being used to measure progress towards the  Sustainable Development Goal Number 6 .  Extreme poverty  and lack of sanitation are statistically linked. Therefore, eliminating open defecation is thought to be an important part of the effort to eliminate poverty. [ 34 ]


The  anus  and  buttocks  may be  cleansed  after defecation with  toilet paper , similar paper products, or other absorbent material. In many cultures, such as Hindu and Muslim, water is used for anal cleansing after defecation, either in addition to using toilet paper or exclusively. When water is used for anal cleansing after defecation, toilet paper may be used for drying the area afterwards. Some doctors and people who work in the science and  hygiene  fields have stated that switching to using a  bidet  as a form of anal cleansing after defecation is both more hygienic and more environmentally friendly. [ 35 ]


Some peoples have culturally significant stories in which defecation plays a role. For example:


Some aspects of  psychology  surround the act of defecation. There is an inherent desire for privacy among humans.  Freud  stipulated a second stage of development, the  Anal Stage , which centers around the release of waste from the bladder and bowels. He categorized two types:  anal retentive  and  anal expulsive .


Digestion  is the breakdown of large insoluble  food  compounds into small water-soluble components so that they can be absorbed into the  blood plasma . In certain organisms, these smaller substances are absorbed through the  small intestine  into the  blood stream . Digestion is a form of  catabolism  that is often divided into two processes based on how food is broken down: mechanical and chemical digestion. The term  mechanical digestion  refers to the physical breakdown of large pieces of food into smaller pieces which can subsequently be accessed by  digestive enzymes . Mechanical digestion takes place in the  mouth  through  mastication  and in the small intestine through  segmentation contractions . In  chemical digestion ,  enzymes  break down food into the small compounds that the body can use.


In the  human digestive system , food enters the mouth and mechanical digestion of the food starts by the action of mastication (chewing), a form of mechanical digestion, and the wetting contact of  saliva . Saliva, a liquid secreted by the  salivary glands , contains  salivary amylase , an enzyme which starts the digestion of  starch  in the food. [ 1 ]  The saliva also contains  mucus , which lubricates the food; the  electrolyte  hydrogencarbonate ( HCO − 3 ), which provides the ideal conditions of pH for amylase to work; and other electrolytes ( Na + ,  K + ,  Cl − ). [ 2 ]  About 30% of starch is  hydrolyzed  into  disaccharide  in the oral cavity (mouth). After undergoing mastication and starch digestion, the food will be in the form of a small, round slurry mass called a  bolus . It will then travel down the  esophagus  and into the  stomach  by the action of  peristalsis .  Gastric juice  in the stomach starts  protein digestion . Gastric juice mainly contains  hydrochloric acid  and  pepsin . In  infants  and  toddlers , gastric juice also contains  rennin  to digest milk proteins. As the first two chemicals may damage the stomach wall, mucus and bicarbonates are secreted by the stomach. They provide a slimy layer that acts as a shield against the damaging effects of chemicals like concentrated hydrochloric acid while also aiding lubrication. [ 3 ]  Hydrochloric acid provides acidic pH for pepsin. At the same time protein digestion is occurring, mechanical mixing occurs by peristalsis, which is waves of muscular contractions that move along the stomach wall. This allows the mass of food to further mix with the digestive enzymes. Pepsin breaks down proteins into  peptides  or  proteoses , which is further broken down into dipeptides and  amino acids  by enzymes in the small intestine. Studies suggest that increasing the number of chews per bite increases relevant gut hormones and may decrease self-reported hunger and food intake. [ 4 ]


When the  pyloric sphincter valve  opens, partially digested food ( chyme ) enters the  duodenum  where it mixes with digestive enzymes from the  pancreas  and bile juice from the  liver  and then passes through the small intestine, in which digestion continues. When the chyme is fully digested, it is absorbed into the blood. 95% of nutrient absorption occurs in the small intestine. Water and minerals are reabsorbed back into the blood in the  colon  (large intestine) where the pH is slightly acidic (about 5.6 ~ 6.9). Some vitamins, such as  biotin  and  vitamin K  (K 2 MK7) produced by bacteria in the colon are also absorbed into the blood in the colon. Absorption of water, simple sugar and alcohol also takes place in stomach. Waste material ( feces ) is eliminated from the  rectum  during  defecation . [ 5 ]


Digestive systems take many forms. There is a fundamental distinction between internal and external digestion. External digestion developed earlier in evolutionary history, and most  fungi  still rely on it. [ 6 ]  In this process,  enzymes  are  secreted  into the environment surrounding the organism, where they break down an organic material, and some of the products  diffuse  back to the organism.  Animals  have a tube ( gastrointestinal tract ) in which internal digestion occurs, which is more efficient because more of the broken down products can be captured, and the internal chemical environment can be more efficiently controlled. [ 7 ]


Some organisms, including nearly all  spiders , secrete biotoxins and digestive chemicals (e.g., enzymes) into the extracellular environment prior to ingestion of the consequent "soup". In others, once potential nutrients or food is inside the  organism , digestion can be conducted to a  vesicle  or a sac-like structure, through a tube, or through several specialized organs aimed at making the absorption of nutrients more efficient.


