Digestive System

∞ generated and posted on 2018.10.08 ∞

The large intestine/colon is where water along with a limited number of additional substances are absorbed and feces are formed.

The large intestine is tasked with temporarily storing what is left over following digestion, absorption, and removing water from chyme, allowing some further digestion and nutrient absorption, and then eliminating the resulting fecal material from the body.

This page contains the following terms: Large intestine, Cecum, Appendix, Colon, Ascending colon, Transverse colon, Descending colon, Sigmoid colon, Rectum, Anal sphincters Cirrhosis, Gallstones, Hepatitis, Hiatal hernia, Irritable bowel syndrome, Inflammatory bowel disease, Crohn's disease, Ulcerative colitis, Microbiome, Normal flora, Beneficial bacteria, Probiotic, Clostridium difficile, Fecal transplant

Large intestine

Region of the alimentary canal in which substantial absorption of water occurs.
The large intestine is described as large because its diameter is somewhat greater than that of the small intestine.

The large intestine is divided, in order going from the small intestine, into (0) the ileocecal valve, (1) the cecum, (2) the ascending colon, (3) the transverse colon, (4) the descending colon, and (5) the sigmoid colon. The rectum follows the sigmoid colon, and is the site of feces storage prior to defecation. The subsequent anus, and its anal sphincter, define the terminus of the alimentary canal.

The terminus of the ileum of the small intestine is at the ileocecal valve, just prior to the cecum. The large intestine, variously descrobed, thus spans from the terminus of the ileum until the anus.

The function of the large intestine is a combination of feces formation, associated removal of water from the forming feces (to prevent excessive fluid loss from the body), and, depending on the species, also some food digestion as well as nutrient absorption.

For the latter, the large intestine basically serves as a rather large fermenter which further digests that material that was not absorbed in the small intestine.

The lumen of the large intestine additionally contains the majority of the microflora (bacteria as well as other microorganisms) that are associated with the body.

Links to terms of possible interest: Anal canal, Ascending colon, Cecum, Descending colon, Large intestine, Sigmoid colon, Smooth muscle, Taenia coli, Transverse colon

The above video walks through the vary basics of why we have a large intestine; note that at 1:36 the narrator misspeaks stating "small intestine" when he means "large intestine".

The above video is quite heavy duty in its discussion but also supplies a pretty amazing perspective on the gross anatomy of the large intestine.


Blind pouch representing the initial section of the large intestine.
The ileocecal valve separates the small intestine from the large intestine. Rather than continuing as a free-flowing tube beyond this valve, however, the alimentary canal instead is pouch-like, that is, having an entrance at one end (the ileocecal valve end, or in us the top or superior end) and no exit at the other, bottom, or inferior end.

This pouch is our cecum and its presense means that chyme does not move quite as easily upon entrance into the large intestine as in the small intestine.

The large diameter of the lumen of the large intestine relative to that of the small intestine/ileum additionally results in a slowing down of the rate of forward movement of chyme.

It is within the cecum that especially difficult-to-digest materials, particularly dietary fiber, may be broken down by the alimentary canal. Indeed, the cecum, as well as appendix, at least in mammals, tends to be larger in herbivores than in carnivores.

It is off of the cecum also that the appendix is found.

Links to terms of possible interest: Appendix, Appendix vermiformis Ascending colon, Cecum, Ileocecal valve, Ileum, Vermiform appendix,

The above video is a short endoscopic examination of a cecum.

OK, the above video is just funny, in a strange kind of way, but does show various endoscopic shots of ceca.


Short, thin, worm-shaped, tubular extension of the cecum.
The appendix is a narrow tube that is closed at one end, and open at the other into the cecum of the large intestine. It is also known, including more formally, as the vermiform appendix.

As with the cecum, and the ascending colon, the appendix is located on the right side of the abdomen, and as the appendix is found below the cecum, it is also found in the lower-right side of the abdomen.

The appendix is typically considered to represent a vestigial structure in humans because its surgical removal, in the course of an appendectomy in response to acute appendicitis, is not known to result in loss of body functioning. Nonetheless, the appendix at least has the potential to play immunological roles in the functioning of the alimentary canal and also at least potentially could serve as a storehouse for microorganisms that the body otherwise "wants" to persist within the large intestine.

