Stage three in the digestive process involves a number of organs. The chyme has reached the bottom of the stomach (the duodenum) and is ready to move to the next phase…

Stage three: Release of pancreatic enzymes 

It is very important that the pH of the stomach is low enough (low pH = highly acidic) to stimulate the production of secretin. Secretin is the hormone that prompts the pancreas to release bicarbonate. The bicarbonate serves to raise the pH of the stomach (higher pH = less acidic) so that when it into the small intestine, it won’t damage the lining of the intestine, which is not designed for acidic substances.

In addition to raising the pH (making it less acidic) of the stomach contents (chyme), the pancreas also releases a number of digestive enzymes including pancreatic lipase, which serves to breakdown fat. Now carbohydrate, protein and fat in our meal should all be sufficiently broken down and in a state where vitamins and minerals can be extracted.

Fat stimulates the release of bile from the gallbladder

Once in the duodenum, the presence of fatty acids in our partially digested food contents will stimulate the gallbladder to release bile. Bile is produced by our liver and then transferred to the bladder for storage purposes. When our gallbladder gets the signal that fat needs emulsifying (breaking down) then the galbladder will release the stored bile. However, if we don’t eat enough fat then this signal never comes and the bile remains in the gallbladder. If this is an ongoing occurrence then overtime bile can become thick and viscous and eventually gallstones can result.

Low-fat diets lead to gallstones

Additionally, a diet high in the wrong kinds of fats can also have a negative effect on the gallbladder. Hydrogenated (link) and rancid fats can cause the texture of the bile to become thick and viscous, meaning it does not flow through to the intestine easily, which also leads to the formation of gallstones.

Gallstones are incredibly painful and often difficult to pass. You can avoid them by eating a diet full of healthy, delicious fats! That means more naturally occurring fats from animals and coconut – not rancid vegetable oils.

Fatty acids play many important roles including formation of hormones, providing integrity to our cells, anti-inflammation and immune responses and many more. If our gallbladder is not functioning effectively and not releasing bile, then we will not absorb the fatty acids our body needs.


The pancrea, liver and gallbladder play very important role in the production and distribution of digestive enzymes and bile.


Stage four: Small intestine

By the time our food enters the small intestine, it should be almost fully digested.

  • Carbohydrates become single glucose molecules
  • Proteins become amino acids and polypeptides (short chains of amino acids)
  • Fats become fatty acids and glycerol molecules.

All of these smaller molecules contain micronutrients (vitamins and minerals) that are absorbed through the slightly-permeable walls of the intestinal lining. The intestinal wall is lined with millions of villi and microvilli – cellular protrusions that increase the surface area of the intestine to enable greater absorption.

From here the glucose, amino acids and fatty acids (carbs, protein and fat) are carried by the villi to the capillaries and then into the liver. The bulk of our vitamins and minerals are also absorbed through the villi.

Damage to the villi

If undigested particles make it to the small intestine still in tact, then they can do significant damage to our delicate microvilli. This inhibits nutrient absorption and can also mean that particles that should not leave the colon can escape and enter the blood stream. The villi and lining of the intestine should provide a critical barrier between the body and what is the waste product of our food. However, if damaged it cannot serve this function and molecules that are actually toxic to the body enter our blood stream.

When the walls of the intestine are permeable it is referred to as leaky gut. I cover this in great detail here.

The main point is that leaky gut can trigger an immune response as our body thinks it is under attack. If left unchecked conditions can escalate into autoimmune responses. Conditions that result from leaky gut include skin problems, hormonal imbalances and autoimmune illness like multiple sclerosis. Leaky gut has incredibly severe health consequences.

Leaky gut results from food not being digested properly – perhaps because we have not chewed our food sufficiently, or because stomach acid is low. It can also occur when we consume foods that our bodies don’t breakdown sufficiently because we lack the right digestive enzymes or hormones. For example grains are foods that contain a host of molecules that humans often lack the digestive capacity for. I cover this in more detail here. Gluten, now a hot topic, is a protein that many people do not fully digest and can contribute to leaky gut. All of these factors contribute to leak gut with profound health consequences.


Stage 4.2: Large intestine

Following extraction of nutrients through the villi in the small intestine, any remaining food contents like indigestible fibres, bile and water are pushed through the ileoceal valve to the large intestine. The large intestine recycles water and waste products and the bacteria that live here produce more of the nutrients that have not yet been absorbed such as Vitamins K, B1, B2 and B12. Importantly the large intestine also forms and expels faeces, which eliminates waste and toxic products from the body.


Again undigested food particles can cause significant issues in the large intestine, which is home to trillions of bacteria. Food particles can disrupt the balance of bacteria and if  “bad bacteria” are able to thrive then the entire body will experience negative consequences. I cover this in detail in my article on the gut microbiome.

Science is only just starting to uncover the truly profound impact of the gut microbiome (ie the bacterial landscape of the gut) and its impacts on human health. There are an increasing number of conditions being linked back to an imbalance of gut flora and the overgrowth of certain products such as yeast (candida albicans). These conditions include depression and anxiety, chronic fatigue, out of control PMS for women and much, much more.

Final words on the four stages of digestion

This series has covered the human digestive process in great detail. The very nature of our digestive system, which centres on our hydrochloric acid based stomach means that we require a balance of animal and plant products for health. Humans are not built to be low-fat, vegetarians.

While we are seeing a huge rise in lifestyle diseases and other illnesses there is significant hope that comes from a true understanding of how the body, and in particular the digestive system works. Ultimately humans are just a collection of chemicals and a lack of any particular vitamin or mineral can have a huge impact on how the body functions. This is why emphasising nutrient density in the diet, and good digestive health to ensure absorption of these nutrients is so critical.

We have a real ability to use food as medicine to heal a whole host of ailments that might not seem related. If you would like to work with me on a specific issue then please get in touch with me.


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