Bacteria  use several systems to obtain nutrients from other organisms in the environments.


In a channel transport system, several proteins form a contiguous channel traversing the inner and outer membranes of the bacteria. It is a simple system, which consists of only three protein subunits: the  ABC protein ,  membrane fusion protein  (MFP), and  outer membrane protein . [ specify ]  This secretion system transports various chemical species, from ions, drugs, to proteins of various sizes (20–900 kDa). The chemical species secreted vary in size from the small  Escherichia coli  peptide colicin V, (10 kDa) to the  Pseudomonas fluorescens  cell adhesion protein LapA of 900 kDa. [ 8 ]


A  type III secretion system  means that a molecular syringe is used through which a bacterium (e.g. certain types of  Salmonella ,  Shigella ,  Yersinia ) can inject nutrients into protist cells. One such mechanism was first discovered in  Y. pestis  and showed that toxins could be injected directly from the bacterial cytoplasm into the cytoplasm of its host's cells rather than be secreted into the extracellular medium. [ 9 ]


The  conjugation  machinery of some bacteria (and archaeal flagella) is capable of transporting both DNA and proteins. It was discovered in  Agrobacterium tumefaciens , which uses this system to introduce the Ti plasmid and proteins into the host, which develops the crown gall (tumor). [ 10 ]  The VirB complex of  Agrobacterium tumefaciens  is the prototypic system. [ 11 ]


In the  nitrogen-fixing   Rhizobia , conjugative elements naturally engage in inter- kingdom  conjugation. Such elements as the  Agrobacterium  Ti or Ri plasmids contain elements that can transfer to plant cells. Transferred genes enter the plant cell nucleus and effectively transform the plant cells into factories for the production of  opines , which the bacteria use as carbon and energy sources. Infected plant cells form  crown gall  or  root tumors . The Ti and Ri plasmids are thus  endosymbionts  of the bacteria, which are in turn endosymbionts (or parasites) of the infected plant.


The Ti and Ri plasmids are themselves conjugative. Ti and Ri transfer between bacteria uses an independent system (the  tra , or transfer, operon) from that for inter-kingdom transfer (the  vir , or  virulence , operon). Such transfer creates virulent strains from previously avirulent  Agrobacteria .


In addition to the use of the multiprotein complexes listed above,  gram-negative bacteria  possess another method for release of material: the formation of  outer membrane vesicles . [ 12 ] [ 13 ]   Portions of the outer membrane pinch off, forming spherical structures made of a lipid bilayer enclosing periplasmic materials.  Vesicles from a number of bacterial species have been found to contain virulence factors, some have immunomodulatory effects, and some can directly adhere to and intoxicate host cells.  While release of vesicles has been demonstrated as a general response to stress conditions, the process of loading cargo proteins seems to be selective. [ 14 ]


The  gastrovascular cavity  functions as a stomach in both digestion and the distribution of nutrients to all parts of the body.  Extracellular digestion takes place within this central cavity, which is lined with the gastrodermis, the internal layer of  epithelium . This cavity has only one opening to the outside that functions as both a  mouth  and an  anus : waste and undigested matter is excreted through the mouth/anus, which can be described as an incomplete  gut .


In a plant such as the  Venus flytrap  that can make its own food through photosynthesis, it does not eat and digest its prey for the traditional objectives of harvesting energy and carbon, but mines prey primarily for essential nutrients (nitrogen and phosphorus in particular) that are in short supply in its boggy, acidic habitat. [ 15 ]


A  phagosome  is a  vacuole  formed around a particle absorbed by  phagocytosis .  The vacuole is formed by the fusion of the  cell membrane  around the particle. A phagosome is a  cellular compartment  in which  pathogenic  microorganisms can be killed and digested. Phagosomes fuse with  lysosomes  in their maturation process, forming  phagolysosomes . In humans,  Entamoeba histolytica  can phagocytose  red blood cells . [ 16 ]


To aid in the digestion of their food, animals evolved organs such as beaks,  tongues ,  radulae , teeth, crops, gizzards, and others.


