Gut Health

Here's How Your Gut Works From Top To Bottom

Here's How Your Gut Works From Top To Bottom

Effective, comfortable digestion of our food needs the whole of our digestive system to be working in harmony.The process starts when we see or smell food, and each step follows in a precise dance where the timing, the movement of the food along the gut, and the release of digestive juices are critical. Some of the key dancers, however, are the myriads of bacteria that live in our gut working on our behalf to digest the foods that we cannot.

The digestive process can be broken down into 12 steps:

  1. Nose, Eyes, Brain
  2. Mouth, Chewing, Saliva
  3. Oesophagus
  4. Stomach
  5. Duodenum (first part of small intestine)
  6. Jejunum
  7. Ileum
  8. Cleaning Up
  9. Appendix
  10. Large Intestine (colon)
  11. Rectum
  12. Anus

Step 1: Nose, Eyes, Brain

When we see, smell or even think about food, the digestive process begins by triggering release of saliva and gastric juices from the stomach.

Step 2: Mouth, Chewing, Saliva

This is the first stage of true digestion. Chemicals (enzymes) in saliva start the break down of starchy foods. Saliva also moistens the food and the mouth generally. It also protects the teeth from decay by digesting and washing away food that becomes stuck in the teeth and it contains antimicrobial substances helping to prevent bad bacteria growing. The process of chewing as well as grinding up the food, allows the tongue to taste the food, firstly to check it is safe to eat and secondly to alert the rest of the body what kind of foodstuff is on the way down.

Chew your food! When the food is well chewed up it is ready to move into the next step. As we swallow, the food passes by a ring of tissue, which includes the tonsils, that is rich in immune cells and which “tastes” the food in a different way to the tongue. This tasting checks for the presence of unwanted microbes as well as helps the immune system to build up a database of foods that are safe to eat.

Step 3: Oesophagus

The oesophagus is made of muscles that contract to move food to the stomach. This process is called peristalsis. At the top and bottom of the oesophagus are rings of muscle. These rings are called sphincters. When food is swallowed, the sphincters relax so food can pass into the stomach. When not in use, they tighten to close the oesophagus so that nothing gets back up. 

Step 4: Stomach

When food enters the stomach, the stomach stretches, and this causes more gastric juice to be made. Chemicals from food directly stimulate the gastric glands to secrete gastric juice. The enzymes in the gastric juices start the digestion of protein components of food. The presence of food dilutes the acid in the stomach which stimulates it to produce more acid. Stomach acid has many vitally important roles in digestion: Gastric juices work best to digest food when there is acid present. Acid kills off potential disease-causing bacteria in the food. It also releases some nutrients from food that would not otherwise be extracted, namely vitamin B12 and minerals such as magnesium and iron. The acidic solution of partially digested food that leaves the stomach stimulates the next phase of digestion that occurs in the small intestine. The acidity of the stomach controls how fast food is released from the stomach into the small intestine, making sure food is not released to the next stage of digestion until the first phase is complete. As acid leaves the stomach it ensures the first part of the small intestine is acidic too which stops unwanted bacteria growing and also creates the right conditions for the enzymes in the small intestine to work optimally. Stomach acid, therefore, is very much the responsible for orchestrating a large part of our digestion.For more on this, read our article on low stomach acid.

Step 5: Duodenum (first part of small intestine)

As the partially digested food enters the duodenum, its presence stimulates release of enzymes from the pancreas. This will complete the process of digestion. The duodenum secretes an alkaline mucus which reduces the acidity present in the mixture coming in from the stomach adjusting it to the right strength for the enzymes to work optimally. Fats in the food stimulate release of bile from the liver and gallbladder. Bile breaks up the fats into small droplets so enzymes from the pancreas can digest it. Other enzymes break up the carbohydrates and proteins.

Slow waves of smooth muscle contraction known as “peristalsis” flow down the length of the duodenum beginning at the stomach and pushing toward the next part of the gut, the jejunum. It takes many peristaltic contractions over the course of an hour for the digested food to travel through the entire length of the duodenum. 

Step 6: The Jejunum

This is where most of the nutrients present in food are absorbed. Only once it has been broken down into the tiniest of constituent parts, can the nutrients in the food be absorbed.

