THE INTESTINAL TRACT & GI MUCOSA THROUGH THE LENS OF A 21st CENTURY FM PRACTITIONER “From mouth to anus, and every other stop in-between”

In-between consulting, coaching & educating people from all over the world; i endeavour to regularly block out time in my diary to write & share some of my own original content based on over a decade of acquired professional knowledge and expertise, as well as extensive  clinical experience in helping individuals restore functional wellness. My aim is for the content i invest time in putting out will hopefully add value to the lives of others done in my own unique way.

In this article I wanted to write a stripped-back, but scientifically detailed anatomy-style lecture, on a subject that has been, and continues to be big part of my personal & professional life as a gut expert & practitioner of Functional Medicine for over 10 years…. that subject is ‘the digestive tract’ and some of its counterparts.

I always like to educate the individuals who work with me throughout the entire process, so they have a greater understanding of what’s going on, and why. Recently I wrote that the explanation I often give to people I work with to describe the gastrointestinal tract (GIT) is that it is a hollow muscular tube running right through the middle of the body that is technically classed as “outside” our physical being. This tube is home to a vast array of different bacteria, protozoa, yeast, fungi, worms & virus’s which reside on its surface, anywhere from one end to the other… ‘the mouth, the anus, and everything else in between’…

To put things into a contextual perspective in terms of scalable ratios – ‘pound for pound’ or ‘cell for cell’ – the human body is made up of 10 x more bacterial cells than human cells – outnumbering our host cells by around 10 trillion to 1. In other words we are a dominant mass of walking, taking bacteria compared to human cells. The key is for the balance between beneficial, commensal or ‘good’ bacteria to be around 80%, and pathogenic or ‘bad’ to be around 20% of the total numbers – however, in a lot of individuals I work with, these numbers look very different, with the latter dominating resulting in a dysbiotic internal eco-system.

The only thing that separates us – the human host – from any invasion of our systemic blood supply, lymphatic system, and cellular DNA by anything from the “outside” world is just a 1 cell-thick layer of mucosal cells which form a protective shield, or membrane, protecting us from anything from a toxic antigen or pathogen that comes knocking at the biological door.

The mucosal membrane is the body’s first line of immune defence who’s job it is to line & protect various structural ‘points of entry’ such as the eyelids, oral cavity, nasal passages, ear & alimentary canal, windpipe, lungs, stomach, bladder, urethra and in protecting the small intestine – who’s chief job is in digestion & absorption of nutrients. 80-90% of all nutrients we ingest get absorbed in the small bowel which highlights its importance. When the absorptive capacity or barrier function is compromised, the health of the host is adversely effected. This is a reason why a number is individuals who consult with me, come to me with compromised immunity, and tend to suffer with one or more of the following, such as allergies, sinus issues, asthma, reoccurring UTI’s, & digestive complaints to name just a few.

In terms of the journey – It all starts from the oral cavity which is where food enters the mouth, and then continues through the pharynx, oesophagus, stomach and intestines to eventually reach the rectum and anus, where food is expelled, and the end product is staring back up at you from the toilet bowl. 

There are various accessory organs that play key parts in this complex process that assist the tract by secreting enzymes to help break down food into its component nutrients. Thus, things like the salivary glands, liver, pancreas and gall bladder all have important roles to play in the digestive system process. 

Once ingested, food is propelled along the length of the GIT by waves of electrical impulses which result in frequent radially peristaltic contraction & relaxation of the smooth-muscular walls triggered by the migrating motor-complex (MMC). The MMC is a system I see dysfunctional in a number of individuals who consult with me which results in undigested food sitting  around for long periods of time allowing pathogenic bacteria to feed on and ferment, consolidating the dysbiosis & thus locking them further in a state of poor health. The body relies on these two important functions to move food through the length of the intestines, from anywhere between the lower oesophagus to the large bowel or colon. I see both of these systems being dysfunctional in a number of people I work with which is often showing up as dysbiotic bacterial, microbial and/or fungal overgrowth (SIBO, SIMO, & SIFO) in the small bowel – however, that’s another very detailed topic for another article, another time. 

As I mentioned earlier, the primary purpose of the gastrointestinal tract is to break food down into nutrients, which can then be absorbed into the body, shuttled into the cells of the mitochondria where they can be burned & provide energy for the body to be able to carry out its functions. 

The very first stop in this digestive journey is the food must be ingested into the mouth in order to be mechanically processed and moistened with the salivary enzyme amylase. This is where the digestive process begins for carbohydrates. Just smelling & chewing the food starts to fire-up other organs further downstream in preparation for what it perceives it’s about to receive. To bring this point to life – when your taste buds sense sweetness, the pancreas is already primed & calculating the release and amount of insulin it thinks that it will need to release in order to manage blood sugar at the point the nutrients reach the bloodstream.

The ‘digestion’ part occurs mainly in the stomach and small intestine where proteins, fats and carbohydrates are chemically broken down into their basic building blocks. Smaller molecules are then absorbed across the epithelium of the small intestine and subsequently enter the circulation. The large intestine plays a key role in reabsorbing excess water. The final stop is where undigested material and secreted waste products are excreted from the body via defecation (passing of faeces).