The latter makes sense at least anatomically as the appendix sits at the beginning of the large intestine, just as the ducts from the pancreas and liver sit at the start of the small intestine. The closed-at-one-end nature of the appendix assures that microorganisms can become reversibly "stuck" within the appendix. This also allows for substantial immunological interaction within the appendix, with retention perhaps especially of more desirable or at least less pathogenic organisms.

Nonetheless, it is by no means certain exactly what role the appendix plays in the normal functioning of our bodies.

Links to terms of possible interest: Appendix, Ascending colon, Cecum, Ileocecal valve, Ileum, Vermiform appendix, Vermiformis appendix

The above video is actually a rather good introduction to the appendix and appendicitis.

An argument for the usefulness of the appendix.


Portion of the large intestine that is found after the cecum and prior to the rectum.
The colon is differentiated into at least four segments. These, as listed in order of the direction of flow of chyme, are the ascending colon, the transverse colon, the descending colon, and the sigmoid colon. The cecum and ileocecal valve are found immediately upstream of the colon and the rectum is found immediately downstream.

The function of the colon is primarily absorption of water as a means of conserving water in terrestrial vertebrates, that is, such as ourselves. It also is involved in absorption of salts and of lipid-soluble substances. Digestion and absorption thus takes place in the alimentary canal through into the cecum, and then anything that has not yet been absorbed that nonetheless is both useful and obtainable by the body is then removed via the colon.

Finally, the product of the colon, essentially the fairly solidified chyme we call feces, is deposited in the rectum where it is stored until defecation.

Links to terms of possible interest: Anal canal, Anus, Ascending colon, Cecum, Colon, Descending colon, Large intestine, Rectum, Sigmoid colon, Smooth muscle, Taenia coli, Transverse colon

The above video does a fairly good job of going through the major features of the colon.

The above video is strangely captivating, a colonoscopy as seen both from the inside and the outside!

Ascending colon

Colon continuation of the cecum.
Peristalsis is responsible for movement of materials through the large intestine and the need for this action is no more apparent than in the ascending colon where, in us, movement of chyme must occur uphill, that is, against the pull of gravity.

Because of the ascending colon's proximity to the small intestine, nutrients that are not absorbed within the small intestine first reach the large numbers of normal microbiota, mostly bacteria, that are found in the large intestine at the cecum and ascending colon. There additional digestion occurs and various substances, such as vitamin K, can be liberated which are then absorbed into the body through the walls of the large intestine.

Transverse colon

Most superior portion of the large intestine and location of substantial amounts of water and salt absorption out of chyme.
The transverse colon connects the ascending to the descending colon but otherwise represents the largest of the four colon sections (the other being the sigmoid colon).

Descending colon

Portion of large intestine that in terms of the flow of chyme connects the superior portion of the large intestine to the inferior portion of the large intestine.
By the time chyme has reached the descending colon, most of the water that is going to be absorbed out of it has been absorbed. Consequently, though some additional water is absorbed, the descending colon nevertheless serves more as a receptacle for storage of hardening chyme. This occurs prior to its movement into the sigmoid colon and then the rectum.

Sigmoid colon

Portion of large intestine found just prior to the rectum.
Due to the shape of the sigmoid colon, it is able to collect gas towards its superior side, found towards the rectum. This gas can then be released through the rectum and anus without also releasing the hardened chyme that is found settled within the sigmoid colon inferior side. Thus you can literally fart (pass gas, i.e., flatus, as in flatulence) without also pooping (defecation).

Links to terms of possible interest: Descending colon, Feces, Flatulence, Rectum, Sigmoid colon

Animated introduction to the sigmoidoscopy procedure.

The above video discusses flatulence, that is, the passing of gas.


Region of the large intestine where fully formed feces is stored prior to defecation.
The rectum is the last region of the large intestine and is found between the sigmoid colon (upstream) and the anus (downstream). Feces itself consists of whatever food materials have not been digested and absorbed, whatever water still remains following absorption, large numbers of microorganisms (that particularly are bacteria), and whatever products our body has secreted or instead that these microorganisms have released.

This is material that has neither been absorbed at some point in the intestine and also which has not been utilized by, again, the microorganisms that are present.

This substantial amount of waste material is, as we know, not released continuously. Instead it is released periodically as it accumulates in the rectum and then otherwise is motivated forward by peristalsis along with various largely voluntary muscular actions.

Links to terms of possible interest: Anal canal, Anal sphincter, Anus, Rectum, Sigmoid colon

Anal sphincters

Smooth as well as skeletal muscles that function to prevent the premature movement of feces out of the body.
There in fact are two anal sphincters, described as internal versus external (internal anal sphincter, a.k.a., sphincter ani internus muscle, versus the external anal sphincter, a.k.a., sphincter ani externus muscle, respectively). These consist of smooth muscle and skeletal muscle, respectively, and thus are under involuntary control and voluntary control, also respectively.

When the internal anal sphincter relaxes, in what is described as the defecation reflex, as occurs in response to increases pressure exerted by feces upon the walls of the rectum, then it is only your external anal sphincter that comes between you and pooping. Otherwise, though, it is primarily the internal anal sphincter that serves to prevent defecation.

Links to terms of possible interest: Anus, External anal sphincter, Internal anal sphincter, Rectum, Skeletal muscle, Smooth muscle

Pretty awesome overview of anal anatomy; discussion of anal sphincters begins at 3:18; discussion of hemorrhoids begins at 9:39.


Loss of liver function associated with replacement of normal liver tissue with various forms of scarring.
Cirrhosis can result from alcoholism, viral infection (most notably as caused by hepatitis B virus or hepatitis C virus), or other causes. It can lead to retention of fluids within the abdominal cavity and other often relatively severe symptoms.

Links to terms of possible interest: Cirrhosis, Excessive alcohol consumption, Liver, Scar tissue,

Considering it has no voice over and is not very detailed, the above video nonetheless is surprisingly effective.


Crystalline precipitation within bile that can lead to pain, obstruction of bile release, and also infections.
Gallstones form particularly within the gallbladder but can pass into the various associated ducts, where obstruction of bile movement can as a consequence occur. Obstruction of ducts can be life threatening particularly to the extent that movement of pancreatic juices is obstructed.

Gallstones can be differentiated particularly into what are known as "cholesterol" stones versus "pigment" stones, depending on their chemical make up. Cholesterol stones consist, not surprisingly, primarily of cholesterol. Pigment stones consist as well of the pigment and heme breakdown compound known as bilirubin.

Links to terms of possible interest: Common bile duct, Choledocholithiasis, Cholelithiasis, Cystic duct, Duodenum, Gallbladder, Gallstone

We're Still Golden owes its title to Kempowski's mother, who, as the Red Army swept into Rostock, remarked: "So long as you don't have gallstones or TB, we're still golden"

— Michael Lipkin, "Gathering Fate", The Nation, Oct. 27, 2014, p. 33


Inflammation of the liver.
Hepatitis is a disease with numerous potential causes but its results can be a degree of liver dysfunction. Symptoms can include jaundice (a yellowing of the skin), loss of appetite, and generally feelings of lack of wellbeing (malaise).

Hepatitis can be distinguished into acute disease versus chronic disease, with the dividing line being six months of duration, that is, with acute hepatitis lasting by definition less than six months while chronic hepatitis lasts longer than six months.

Causes of hepatitis include alcohol abuse and drug abuse, other non-infectious causes, and that caused by infections by viruses. The viruses hepatitis A virus, hepatitis B virus, and hepatitis C virus are the most common causes of hepatitis.

The above video begins with discussion of what the liver does, moves into what symptoms can coincide with low liver function, and then spends more than the second half of the video consider specifically hepatitis C.

Hiatal hernia

Imperfection in the thoracic diaphragm that allows the stomach to protrude into the thoracic cavity.
Part of the means by which the stomach contents are kept separate from the esophagus, in addition to the presence of the lower esophageal sphincter, is the presence of the stomach below rather than above the thoracic diaphragm, which is the muscle which separates the thoracic cavity from the abdominal cavity and which we employ in breathing.

The esophagus normally passes through the diaphragm whereas with a hiatal hernia the stomach is found in this opening instead of the esophagus or the stomach protrudes into the thoracic cavity, through the diaphragm.

Hiatal hernias become increasingly common with age and are associated with a fairly large number of symptoms, most notably acid reflux/heartburn.

The above video considers what a hiatal hernias is, what are some of the resulting symptoms, and how hiatal hernias can be treated, including a fascinating look at robotic surgery.

