The process of digestion is quite complex but also very sensitive to what we eat and in many cases our gut is the mirror of our health.

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The importance of the gut

It is no wonder that the gut is called the second brain. The gut controls everything and so many of us have issues that even if we don’t realise it might begin from the gut. The gut is central to 3 of the 4 steps of how our body processes food.





The main function of the digestive system is to 

1. Digest the food by breaking it down

2. Absorb nutrients from the small intestine into the circulatory system. Digestion can be divided roughly into two functional phases: mechanical digestion (the food is broken into smaller pieces by chewing) and chemical digestion (enzymes break down food into molecules).

3. Eliminate waste products by forming of feces.


The digestive tract reaches from the mouth all the way to the anus. The most important parts of the digestive tract in terms of functions are the esophagus, stomach, and duodenum in the upper gastrointestinal tract and the jejunum, ileum, colon and rectum in the lower gastrointestinal tract. The digestive system also includes the salivary glands, pancreas, liver, spleen and gallbladder, each with their own role in digestion.  Every single organ in your body basically!

What is proper digestion

A lot happens between the time you eat a piece of food and the time you go to the bathroom. Most people are concerned only with the two parts of the digestive system that require some active participation on their part, the food going in and the waste coming out. The multitude of other steps between these two poles are involuntary, and you probably don’t pay a lot of attention to them.


When it’s all working well, normal digestion is an unremarkable experience. 

  • You typically have one bowel movements per day. 
  • They aren’t urgent, they don’t cause any discomfort, there is very little noticeable gas production, and they only take about five minutes.
  • Stools should be well-formed and not watery, generally dark brown in color, and passed easily without straining, cramping, or pain. And a healthy stool does not float in the water.
  • Ideally, at the end of the bowel movement, you should feel like you are fully through, and you shouldn’t need to wipe much. Pooping is a natural experience and should be comfortable and can even bring an enjoyable feeling of release.


As food travels through your digestive tract, it moves down the tube by an involuntary process called peristalsis, a wavelike muscular contraction that carries the nutrients and subsequent waste products from top to bottom. This movement is controlled by the digestive tract’s private nervous system. Eating triggers peristalsis. Therefore, about 30 to 60 minutes after eating, depending on various factors including how much was in the intestinal tract to begin with, a person may feel the urge to have a bowel movement. This bowel movement is not the same food you just ate.

Technically speaking, anything inside this tube is not really inside your body. It is still part of the exterior world. Only once it has been processed and broken down does it pass through the intestinal wall at a cellular level and actually move to the inside your body. This tissue wall is a permeable “skin,” similar in many respects to the skin that protects you on your other exterior surfaces like your arms, legs, torso, and face. Like your outer skin, this layer of tissue is protective, but unlike the skin that you see, it is highly specialized for digestion and absorption.

The food breaks down into smaller and smaller substances as it moves down the tube in stages. Chemicals necessary for digestion and absorption, including acid and enzymes, are secreted into different sections of the tube. Muscular valves close off portions of the tube while chemical processes are carried out at each stage.

Different areas of the digestive tract absorb different materials needed for life: vitamins, minerals, fats, amino acids (proteins), sugars (carbohydrates,) and even water. Waste is also created at each step and moves down the tube toward the exit. All of these functions are highly coordinated, working together to provide you with proper nutrition.

About 60 percent of the fecal mass is made up of water, although this figure can vary widely. When you have diarrhea, for example, the percentage of water is much higher.

Another 30 percent of a normal stool consists of dead bacteria, which gives feces its characteristic odor. These bacteria are from the vast ecosystem of bacteria that lives in the digestive tract. The rest of the stool is made up of indigestible fiber, fats (such as cholesterol), inorganic salts, live bacteria, dead cells and mucus from your intestinal lining, and protein.