In the case of various gastrointestinal disorders & dysfunctions, these functions are not achieved successfully. Patients may develop symptoms of nausea, vomiting, diarrhoea, malabsorption, bloating, allergies, food reactions, constipation or obstruction. Gastrointestinal problems, along with other body-system issues are very commonplace for me in Functional Medicine.

The GIT is essentially a muscular tube lined by a special layer of cells, called epithelium. As I mentioned earlier, the contents of the tube are considered external to the body and are in continuity with the outside world at the point of the mouth and the anus. Although each section of the tract has specialised functions, the entire tract has a similar basic structure with regional variations.

To expand a little on the anatomy side of things, I have broken down the Individual components of the gastrointestinal system to add a little more clarity on the subject.

Oral cavity

The oral cavity or mouth is responsible for the intake of food and is lined by a stratified squamous oral mucosa with keratin covering those areas subject to significant abrasion, such as the tongue, hard palate and roof of the mouth. Mastication refers to the mechanical breakdown of food by the chewing and chopping actions of the teeth. The tongue, a strong muscular organ, manipulates the food bolus to come in contact with the teeth. It is also the sensing organ of the mouth for touch, temperature and taste using its specialised sensors known as papillae.

Insalivation refers to the mixing of the oral cavity contents with salivary gland secretions. 

The mucin (a glycoprotein) in saliva acts as a lubricant, as well as playing a small cameo role in the digestion of carbohydrates. The enzyme serum amylase, a component of saliva, starts the process of digestion of complex carbohydrates. The final function of the oral cavity is absorption of small molecules such as glucose and water, across the mucosa. From the mouth, food passes through the pharynx and oesophagus via the action of swallowing.

Salivary glands

Three pairs of salivary glands communicate with the oral cavity. Each is a complex gland with numerous acini lined by secretory epithelium. The acini secrete their contents into specialised ducts. Each gland is divided into smaller segments called lobes. Salivation occurs in response to the taste, smell or even appearance of food. This occurs due to nerve signals that tell the salivary glands to secrete saliva to prepare and moisten the mouth. Each pair of salivary glands secretes saliva with slightly different compositions.


The parotid glands are large, irregular shaped glands located under the skin on the side of the face. These glands secrete around 25% of the saliva, and are situated below the zygomatic arch (cheekbone) and cover part of the mandible (lower jaw bone). An enlarged parotid gland can be easier felt when one clenches their teeth. The parotids produce a watery secretion which is also rich in proteins, immunoglobulins that help to fight microorganisms at an oral level, as well as the a-amylase proteins previously mentioned that start to break down complex carbohydrates in the mouth.


The submandibular glands secrete 70% of the saliva in the mouth. They are found in the floor of the mouth, in a groove along the inner surface of the mandible. These glands produce a more viscid (thick) secretion, rich in mucin and with a smaller amount of protein. Mucin is a glycoprotein that acts as a lubricant.


The sublinguals are the smallest salivary glands, covered by a thin layer of tissue at the floor of the mouth. They produce approximately 5% of the saliva and their secretions are very sticky due to the large concentration of mucin. The main functions are to provide buffers and lubrication.


The oesophagus is a muscular tube of approximately 25cm in length and 2cm in diameter. It extends from the pharynx to the stomach after passing through an opening in the diaphragm. The wall of the oesophagus is made up of inner circular and outer longitudinal layers of muscle that are supplied by the oesophageal nerve plexus. This nerve plexus surrounds the lower portion of the oesophagus. The oesophagus functions primarily as a transport medium between compartments.


The stomach is a J shaped expanded bag, located just left of the midline between the oesophagus and small intestine. It is divided into four main regions and has two borders called the greater and lesser curvatures. The first section is the cardia which surrounds the cardial orifice where the oesophagus enters the stomach. The fundus is the superior, dilated portion of the stomach that has contact with the left dome of the diaphragm. The body is the largest section between the fundus and the curved portion of the J.

This is where most gastric glands are located and where most mixing of the food occurs. Finally the pylorus is the curved base of the stomach. Gastric contents are expelled into the proximal duodenum via the pyloric sphincter. The inner surface of the stomach is contracted into numerous longitudinal folds called rugae. These allow the stomach to stretch and expand when food enters. The stomach can hold up to 1.5 litres of material. 

The functions of the stomach include:

  • The short-term storage of ingested food.
  • Mechanical breakdown of food by churning and mixing motions, very much like a biological cement-mixer
  • Chemical digestion of proteins by acids and enzymes.
  • Maintaining the correct pH to keep the keep the environment hostile for pathogenic organisms 
  • Absorption of limited substance such as aspirin, NSAIDS, & alcohol/ethanol

Small intestine

The small intestine is composed of the duodenum, jejunum, and ileum respectively. It averages approximately 6m in length, extending from the pyloric sphincter of the stomach to the ileo-caecal valve separating the ileum from the caecum. The small intestine is compressed into numerous folds and occupies a large proportion of the abdominal cavity.