Irritable bowel syndrome

Symptoms characterized by abdominal pain over extended periods, excessive intestinal gas, and diarrhea or constipation or alternating bouts of both.
Irritable bowel syndrome, or IBS, is distinct from inflammatory bowel disease and can be associated with gastrointestinal infections as well as in response to otherwise stressful situations or anxiety. Frequency of symptoms of at least three affected days per month for three months are consistent with a diagnosis of IBS.

Treatment can include medications as well as dietary changes, the latter including changes in response to possible lactose intolerance as symptoms of lactose intolerance can be similar to those of IBS. Celiac disease as well as colon cancer can also mimic IBS. Caffeine, large meals, lack of exercise, poor sleep habits, and diets that are low in fiber can exacerbate symptoms. IBS is not known to impact life expectancy.

The above video provides a nice introduction to irritable bowel syndrome.

Inflammatory bowel disease

Gastrointestinal tract immunological disorders associated especially with ulcerations of the intestines.
Inflammatory bowel disease, or IBD, can be differentiated especially into at least two mostly distinct diseases known as Crohn's disease versus ulcerative colitis. Symptoms are gastrointestinal including pain in the abdominal area and diarrhea and potentially also vomiting and weight loss.

Causes of IBD are a combination of genetic and environmental with some association with antibiotic use, the latter which can cause changes in the types of bacteria that reside in your gut (i.e., your normal microbiota or microbiome). These changes in some manner leads to an immune response that attacks the body's own tissues.

IBD often is characterized by periods of active disease that are interspersed with periods of remission.

The above video provides an excellent overview of inflammatory bowel disease.

Crohn's disease

Non-autoimmune inflammatory disease of the gastrointestinal tract.
Crohn's disease is considered to be a form of inflammatory bowel disease, but that can affect more than the bowel. It is a chronic inflammatory disease that can result in numerous gastrointestinal symptoms, including diarrhea, but also symptoms seen outside of the gastrointestinal tract.

Despite not being an autoimmune disease, symptoms nonetheless stem from immune system attack of gastrointestinal tract tissues. Smoking cigarettes can substantially increase one's risk for Crohn's disease though there are other environmental as well as genetic risk factors as well.

The above video is a well done, professionally produced video on Crohn's disease.

The above video can best be thought of as a "cute", and brief, introduction to Crohn's disease.

The above video provides a more in-depth overview of Crohn's disease.

Ulcerative colitis

Non-autoimmune inflammatory disease especially of the large intestine.
Ulcerative colitis is considered to be a form of inflammatory bowel disease. Contrasting Crohn's disease, ulcerative colitis predominantly affects the large intestine rather than the small intestine. In addition, with ulcerative colitis the rectum is always involved.

Ulcerative colitis is a chronic inflammatory disease that can result in numerous gastrointestinal symptoms, including bloody diarrhea, but also symptoms seen outside of the gastrointestinal tract. Despite not being an autoimmune disease, symptoms nonetheless stem from immune system attack of gastrointestinal tract tissues.

The above video provides an excellent overview of ulcerative colitis.

The above video provides a brief overview of ulcerative colitis and is particularly good in terms of its illustrated depiction of what the ulcerations look like.


Those microorganisms found in association with a given environment and particularly from the perspective of what genes they carry as well as what impact they have.
All environments that possess living things possess microbiomes, and especially in more severe environments they possess only microbiomes among living things. The concept of microbiome, however, goes beyond the existence of the microorganisms that live within environments but also considers the genes associated with those microorganisms.

These genes to a large extent contribute to the survival, propagation, and otherwise functioning of the microorganisms found in environments. In addition, however, these genes can play beneficial (e.g., stabilizing) as well as detrimental roles (disruptive ones) within these environments.

Included among environments are those associated with larger organisms such as ourselves, e.g., such as is found within our gastrointestinal tracts.

The above video provides a nice introduction to the concept of microbiome.

The above video provides a rather pretty introduction to the concept of microbiome.

Normal flora

Those microorganisms consistently present within a specific environment.
Also known as normal microbiota, the normal flora can be viewed as equivalent to microbiomes but especially from the perspective of individual hosting organisms, and their more organismal properties, or microrganismal properties, rather than as viewed particularly from the perspective of their genes.