Villi and microvilli: the small intestine is lined with tiny finger-like projections, called villi, and each finger is covered with a fine velvet-like layer of tinier villi, called microvilli. These microvilli form the outer surface of the intestinal cells that line the gut. Each epithelial cell is closely linked to its neighbours so that the only way that nutrients can enter the body is to pass through the epithelial cells. After passing through, nutrients are fed into the tiny blood vessel (capillary) that is found in each of the villi, which transports them first to liver.


Step 7: The Ileum

This the last part of the small intestine, where any last nutrients are absorbed before the indigestible constituents of food are moved into the large intestine.

Step 8: Cleaning Up

Once the food moves into the large intestine, the small intestine is virtually clear of any residue. Just to be sure, the small intestine does a little cleaning up routine. This happens about an hour after the digestive processes in the small intestine are completed or about 3-5 hours after eating. A powerful wave of contraction passes along the intestine clearing out any left-overs or unwanted bacteria or other particles into the large intestine. Often you can hear this happening as tummy rumbles. You might think tummy rumbles are a sign of hunger but actually they are the sound of the housekeeper at work tidying up. This work is a vital part of a healthy gut: constant snacking prevents it from happening.

Step 9. The Appendix

Just before the remains of the meal pass into the large intestine, they pass by the appendix. Often thought of as just a cause of trouble, in fact the appendix has an important role. It acts, much like tonsils, to monitor for bad bacteria and activate the immune system if needed. It also is thought to store a supply of good bacteria which can help keep the population of bacteria in the large intestine in good shape.

Step 10. The Large Intestine (colon)

This is where the much of the fibrous components of our food that cannot be digested by the enzymes of the upper parts of the gut are broken down. About 90% of the nutrients present in digested food have been absorbed by the time it reaches the large intestine. The work of digesting what’s left is done by our gut bacteria. The acid from the stomach that prevents bacteria growing in the small intestine has been neutralised by the time it reaches the large intestine which allows bacteria to thrive. They ferment the fibres in our food and produce substances that not only feed themselves but also supply extra nutrients to us. Some important nutrients provided by are gut bacteria are vitamins K, B1, B2, B6, B12, and biotin and a type of small fat molecule called short chain fatty acids (SCFA). The walls of the colon absorb these vitamins along with most of the water present. SCFA are used as a source of energy by the cells lining the colon. The work of the large intestine is very slow compared with the first part of digestion, taking around 36 hours on average. The diagram shows the large intestine as being rather lumpy. This is because the contents tend to stay in one place for a long time, in distinct “pouches” (those are the bulges). A few times a day, a wave of peristalsis shoves the contents along a bit, particularly after a meal (to make way for a new batch). Often the fermentation process results in gas, such as carbon dioxide and methane being formed. Some foods and some kinds of bacteria will cause more gas than others.

Step 11: The Rectum

Most of the water, vitamins and products of fermentation have been absorbed by the time the contents reach this last part of the colon. Here, the faeces, consisting of fibres and waste material that cannot be broken down, are stored ready for defaecation. Water continues to be absorbed throughout this storage time, making the faeces gradually more solid as time passes. As faeces accumulate and fill the rectum, the resulting stretching of the rectal walls sends nerve signals to the brain, suggesting it is time to empty the rectum through defaecation.

Step 12: Anus

Like the oesophagus above, there are two sphincters at each end of the anus that keep the gut contents from spilling out until desired. Between the inner and outer sphincters there are some specialised sensory cells that detect presence of faeces/gas. As pressure builds up in the rectum, the first sphincter lets through a taster for these sensory cells determine if it is gas or faeces causing the pressure. The outer sphincter opens only if it is appropriate. When our conscious brain deems that the time is right, both sphincters relax and a powerful wave of peristalsis, backed up by contraction of the abdominal muscles pushes the faeces out.

Learn more about the digestive system in Episode 1 of the Gutology Podcast

Gutology Digest Box
Gutology Digest Box
Regular price £29.97
Regular price Sale price £29.97

Take the gut health quiz!

Get articles, product recommendations & information based on your symptoms.

Start now


  1. Enders, G. Gut. (Scribe Publications, 2015).
  2. Innerbody. Digestive System: Everything You Need to Know, Including Pictures. Available at: