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How does digestion actually work?

March 4th, 2021  

Or right to the point: how does pooping work?

Most people don’t talk about it, but the majority of us do it every day, or at least every other day. For many it is part of the morning routine. Pooping! We don’t understand why this important topic is a taboo for many people. We go into detail and look at exactly how digestion actually works. What happens inside us before we go to the toilet? When and where does digestion begin? A favourite topic for us and hopefully soon for you too. 

The little helpers inside you: your gut bacteria

Before we go into the subject of digestion in more detail, you should know that over 90% of the food we eat is absorbed, broken down and converted by our gut bacteria. Each bacterium performs different functions. Some produce vitamins, others participate in carbohydrate, fat or protein metabolism. They assist us in digestion and nutrient absorption. In addition, our intestinal bacteria help us supply energy, regenerate the intestine and control the transport of substances (1). 

Our digestive system is a complex and clever interaction of our body and our intestinal bacteria. Our body has two metabolic systems. If our body metabolism cannot utilize certain nutrients, the bacterial metabolism will help us.  

Well chewed is half digested – this is where digestion begins!

Let us imagine that we are eating a sandwich with cheese. Interestingly, just by thinking about our snack, we begin to produce stomach acid and saliva. That’s where the saying comes from, „My mouth is watering just thinking about it.” Our body is preparing for the meal! This is how our body prepares for the meal.

Just by thinking about food, we start to produce stomach acid & saliva.

From the moment we bite into the sandwich, it’s already happening: chewing turns our food into mush. Antibodies and lysozymes carry out the disinfection work and mucins (=mucous substances) make our porridge slimy and ready to swallow.

Carbohydrates, proteins and fats are digested differently

The alpha-amylase ptyalin is an enzyme that is actively involved in nutrient processing in the mouth due to the hydrogen carbonate buffer (pH= 7-8) present there. Carbohydrate digestion thus begins in the mouth. We have the hydrogen carbonate buffer to thank for the fact that acidic foods do not attack our tooth enamel. However, since there is a much more acidic environment in the stomach (pH=1), the alpha-amylase ptyalin is inactive in the stomach. However, the acidic environment in the stomach is important because the hydrochloric acid there has an antibacterial effect. It is good that the so-called tongue base lipase is present in saliva, because it loves the acidic environment in the stomach and helps digest fat there. Fat digestion does not take place in the mouth. (2) 

Now the bread pulp continues through the telephone cable-like esophagus into the right side of the stomach. In the stomach, muscle activity breaks down our porridge. Protein cleavage begins: the hydrochloric acid mentioned earlier activates pepsinogens to pepsins and the trivalent iron is reduced to bivalent iron. (For those of you interested in chemistry: Fe3+ -> Fe2+). Pepsins convert proteins and polypeptides to peptides. 

In the next step, tongue base lipase and gastric lipase help with fat digestion in the stomach. Something else very important happens: the intrinsic factor (=glycoprotein) binds to vitamin B 12. Why do I mention this separately? Only in this way vitamin B 12 can be absorbed into the small intestine. Vitamin B 12 is an important coenzyme for us, which together with folate is involved in the regulation of homocysteine concentration in blood. The interaction of folate and vitamin B 12 is essential for cell differentiation and division – e.g. in DNA synthesis and blood formation.

How the small intestine works

After the stomach, food first enters the small intestine. This consists of three sections: Duodenum (duodenum), Jejunum (jejunum) and Ileum (ileum). In the duodenum, bile and pancreatic ducts are now added. (3)

The small intestine consists of three sections: Duodenum, jejunum and ileum. 

The entire intestine is surrounded by blood vessels that absorb and carry away nutrients. The blood vessels end in the portal vein, which leads to the liver. Our liver is our central metabolic organ and loves to store nutrients to have them handy for us. After the sugar broken down in the small intestine passes through the intestinal wall, our liver takes a lot of glucose and stores it, but as a long-chain carbohydrate (glycogen) so that we have sugar available later when we need it. The remaining glucose floats into the general bloodstream. At night, when we sleep, the liver provides us with sugar when needed and in turn protects us from hyperglycemia after eating. (2)  

What insulin is all about

(A little side fact: As soon as sugar enters the blood, the hormone insulin, which is produced in the ß-cells of the islets of Langerhans in the pancreas, is released. Like a key, insulin unlocks cells to let the sugar in. That’s why blood sugar levels drop – because of insulin. The pancreas acts like a blood sugar meter. The more and simpler the sugar we eat, the more insulin has to be produced and released. Therefore, complex carbohydrates are an important part of a healthy diet because it is more complicated, energy- and time consuming for enzymes to break down such carbohydrates.  Thus, with complex carbohydrates, there is a slower rise in blood sugar and a longer feeling of satiety. Complex carbohydrates include starch (cereals, potatoes), glycogen (=storage carbohydrate in liver and muscles) and dietary fiber (legumes, nuts, vegetables, fruits). In addition, insulin is also secreted during fat and protein intake, but it reacts most strongly during a rise in blood glucose. (2) Intestinal bacteria live in our intestines and produce their own enzymes that help us with this carbohydrate splitting.