Digestion and our immune system

Inside of your digestive tube is a vast ecosystem where some 100 trillion bacteria live, and this should not alarm you. We have been conditioned to think of bacteria as something bad, and the thought that we have 100 trillion “bugs” inhabiting our body can make us feel slightly queasy. But we now are beginning to appreciate the importance of these bacteria, and they have become known as the microbiome.


Although some bacteria are bad, others are very good. In fact, if you don’t have them, you feel very bad, because they are critical for proper digestion.


These bacteria have several important jobs: They help to break down food, they create some vitamins, yhey work directly with the immune system surrounding the digestive tract to protect us from bad guys, they also independently protect us against invading organisms.


Our relationship with the 100 trillion bacteria in our digestive tract is not new. It has developed over hundreds of thousands of years. There should be no doubt about the importance of this ecosystem to good health.


The digestive system also contains 80 percent of your immune system, which defends you from invaders coming down the pipe. The immune system is critically important in helping the digestive system react to bad bacteria and viruses that may be found in our food or accidentally ingested. Possibly the greatest challenge to the digestive tract’s immune system is to correctly tell the difference between what is bad, such as viruses and bad bacteria, and what is good, such as nutrients and good bacteria.


Recent advances in DNA analysis have enabled us to determine the different kinds of organisms living in the digestive tract. In just the last few years, researchers have created tests that analyze the DNA of these organisms and can determine which are healthy microbes and which are pathogenic microbes. This dramatic advance is available to physicians, though they are mostly used only in research facilities.


Your immune system must also determine whether or not to develop a reaction to everything that you put into your mouth. Whenever you try a new food, it must decide, “do I like this and let it go, or do I attack and kill it?”


You are always ingesting bacteria and other substances with your food, no matter how fresh and clean it is, so these must be screened out. While your immune system will say okay to most foods, genetic and other issues may affect its decision.


Recent studies also suggest your immune system’s ability to develop correct tolerances depends a great deal on the balance of good bacteria inside your intestinal tract. When you put something into your mouth that the immune system doesn’t like, it attacks with inflammation and excess mucus production. If your immune system is continually bombarded with messages to attack, its reactions can lead to long term inflammatory consequences.


Inflammation of the digestive tube can, in turn, lead to damage of the lining of this tube, often resulting in something called leaky gut or gut hyperpermeability. These two terms are simply descriptions of the damage to the digestive tract that is a result of something triggering an immune response.

Symptoms of poor digestion

Understanding the qualities of normal good digestion is vitally important to maintaining optimal health. If your digestion is anything less than perfect, your health is going to suffer. The entire digestive process should be unremarkable, meaning there is nothing to remark about it, because it’s functioning in the background and there is no reason for you to notice it.


If you are noticing your digestion, then it isn’t working properly. Likely you are suffering from some kind of digestive upset, such as abdominal pain, gas, urgent diarrhea, uncomfortable or incomplete bowel movements, or bloating. If anything like this is happening, then your digestive system is sending you a message. It’s saying, “Help me!”


If all you do is take something for the gas, or something to create a solid bowel movement or something to make you have a bowel movement, then you’ve only treated the symptom. Your digestion still isn’t working properly, and your health is still going to suffer.


The entire digestive function is based on relaxation and this is why stress is often blamed for bad digestion. When you are relaxed, the parasympathetic part of your nervous system is dominant. This same part allows your digestive system to do its thing an operate normally.

Low Stomach Acid

Stomach acid is vital to good health. It is the first major step, after chewing and saliva, in breaking down your food. Acid is especially important for breaking down proteins into amino acids and is required for the optimal release, preparation, and absorption of minerals, such as calcium, magnesium, and iron.


Decreased acid levels can also cause digestive problems further on down the line. Pancreatic enzymes, bicarbonate, and bile are all released in the small intestine in response to the acidity (pH) of the food that normally leaves the stomach.


Without these, digestion continues to degenerate, resulting in a far less than optimal nutritional gain from your food and potentially damaging byproducts. The pH, now improperly balanced further down the digestive tract, damages the environment for billions of normal/good bacteria, which are critical to proper digestion and good health.


