Gut: The Inside Story of Our Body’s Most Underrated Organ

Gut: The Inside Story of Our Body’s Most Underrated Organ

by Giulia Enders

The gut was one of the most ignored organs within the body for decades, but recent research showed that it is responsible for a lot more than we think. Giulia Enders, a gastroenterologist, explains the gut's inner workings, including its inner structure, the reasons for our gluten allergies, the role of the appendix, and many others. It also touches on human feces—an important topic we often overlook. Most importantly, the author sheds light on the connection between the gut and the brain and how our gut can influence our mental health.

Summary Notes

How Does Pooping Work?

“Squatting has been the natural defecation position for humans since time immemorial.”

To understand how our gut works, we’ll have first to understand the inner workings of our body’s waste management system, of which, two sphincters are the most important parts.

The first is the external sphincter,  a layer of striated muscle encircling the outside wall of the anal canal and can be consciously controlled. The second part is the inner sphincter, unconsciously controlled by our smooth muscles. 

The inner sphincter is a part of the inner surface canal that identifies whether what is about to come out is fart or fecal matter. Once the ambiguous stimulus is identified, the outer sphincter permits us to dispose of it.

Aside from these sphincters, the position we defecate can also influence our gut. Research shows that squatting is the most beneficial position when we defecate. When we sit on a toilet, the muscle surrounding our intestines almost strangles them. When we squat, the muscle relaxes, allowing us to defecate comfortably.

This explains why people in countries with squatting toilets are less prone to diverticulitis, hemorrhoids, and other health-related issues.

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The Gateway to the Gut

“Our saliva contains one painkiller that is stronger than morphine.”

The gateway to the gut starts with our mouth—specifically, the parotid papillae, two forgettable bumps on the tongue that help with the secretion of saliva. Saliva is one of our strongest forces against bacteria and helps us predigest food. It contains opiorphin, a natural painkiller that our body secretes in small amounts; otherwise, we would all be high on our saliva.

The concentration of bacteria in our mouths tends to peak in the morning and at night. We produce very little saliva while asleep, so brushing our teeth every morning is especially important. Since only small amounts of saliva are produced at night, it causes the bacteria to increase. If you do not eliminate the bacteria in the morning, you may develop a sore throat, bad breath, and endanger your teeth.

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What We Really Eat

“So, whether it’s extra virgin olive oil or cheap fat from french fries, it all goes straight into the heart—there is no detoxing detour via the liver as there is for everything else we digest.”

Digestion starts in our mouth, where saliva breaks down the food we ingest. Food then travels into the stomach and is further broken down through mechanical movements and gastric juices before moving to the small intestine. 

In the small intestine, digestive enzymes from the pancreas and bile from the liver break our food down further, which is then squeezed into the lower parts of the small intestine (the jejunum and ileum), where nutrients are absorbed.

Our ileum is covered with millions of finger-like projections called villi, which help absorb nutrients. Each villus is connected to a series of capillaries through which nutrients travel to reach our main bloodstream. Once our villi absorb all these nutrients, the remaining waste is moved into the large intestine to be excreted.

The digestion of bad fat can be highly dangerous for your health as it is susceptible to oxidation, leading to the deterioration of the fatty acids. For example, polyunsaturated fats like canola or sunflower oil can become toxic when cooked at high heat. Unlike other nutrients, fat cannot be absorbed straight into the gut because it’s not water-soluble, so it must be absorbed through the lymphatic system.

After eating a fatty meal, many tiny fat droplets end up in our thoracic duct that skirts the belly, passes through the diaphragm, and heads straight for the heart. Whether it is healthy olive oil or the cheap fat from fast-food fries, the fat you ingest impacts your blood vessels.

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Allergies and Intolerances

“Instead of creating an emotional scene, plants respond by making their seeds slightly poisonous.”

If you’re allergic to peanuts, you may have experienced diarrhea, nausea, vomiting, or shortness of breath, even if you tried eating only a few peanuts. Why does that happen?