The concept of "normal" to a degree implies that these are the microorganisms that contribute the "normal" functioning of environments, which for us would be those microorganisms that are other than pathogens which are actively causing disease.

Normal flora microorganisms can be differentiated into those which can be viewed as resident normal flora versus transient normal flora. Disease-causing microorganisms as well as what can be described as probiotics are included among the latter. The goal with fecal transplants is to replace the former.

Resident normal flora can be harmful as well, though more chronic rather than acute in their impact, e.g., such as contributing to weight gain.

Beneficial bacteria

Particularly those normal flora members that contribute to healthy or optimal functioning of the environment in which they are able to reside though also which can be temporarily added to those environments.
Beneficial bacteria can be either resident normal flora or transient normal flora, which are microorganisms that live as populations in association with our bodies either over long periods (years) or instead short periods (e.g., less than a month).

The goal with a fecal transplant is to replace less beneficial bacteria that make up resistant normal flora with more beneficial bacteria, that is, which are more effective in contributing to the health of environment in which they reside (e.g., such as the environment found within the lumen of our gastrointestinal tracts). Alternatively, probiotics ideally serve as beneficial bacteria, though ones that can serve more as transient normal flora rather than as resident normal flora.

Thus, beneficial bacteria contribute to good, better, or optimal functioning of the environments in which they reside though their residence may or may not be permanent but instead, such as in terms of probiotics, can require periodic reinoculation.


Microorganisms that can contribute to healthy or optimal functioning of especially gastrointestinal tract environments when they are temporarily added to those environments as when eaten.
Generally the health claims associated with probiotic microorganisms have not been extremely well substantiated, though in part this may be a consequence of difficulties in substantiating any procedure that has small or variable effects. That is, such substantiation at a minimum often requires fairly large inputs of money and other resources so as to perform efficacy trials (i.e., phase III medical trials). Alternatively, tendencies may be identified and, at least to a first approximation, can be safely ascertained.

There thus exist a number of probiotic products with possible health benefits and that probably are not harmful. The question then comes down to ones of convenience, perceived utility, appreciation (such as in terms of taste), and overall cost. Historically, note that it has been common to consume foods that possess living microorganisms in them, e.g., yogurt and other fermented foods, so actually consuming microorganisms in one's diet should not be viewed as inherently problematic. To what degree these microorganisms are actually providing us with health benefits, however, is not highly rigorously understood.

Clostridium difficile

Cause of severe, antibiotic-associated diarrhea.
Clostridium difficile, or "C. diff", is normally a soil bacterium though in a subset of adults it is also a member of the gastrointestinal normal flora. C. diff produces endospores that are highly durable and can be ingested, thereby allowing passage of this organism between adults.

Typically the presence of C. diff within gastrointestinal tracts does not cause disease because resident normal flora tend to display what is known as microbial antagonism, that is, various means by which they can serve to keep other, including potentially harmful microorganisms, i.e., pathogens, from excessively increasing in numbers.

It is only when these resident normal flora are severely disrupted, such as in the course of antibiotic treatment, can these other, potentially pathogenic microorganisms excessively increase in numbers, resulting in what is described as an antibiotic-associated superinfection. C. diff infections occur by this route, resulting in harmful and even potentially deadly colitis that tends to be fairly resistant to treatment using standard antibiotics.

The above video provides a pretty good overview of Clostridium difficile infection.

The above video considers Clostridium difficile from a fairly sophisticated perspective.

Fecal transplant

Intentional movement of especially beneficial bacteria from one individual's gastrointestinal tract to another's, particularly as a medical procedure.
Fecal transplantation literally is the movement of feces from a healthy donor to a typically unhealthy recipient. This is as equivalent to the transplantation of cells, tissues, organs, etc. from one individual to another. A distinction, though, is that feces typically are not missed by the donor individual (e.g., just as, to a lesser extent, blood is not missed by donors) and issues of rejection by the recipient are either not an issue or otherwise are not well understood.

The fecal transplantation procedure itself involves a degree of processing of the feces, particularly to separate bacteria from more solid materials, and then exposure, often post-stomach, of a patient to the potentially beneficial bacteria found within the transplanted feces. Ideally these bacteria will take up residence and contribute to an improvement in the health of the recipient, such as in terms of fighting C. diff infections, which have been found to respond favorably to fecal transplantation.

The above video provides a nice primer on fecal transplantation.