Birds  have bony  beaks  that are specialised according to the bird's  ecological niche . For example,  macaws  primarily eat seeds, nuts, and fruit, using their beaks to open even the toughest seed. First they scratch a thin line with the sharp point of the beak, then they shear the seed open with the sides of the beak.


The mouth of the  squid  is equipped with a sharp horny beak mainly made of cross-linked  proteins . It is used to kill and tear prey into manageable pieces. The beak is very robust, but does not contain any minerals, unlike the teeth and jaws of many other organisms, including marine species. [ 17 ]  The beak is the only indigestible part of the squid.


The  tongue  is skeletal muscle on the floor of the  mouth  of most vertebrates, that manipulates  food  for chewing ( mastication ) and  swallowing  (deglutition). It is sensitive and kept moist by  saliva . The underside of the tongue is covered with a smooth  mucous membrane . The tongue also has a touch sense for locating and positioning food particles that require further chewing. The tongue is used to roll food particles into a  bolus  before being transported down the  esophagus  through  peristalsis .


The  sublingual  region underneath the front of the tongue is a location where the  oral mucosa  is very thin, and underlain by a plexus of veins. This is an ideal location for introducing certain medications to the body. The sublingual route takes advantage of the highly  vascular  quality of the oral cavity, and allows for the speedy application of medication into the cardiovascular system, bypassing the gastrointestinal tract.


Teeth (singular tooth) are small whitish structures found in the jaws (or mouths) of many vertebrates that are used to tear, scrape, milk and chew food. Teeth are not made of bone, but rather of tissues of varying density and hardness, such as enamel, dentine and cementum. Human teeth have a blood and nerve supply which enables proprioception. This is the ability of sensation when chewing, for example if we were to bite into something too hard for our teeth, such as a chipped plate mixed in food, our teeth send a message to our brain and we realise that it cannot be chewed, so we stop trying.


The shapes, sizes and numbers of types of animals' teeth are related to their diets. For example, herbivores have a number of molars which are used to grind plant matter, which is difficult to digest.  Carnivores  have  canine teeth  which are used to kill and tear meat.


A  crop , or croup, is a thin-walled expanded portion of the  alimentary tract  used for the storage of food prior to digestion. In some birds it is an expanded, muscular pouch near the  gullet  or throat. In adult doves and pigeons, the crop can produce  crop milk  to feed newly hatched birds. [ 18 ]


Certain insects may have a crop or enlarged  esophagus .


Herbivores  have evolved  cecums  (or an  abomasum  in the case of  ruminants ). Ruminants have a fore-stomach with four chambers. These are the  rumen ,  reticulum ,  omasum , and abomasum. In the first two chambers, the rumen and the reticulum, the food is mixed with saliva and separates into layers of solid and liquid material.  Solids clump together to form the cud (or  bolus ). The cud is then regurgitated, chewed slowly to completely mix it with saliva and to break down the particle size.


Fibre, especially  cellulose  and  hemi-cellulose , is primarily broken down into the  volatile fatty acids ,  acetic acid ,  propionic acid  and  butyric acid  in these chambers (the reticulo-rumen) by microbes: ( bacteria ,  protozoa , and fungi). In the omasum, water and many of the inorganic mineral elements are absorbed into the blood stream.


The abomasum is the fourth and final stomach compartment in ruminants. It is a close equivalent of a monogastric stomach (e.g., those in humans or pigs), and digesta is processed here in much the same way. It serves primarily as a site for acid hydrolysis of microbial and dietary protein, preparing these protein sources for further digestion and absorption in the small intestine.  Digesta is finally moved into the small intestine, where the digestion and absorption of nutrients occurs. Microbes produced in the reticulo-rumen are also digested in the small intestine.


Regurgitation  has been mentioned above under abomasum and crop, referring to crop milk, a secretion from the lining of the crop of  pigeons and doves  with which the parents feed their young by regurgitation. [ 19 ]


Many  sharks  have the ability to turn their stomachs inside out and evert it out of their mouths in order to get rid of unwanted contents (perhaps developed as a way to reduce exposure to toxins).


Other animals, such as  rabbits  and  rodents , practise  coprophagia  behaviours – eating specialised faeces in order to re-digest food, especially in the case of roughage. Capybara, rabbits, hamsters and other related species do not have a complex digestive system as do, for example, ruminants. Instead they extract more  nutrition  from grass by giving their food a second pass through the  gut . Soft faecal pellets of partially digested food are excreted and generally consumed immediately. They also produce normal droppings, which are not eaten.