If we fail to break down the protein particles from a peanut into its constituent amino acids, tiny bits of it will remain undigested. Under normal conditions, those tiny particles don’t make it into the bloodstream. Nevertheless, they can sometimes infiltrate the lymphatic system. 

Those particles become embedded in fat droplets, which are then attacked by the immune system once discovered. The problem is not that the immune system removes that foreign body from the lymphatic system; rather, the problem is that each time it occurs, the immune system attacks more aggressively. 

The immune reaction to peanut particles can become so severe that simply putting a peanut in your mouth can cause severe allergic reactions such as extreme swelling of the face or tongue.

Intolerances happen in part because plants don’t like to be eaten, so they make their seeds slightly poisonous. While we evolved in such a way that we can easily digest a wide range of plants, some people are still more sensitive to the toxic parts of plants. 

In the case of gluten, it can pass into the gut cells in a partially undigested state. Once there, it can slacken the connections between individual cells, allowing wheat proteins to enter areas of the body where they should not be, raising the alarms of our immune system.

Allergies and intolerances can affect how our feces look, giving us details about the health of our digestive system. One way to identify the way healthy feces should look is the Bristol stool scale.

The Bristol stool scale is a medical tool designed to classify the form of human feces into seven categories. Characterizing the stool based on its consistency can help identify healthy bowel movements. Ideally, your feces should be of type 3 or 4. 

The seven categories are the following:

  • Type 1: Separate hard lumps - Very constipated
  • Type 2: Lumpy and sausage-like - Slightly constipated
  • Type 3: A sausage shape with cracks in the surface - Normal
  • Type 4: Like a smooth, soft sausage or snake - Normal
  • Type 5: Soft blobs with clear-cut edges - Lacking fiber
  • Type 6: Mushy consistency with ragged edges - Inflammation
  • Type 7: Liquid consistency with no solid pieces - Inflammation and diarrhea

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How Organs Transport Food

“So, really, we have reason to be proud of our body’s abilities whenever we find ourselves crouched over the toilet bowl throwing our guts up.”

The gut is cosseted by three coats of smooth muscle tissue that we do not consciously control. Instead, the gut’s enteric nervous system controls all processes in the digestive tract, which is highly autonomous.

For example, the enteric nervous system controls the important process of vomiting. Vomiting follows a precise plan; millions of tiny receptors test our stomach contents, examine our blood, and process impressions from the brain. If something we ate is deemed to be harmful, an emergency procedure starts, and the harmful contents are evacuated. 

On the other hand, motion sickness occurs when information sent to the brain from the eyes doesn’t match the information sent by the ears. The brain becomes confused and enters a state of alarm, slamming any emergency break at its disposal. 

Understanding all of this will help you reconsider the process of vomiting as something beneficial and useful rather than something disgusting for no particular reason.

Actions to take


“The best parameter for assessing constipation is not how often you need to go to the toilet, but how difficult it is.”

Constipation results from a disconnect between the nerves and the muscles of the gut when they are no longer working toward the same goal. Going to the toilet three times a day is still healthy; however, frequency is not the best parameter for assessing constipation. Your difficulty on the toilet is a much better factor to consider since time spent on the toilet shouldn’t be troubling.

Temporary constipation can be due to traveling, illness, or stress, but more persistent constipation can indicate long-term problems. Constipation while traveling occurs because our gut is a creature of habit; it knows when we should eat, what type of food we eat, how much water we drink, and even how much we move around. Changing these habits can put our gut in a state of alarm, temporarily postponing the normal excreting processes until things return to normal.

Actions to take

The Brain and the Gut

“When a gut is irritated, its connection to the brain can make life extremely unpleasant.”

The gut possesses an unimaginable number of nerves that differ from the rest of the body.  This is called the gut-brain because it is just as large and chemically complex as our brain. The gut can reach various brain regions, such as the insula, the limbic system, the prefrontal cortex, and others. 

There is a deep relationship between the gut and the brain. We can see this reflected in both animal and human studies. 