Vitamin B12 also isn’t adsorbed without stomach acid. The same cells that produce acid produce intrinsic factor, which is required for vitamin B12 absorption. Without B12, you become B12 deficient, which can lead to fatigue and neurological problems.


The acidity of gastric juice destroys harmful micro-organisms present in food. However, many people suffer from a deficiency in the production of hydrochloric acid due to stress, poor diet, or harmful chemicals. Hypochlorhydria (the low level of hydrochloric acid) contributes to nutritional deficiencies, osteoporosis, various infections, and stomach cancer. Stomach acid is also your primary defense against food-borne infections. Bacteria don’t usually survive the stomach, so decreased acid increases your risk of food poisoning. Another risk of low stomach acid is poor calcium absorption and therefore low bone density.


The long-term use of acid blockers may cause anemia, vitamin B12 deficiency, and overgrowth of stomach and small intestinal bacteria (SIBO). In addition, acid blockers (proton pump inhibitors [PPIs]) have been found to predispose to the development of food hypersensitivity with gastroesophageal reflux disease. 


Nutrients provide the building blocks for our entire biochemistry. Optimal health requires optimal nutrition which is why you need stomach acid.

If you have low stomach acid you most probably will have some of the below symptoms

  •  Abdominal bloating after food
  • Belching
  • Heartburn
  • Stomach pains
  • Diarrhea or constipation
  • Non-digestible food in stool
  • Bad breath
  • Splitting nails, Acne, Anemia
  • Depression/fatigue (due to low levels of vitamin B12 absorption)


Dyspepsia refers to unspecified upper abdominal discomfort. The underlying problem may be more of a functional reason, the most important of which are motility problems (the problem of gastric motility and in electric activity), abnormal touch sensation of internal organs and visceral hypersensitivity.

Symptoms of dyspepsia include, but are not limited to

  • Pain or discomfort in the upper abdomen
  • Feelings of “full stomach”
  • Rapid feeling of satiety, belching
  • Abdominal bloating
  • Nausea

It is important to note that dyspepsia can be due to some more serious underlying reasons such as stomach ulcer, gallstone disease, cancer, etc.

As always lifestyle plays an important factor. Consider addressing the below areas

  • Smoking
  • High caffeine use
  • Alcohol consumption
  • High-fat processed food
  • Large-portioned meals
  • Extra kilos


Gastroesophageal reflux disease (GERD) is the reflux of food or gastric fluids back into the esophagus.  and is caused by an increase in intra-abdominal pressure.

Main symptoms is usually heartburn. 

Two types of reflux disease can be distinguished: non-erosive reflux disease (NERD) and erosive reflux disease (ERD). Of these, NERD is far more common. 

Reflux itself is a normal physiological phenomenon during relaxation of the esophageal sphincter. However, in reflux disease these relaxations last longer than usual, leading to symptoms. 

Coffee, alcohol, chocolate, fatty meals, and many drugs such as beta-blockers, nitrates, calcium channel blockers, and anticholinergics all enhance and prolong LES relaxation. 

Also, progesterone (a glandular hormone) and nicotine increase the relaxation of the esophageal sphincter. Intra-abdominal or intraperitoneal pressure will increase further (perhaps unexpectedly) by low gastric acid level (hypochlorhydria), which in turn may lead to small intestinal bacteria overgrowth (SIBO) and carbohydrate absorption problems. Treating GERD with acid blockers does not focus on the actual causes of the problems, since reflux disease is rarely caused by excess acid production in the stomach. The use of acid blockers masks and removes the symptoms momentarily but has no effect on intra-abdominal pressure or the function of the lower esophageal sphincter.

Bile and Enzymes

The small intestine receives pre-digested food from the stomach and continues to break down ingredients. 

The digestive process is assisted by bile (formed in the liver but secreted through the gallbladder) as well as pancreatic juice, which contains plenty of digestive enzymes. The small intestine breaks down three main groups of nutrients: proteins, fats, and carbohydrates. 