Another function of our liver is the production of bile. The bile is stored in the gallbladder. Bile acid neutralizes hydrochloric acid through hydrogen carbonate. Bile salts, which are produced in the liver from cholesterol, and phospholipids form micelles (=fat droplets) in the duodenum. 

The diversity of our microbiome plays an important role, because a lack of gut bacteria can have a negative impact on liver metabolism.

Liver and intestine are in communication. This circuit is called enterohepatic circuit. About 98% of the bile salts produced in the liver are involved. Other substances such as estrogens, drugs, cardiac glycosides, vitamin D, folic acid, vitamin B9, vitamin B12, bile pigment from hemoglobin (about 15%) and other toxins are not so easily removed with the stool, but are reabsorbed. (2) The diversity of our microbiome plays an important role here, because a lack of intestinal bacteria can have a negative effect on liver metabolism (4). In fact, our gut bacteria can also influence the properties of bile acid and therefore play a very important role (5).

And what’s the deal with the pancreas? Hydrogen carbonate neutralizes hydrochloric acid, and in the duodenum, pancreas helps break down fat using lipases. These lipases convert fat to free fatty acids and monoglycerides. Starch and glycogen are converted to dextrin and maltose by alpha-amylase (= the amylase that already breaks down carbohydrates in the mouth).

What happens inside us when we are lactose intolerant

If carbohydrates cannot be completely digested, as in the case of lactose intolerance, for example, the lactose cannot be absorbed by the intestinal cells and migrates into the large intestine. Here, our intestinal bacteria take care of the lactose and break it down. This process produces unpleasant by-products, which can be the reason for flatulence, abdominal pain and other complaints. (2) 

And what do small intestinal secretions of microvilli do? They complete the whole procedure: they ensure that our food becomes absorbable molecules. However, what actually are microvilli? To explain this, let’s take a short trip to the wall of the small intestine. It is folded several times to create a large contact area. This contact area is used to absorb the nutrient building blocks into the blood. The folds of the small intestine have protrusions called intestinal villi. These villi in turn have further projections, the microvilli.

The end of the food journey: The large intestine

And the best comes at the end: the large intestine. It is divided into transverse colon, ascending colon, caecum with vermiform appendix, descending colon, sigmoid colon and rectum (2). (Side Fact: each of us has an appendix. It is in this appendix that bad germs in particular are fought. In case of inflammation of that one speaks of appendicitis).

The task of the large intestine is to absorb the mush from the small intestine, thicken it into feces by extracting water and electrolytes. It also absorbs important short-chain fatty acids, the food for our intestinal bacteria.  These short-chain fatty acids, acetic, propionic and butyric acids, help modulate hunger and satiety. The salt of acetic acid binds to specific receptors and triggers feelings of satiety (1). The feces is then transported further and stored in the rectum. Finally, it is excreted. This is where the exciting journey ends for our cheese bread 😉.

How about an oatmeal porridge with psyllium husks, berries and kiwi? Fiber for your microbiome <3 

In conlcusion, our dietary choices influences our microbiome and our microbiome influences how we utilize our food intake. Thus, it would only be fair to take care of our gut bacteria and feed them their favorite food: fiber. Bon appetit! 🙂 

Now, if you want to find out how diligently your own gut bacteria are working for you, you can have your gut microbiome analysed with myBioma and learn more. We hope we’ve been able to de-taboo the subject of digestion a little. It’s important to talk about it! If you have serious problems, we recommend you talk to an expert about it. Check out our network of therapists. If you have any questions, you can always contact us at:


1.           Fachgesellschaft für Ernährungstherapie und Prävention (FET) eV.

2.           Elmadfa I. Ernährungslehre: UTB GmbH; 2019.

3.           Silbernagl S, Draguhn A. Taschenatlas Physiologie: Thieme; 2018.

4.           Schneider KM, Trautwein C. Die Darm-Leber-Achse bei nichtalkoholischer Fettlebererkrankung: molekulare Mechanismen und neue Targets. Der Gastroenterologe. 2020;15(2):112-22.

5.           Chiang JYL, Ferrell JM. Bile Acid Metabolism in Liver Pathobiology. Gene Expression. 2018;18(2):71-87.

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