One example is a study where a small balloon was inflated inside the participants' intestines, showing differences in their brain activity. Those who suffered from irritable bowel syndrome showed increased brain activity in the areas associated with unpleasant feelings, while the healthy participants showed normal activity.

Another example is an experiment conducted on mice. When they were fed good bacteria, their performance on a swimming test improved, and their stress levels decreased. 

The impact of the bacteria within our gut is clearly shown in the experiments with germ-free mice. They are the cleanest creatures in the world. They are born via sterile cesarean section, eat steam-sterilized food, and live in antiseptic cages. They have abnormal behavior characterized by hyperactivity and caution, take longer to digest food, and have a reduced number of immune cells. They are easy prey even for relatively harmless pathogens. 

Feeding them cocktails of bacteria taken from other mice produces astonishing results. If they are given bacteria from mice with type 2 diabetes, they soon begin to develop problems metabolizing sugar. Our microbiome (the bacteria living in our gut and their genetic material) plays a huge role in how our body systems work.

Actions to take

The Development of Gut Flora

When you were still a baby in your mother's womb, you were in one of the most germ-free environments you will ever be in. For about nine months, you will have no contact with the outside world except through your mother. Your mother's lungs and gut filter everything before it reaches you.

Natural births help babies get in touch with the helpful microbes in the protective vagina flora, a part of the body where bacteria beneficial to the baby's sterile body are carefully selected. This is not the case for babies born through a cesarian section; they will get in contact with whatever bacteria from the people that will handle them in their early days. That’s why this type of birth increases the baby's chances of developing allergies or asthma.

Breast milk also has an extremely beneficial effect on building babies’ health. It is simply the best food for a baby, with all the necessary nutrients and antibodies to protect them against dangerous bacteria.

Actions to take

The Role of Gut Flora & the Bad Guys – Harmful bacteria and Parasites

“There are good guys, and there are bad guts in the world, and the same goes for the world of our microbes.”

Gut bacteria process food we cannot break down otherwise (for example, lactose). We can also use the same bacteria in our kitchens to ferment food, such as when we ferment cabbage to make vitamin-rich sauerkraut.  

Some bacteria can hinder our efforts to lose weight and are associated with chubbiness. These bacteria are found in the gut floras of obese individuals or in experiments with obese mice. They are highly efficient at breaking down carbohydrates. In mice studies, it has been shown that skinny mice excrete a certain quantity of indigestible calories while their overweight peers excrete significantly fewer.

Nevertheless, the chubbiness bacteria are not inherently harmful, unlike Salmonella, which can be found in the gut flora of contaminated chicken. Once in contact with a host, Salmonella can wreak havoc on the human body. 

Another type of bacteria that can be harmful is Helicobacter pylori. This type of bacteria is not inherently dangerous because it can help decrease the probability of asthma, but it can lead to ulcers and gastritis for some people.

Actions to take

The Cleanliness and Good Bacteria

“Preventing deadly disease by banning pupils from spitting at school seemed like a simple and effective idea.”

More than 95% of the world’s bacteria are harmless. That means you don’t need as much disinfectant as you think. In fact, many bacteria are even extremely beneficial!

If your floor is covered with dirty footprints, all you need is water and a drop of cleaning fluid to reduce the bacteria population on your floor by 90%. This method allows the normal, healthy population of the floor’s bacteria to recolonize the territory.

The aim of cleaning should be to reduce bacteria but not to eliminate them completely. Even harmful bacteria can sometimes be good for us since our immune system strengthens in response to mild exposure. You can think of a couple of thousand Salmonella bacteria in the kitchen sink as a chance for our immune system to do some weight training. Salmonella is only dangerous when it comes in greater numbers.

Antibiotics are a way to erase the bad bacteria from our gut. Nonetheless, they will also kill good bacteria. They are overprescribed for colds caused by viruses, for which the antibiotics are useless. A doctor can perform a procalcitonin test, which indicates whether a bacterial or viral infection causes cold-like symptoms. 

Avoiding overusing antibiotics is essential, as you can develop antibiotic resistance and negatively affect the gut flora in the long term, especially in the elderly and children.

Actions to take

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