  • Proteins are broken down into peptides and amino acids. 
  • Fats are broken down into fatty acids and glycerol. 
  • Carbohydrates are broken down into monosaccharides (e.g., glucose) and starch into oligosaccharides. 

Once broken down, the nutrients are absorbed through the intestinal wall. 

Thanks to the structure of the small intestine villi and microvilli, the surface area available for nutrient absorption is enormous—roughly one half of a badminton court.

If you don’t produce enough enzymes you might face some of the below symptoms

  • Food sensitivities
  • Abdominal bloating
  • Stomach pain
  • Heartburn
  • Non-digestible foods in stool
  • Fatigue

On the other hand, Bile is secreted from the gallbladder into the small intestine during the digestive process. The gallbladder is located below the right lobe of the liver. It is a small organ, approximately 8 centimeters in length, and its main function is to store the bile produced by the liver. The gallbladder and the hepatic duct merge to form the bile duct, which leads bile into the small intestine from the ampulla of Vater (a merging point with the pancreatic duct).


Bile facilitates the formation of micelles, which are essential for the absorption of fats. Bile also has an important role in the absorption of fat-soluble vitamins (A, D, E, and K) and the recycling of bilirubin in the body. 

Bile acids function in a manner similar to hormones, participating in metabolism (energy balance, regulation of fat metabolism and glycemic control). Deficiency in the production of bile and bile acids may cause significant health problems such as excess weight and insulin resistance. The gallbladder may also form gallstones due to indigestion or imbalanced diet. For instance, a deficiency in the production of bile salts in the liver, in combination with a diet rich in cholesterol, may be a predisposing factor for the formation of gallstones. 

Risk factors contributing to the formation of gallstones include excess weight, rapid weight loss, constipation and the decreased intake of fiber and nutrients (folate, magnesium, calcium and vitamin C). 

Symptoms of little Bile production may include


  • Heartburn
  • Upper abdomen bloating
  • Fat digestion problem/fatty diarrhea
  • Fat-soluble vitamin absorption problems and deficiencies


Constipation is one of the most common stomach problems besides diarrhea and bloating. 

There are many reasons for this, but here is a look at the most important reasons for constipation. 

When functioning optimally, you may go to bathroom for a ”poop” every day. This is called gastrocolic reflex where stretching of the stomach lining activates bowel movements. This is a very logical reaction: when food is introduced into the body, waste comes out at one end. However, for many, this reflex does not work optimally. Textbooks define constipation as a condition where the bowel empties fewer than three times a week. Normally, the intestines should empty on a daily basis so that removing waste products from the system is optimal.

The most common causes of constipation are

  • Chronic stress (can also cause diarrhea)
  • Imbalance of the bacterial strain in the gut (dysbiosis)
  • Irritable bowel syndrome
  • Drugs (opiate-based painkillers, numerous antipsychotics, iron medications,diuretics, etc.)
  • Hormonal imbalance (especially hypothyroidism)

Leaky Gut

Gut permeability refers to the changed state of the epithelial cells on the surface of the intestine. 

Normally nutrients are absorbed through the epithelial cells. However, sometimes, the cells and the tight junctions between them start to “leak” and allow harmful substances into the circulation. Celiac disease is a typical example of an autoimmune disease involving gut permeability. Increased gut permeability (leaky gut syndrome) is one of the key factors in the development of autoimmune diseases. However, whether it is a cause or an effect is currently not known.

The continuous inflammatory condition or imbalance of the intestine may cause deterioration of the links between the enterocytes on the surface of the intestine, causing gut permeability. Similarly, impaired brain function or stress-related hyperactivity of the sympathetic nervous system undermines the function of the vagus nerve. This impairs the function of the immune system and reduces blood circulation in the intestine, which in turn increases the growth of harmful fungi and bacteria in the intestine. They can damage the surface tissue of the intestine and aggravate gut permeability (leaky gut).