The duodenum is the proximal (closest to) C-shaped section that curves around the head of the pancreas. The duodenum serves a mixing function as it combines digestive secretions from the pancreas and liver with the contents expelled from the stomach. The start of the jejunum is marked by a sharp bend, the duodenojejunal flexure. It is in the jejunum where the majority of digestion and absorption occurs. The final portion, the ileum, is the longest segment and empties into the caecum at the ileocaecal junction.

The small intestine performs the majority of digestion and absorption of nutrients. Up to 90% to be precise. Partly digested food from the stomach is further broken down by enzymes from the pancreas and bile salts from the liver and gallbladder. These secretions enter the duodenum at the Ampulla of Vater. After further digestion, food constituents such as proteins, fats, and carbohydrates are broken down to small building blocks and absorbed into the body’s blood stream.

The lining of the small intestine is made up of numerous permanent folds called plicae circulares. Each plica has numerous finger-like structures called villi (folds of mucosa) and each villus is covered by epithelium with projecting microvilli (brush border). This increases the surface area for absorption by a factor of several hundred. The mucosa of the small intestine contains several specialised cells. Some are responsible for absorption, whilst others secrete digestive enzymes which reside on layer of mucosal cells, as well as they mucous itself, which protects the intestinal lining from digestive actions.

Large intestine

The large intestine is horse-shoe shaped and extends around the small intestine like a frame. It consists of the appendix, caecum, ascending, transverse, descending and sigmoid colon, and the rectum. It has a length of approximately 1.5m and a width of 7.5cm.

The caecum is the expanded pouch that receives material from the ileum and starts to compress food products into faecal material. Food then travels along the colon. The wall of the colon is made up of several pouches (haustra) that are held under tension by three thick bands of muscle (taenia coli).

The rectum is the final 15cm of the large intestine. It expands to hold faecal matter before it passes through the anorectal canal to the anus. Thick bands of muscle, known as sphincters, control the passage of faeces.

The mucosa of the large intestine lacks villi seen in the small intestine. The mucosal surface in the large bowel is flat with several deep intestinal glands. Numerous goblet cells line the glands that secrete mucous to lubricate faecal matter as it solidifies. The functions of the large intestine can be summarised as:

  • The accumulation of unabsorbed material to form faeces.
  • Some digestion by bacteria. The bacteria are responsible for the formation of intestinal gas.
  • Reabsorption of water, salts, sugar and vitamins.


The liver is a large, reddish-brown organ situated in the right upper quadrant of the abdomen. It is surrounded by a strong capsule and divided into four lobes namely the right, left, caudate and quadrate lobes. The liver has several important functions. It acts as a mechanical filter by filtering blood that travels from the intestinal system. It detoxifies several metabolites including the breakdown of bilirubin and oestrogen. In addition, the liver has synthetic functions, producing albumin and blood clotting factors. However, its main roles in digestion are in the production of bile and metabolism of nutrients. 

All nutrients absorbed by the intestines pass through the liver and are processed before traveling to the rest of the body. The bile produced by cells of the liver, enters the intestines at the duodenum. Here, bile salts break down lipids into smaller particles so there is a greater surface area for digestive enzymes to act.

Gall bladder

The gallbladder is a hollow, pear shaped organ that sits in a depression on the posterior surface of the liver’s right lobe. It consists of a fundus, body and neck. It empties via the cystic duct into the biliary duct system. The main functions of the gall bladder are storage and concentration of bile. Bile is a thick fluid that contains enzymes to help dissolve fat in the intestines. Bile is produced by the liver but stored in the gallbladder until it is needed. Bile is released from the gall bladder by contraction of its muscular walls in response to hormone signals from the duodenum in the presence of food.


Finally, the pancreas is a lobular, pinkish-grey organ that lies behind the stomach. Its head communicates with the duodenum and its tail extends to the spleen. The organ is approximately 15cm in length with a long, slender body connecting the head and tail segments. The pancreas has both exocrine and endocrine functions. Endocrine refers to production of hormones which occurs in the Islets of Langerhans. The Islets produce insulin, glucagon and other substances and these are the areas damaged in diabetes mellitus. The exocrine (secretrory) portion makes up 80-85% of the pancreas and is the area relevant to the gastrointestinal tract.

It is made up of numerous acini (small glands) that secrete contents into ducts which eventually lead to the duodenum. The pancreas secretes fluid rich in carbohydrates and inactive enzymes. Secretion is triggered by the hormones released by the duodenum in the presence of food. Pancreatic enzymes include carbohydrases, lipases, nucleases and proteolytic enzymes that can break down different components of food. These are secreted in an inactive form to prevent digestion of the pancreas itself. The enzymes become active once they reach the duodenum.

Now I only kept things light as this subject, like many others goes way deeper, which I tend to go more into when working with individuals on a 1 to 1 basis. Hopefully now you can appreciate the complexity in just one snapshot of the intestinal system and some of its other functional moving parts.

If you’ve lost your way on the journey towards good health, and need an experienced guide to help you get back on the right path to functional wellness, then feel free to head on over to book a free 30 minute consult to see whether we are the right fit to take that journey together.

Thank you for your attention.

*By Steve Hawes