A continuous low-grade inflammation of the system may also aggravate gut permeability.This results in the production of cytokines (inflammatory messenger substances) in the intestine. Due to gut permeability, the messenger substances are able to enter the circulation and the brain via the blood-brain barrier. The inflammation causes the blood-brain barrier to also become permeable, which in turn activates the connective tissue cells of the brain, also known as microglia cells. The result is a chronic inflammatory condition of the brain that impairs brain function and may cause anxiety and depression. Thus completing the vicious circle, which will get worse unless corrective measures such as those outlined in this web course are implemented.

Possible symptoms are

  • Bloating
  • Food hypersensitivity
  • Hypothyroidism
  • Joint pain
  • Headaches
  • Various skin problems
  • Digestive problems
  • Weight gain
  • Metabolic syndrome
  • Malabsorption & nutrient deficiency states


Irritable bowel syndrome is a syndrome may have a number of different reasons. 

The affliction of IBS is very common, probably more common than studies show. 

Globally, irritable bowelsyndrome affects about 11 % of the total world population. Only about 30 % of people who suffer from IBS are in contact with their doctors. Irritable bowel syndrome may be classified into three major types


In IBS, the gas production in the gut is markedly increased. 

Typical of IBS is the fluctuation of symptoms and possible other symptoms associated with abdominal symptoms (arthralgia, mood swings, fluctuations in energy levels etc.). 

The most common intestinal symptoms in IBS are abdominal pain, straining stomach, muscle aches, rushing to the toilet, bloating, and general feelings of illness. In the development of IBS there has also been identified a genetic component, but its significance and importance has not yet been established. Indeed, environmental factors play a greater role in this syndrome.

  • Increased food processing (e.g. modified starches, additives, sweeteners, polydextrose, etc.)
  • Abundant use of cereals and legumes and heavy drinking of milk
  • Changes in intestinal bacterial balance and dysbiosis (including unnecessary antibiotic use)
  • Silent (low-level) inflammation of the body
  • Chronic stress
  • Small intestinal bacterial overgrowth (SIBO)
  • Malfunctions of the gut-brain-microbiota axis
  • Serotonin metabolism disorders (especially 5-HT3 and 5-HT4 receptors)
  • Sitting and lack of exercise

The treatment of IBS is quite difficult since it is not just an intestinal disease, but rather a systemic syndrome created by environmental, physiological and psychosocial factors. Often, diet alone is not enough, and treatment requires a systematic self-assessment of lifestyle and, in particular, high-quality stress management measures.


Small intestinal bacterial overgrowth growth literally means just that: an excess of bacteria growing in the small intestine. 

Although many doctors do not yet recognize SIBO as a medical diagnosis, it has accumulated quite a bit of medical research over the last 10 years, which will lead to increased knowledge on the existence of SIBO. Normally, only small amounts of bacteria grow in the small intestine. Most bacteria live in the colon (large intestine). However, there are situations where the level of bacteria in the small intestine may increase to harmful levels and lead to many serious health problems. 


When bacteria ferment fibers, they produce hydrogen gas. Similarly, so-called arcanobacteria live on hydrogen and produce methane gas. Methane is usually associated with constipation-prone bacterial overgrowth, while diarrhea-prone bacterial overgrowth is caused by hydrogen. Hydrogen-dominant SIBO is usually easier to treat than methane-dominant SIBO.

  • Diarrhea (hydrogen is dominant in gas formation)
  • Constipation (methane is dominant in gas formation)
  • Intestinal cramps and pains
  • Fatigue, joint pain, anxiety, depression

Health factors to be considered

  • • Reduced gastric acid production 
  • Disorders of pancreatic digestive enzyme production
  • Systemic diseases (celiac disease, Crohn’s disease, fatty liver)
  • Intestinal surgery
  • Intestinal blocks (strictures, tumors, ulcers)

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