Inflammation, leaky gut and dysbiosis


The other day, while I was trying to make french toast with old bread, I cut myself. It hurt me instantly, but the pain really felt the next day. The cut became swollen and red.

Why is this phenomenon being observed?

When our organism is attacked by pathogens, it defends itself. Immune cells are sent to the battlefield, and their actions will cause inflammation.



Okay, but what does that have to do with our intestines?

Wait a minute…

You may recall that 80% of our immune cells are in our digestive tract. They help protect us from the microorganisms that may be in our food.
If our intestines are attacked all the time, and besides, our microbiota is not in great shape, the intestinal cells ignite, like my cut on my finger!


It is not possible to feel the inflammation that takes place in our belly in the same way as that caused by a cut. Yet, it is identifiable by visible signs.

At this point, you’re probably wondering, but why can’t our microbiota protect us from everything, and why are our intestines igniting?

The purpose of this article is to explain to you how an imbalance of the microbiota induces a permeability of the intestinal wall, causing an inflammation that is at the origin of many evils.


Let’s talk first about inflammation

Two types of inflammation

It is necessary to distinguish between acute inflammation, that is to say temporary (appendicitis or gastroenteric for example), and chronic inflammation. In the latter case, chronic inflammatory bowel disease is referred to as IBD. Crohn’s Disease and Rectocolitis Hemorrhagic. They manifest themselves in phases: the phase of pain, called the phase of thrust, and the so-called periods of remission.

NB: Irritable bowel syndrome is not considered a disease, but a set of symptoms. For more information, find my full article on this subject.

In IBD, inflammation is visible and causes a set of symptoms that have been identified and grouped together to give them a name.

However, many of us suffer from chronic inflammation without suffering of IBD and without knowing it.


What trigger inflammation?

Acute inflammation is usually caused by an infection. It can be viral, bacterial or parasitic.

Chronic inflammation is more complicated. A combination of factors can cause and sustain inflammation: poor eating habits, medication, contraception, smoking, pollution, untreated acute inflammation…

In all cases, the inflammation is due to an intestinal permeability, itself caused by an imbalance of our intestinal flora.


Imagine that our intestinal cells are a barrier. They are stuck together, but they are not completely sealed. They allow the nutrients that are very small to enter in the bloodstream, but protect us from pathogens or other toxic substances. Sometimes, however, the space between our cells grows, they no longer play their protective role, and fragments of food (peptides) and toxins can enter the bloodstream. The organism can then trigger artillery against these protein factions which they consider as enemies. Our immune system is overexcited: it’s inflammation.


Why is our intestine becoming permeable?

The main reason for leaky gut is dysbiosis, which means an imbalance of our microbiota. The main causes are:

  • A imbalanced diet:
    • Excess of sugars, promoting among other things the growth of yeasts such as Candida spp. SIBO (Small Intestine Bacterial Overgrowth) may be observed in some cases.
    • Excess of protein (animal) that will induce the production of toxic metabolites for the cells of the intestinal mucosa by our microbiota (hydrogen sulphide, p-cresol…) and promote methane-generating fermentation.
    • Excess of fat. A study in mice showed that after only one month of a diet composed of 70% lipids, their microbiota was modified: some bacteria proliferated, others disappeared. In addition, the epithelium (intestinal tissue) produces antimicrobial peptides and mucus, preventing bacteria from passing through the wall and thus ending up in our blood. This production of peptides and mucus also decreased in mice during the experiment. Certainly, the percentage of fat was very high, but this study may be of interest to ‘ketogenic pro-diets’. 
    • Industrial food which contains a lot of preservatives which interfere with the microbiome



    • Consumption of products containing sweeteners that may, for example, inhibit the growth or functions of many micro-organisms.
    • The lack of plants, therefore fibres, prebiotics and minerals essential to bacteria.
    • Consumption of hydrogenated fats (that is to say that we have added molecules of hydrogen in order to make them more stable in heat, ultra-convenient for industrialists…less for our microbiota!). Trans fatty acids are partially hydrogenated and/or deodorized and/or heated fats at high temperatures. Trans fats are suspected to affect the production of short-chain fatty acids, which play an important role in the communication between the immune system, microbiota and fat metabolism.
    • Unbalanced omega-6/omega-3 ratio. The ratio should be 4:1, but in Western societies it is closer to 15:1. Omega-6s that are out of balance with omega-3s are pro-inflammatory.


  • Bad eating habits
    • Not chewing enough. Carbohydrate digestion begins in the mouth thanks to the action of enzymes contained in saliva. If carbohydrates are only partially cut when they enter the intestine, they are poorly digested and can ferment.
    • Excessive and regular alcohol consumption. It has been shown that the microbiota of large alcohol consumers have less Lactobacilli (anti-inflammatory bacteria), but more bacteria of the family of Actinomyces, Leptotrichia, Cardiobacterium and Neisseria, which too much can become dangerous.
    • Very frequent food outlets. Our body is equipped with migrant myoelectric complexes (or migrant motor complex). It is a muscle contraction in the stomach that is responsible for peristalsis. The complexes are separated into 3 phases. When the stomach is empty, we go to phase 3, which is a series of regular contractions pushing food residues towards the colon. You have most certainly heard your CMM in Phase 3 when you heard your stomach gurgling. The MMC is kind of a broom that cleans food residues. If your food intake is very close (less than 3 hours between each), the MMC does not enter in phase 3, and does not play its role as a housekeeper of the intestine. t’s kind of like you’re soiling your house before you even finish cleaning it. Food residues in your intestines do not drain properly, and can rot and feed some bacteria that, for our sake, should ‘be on a diet’.


  • Médicine consumption
    • Antibiotics. As seen in my article on IBS and microbiota, antibiotics are bulldozers that destroy all in their path. If one does not take care to regenerate its flora after treatment, an imbalance may appear.
    • The contraceptive pill
    • Proton pump inhibitors (or antacids). These drugs block the secretion of hydrochloric acid in the stomach. However, we saw in this article, if the body produces acidity, it is because it needs it! Without hydrochloric acid, the food bowl cannot be sanitized properly.


  •  Uncontrolled stress

You have to distinguish between the good stress that pushes you beyond your limits and the one that dominates you and prevents you from living serenely.

  • High intensity sports activity

Endurance athletes are much more likely to develop a dysbiosis because during long-time exercice, blood supply muscles in priority. As the digestive tube doesn’t receive enough oxygen, some cells die, and some micro-organisms as well.


  • Constipation

If waste is not disposed of properly, microorganisms can grow and produce their own waste that can weaken the mucous membrane and induce intestinal permeability. For more information, find my article on the subject.


Here is a little experience explained by Tim Spector in his book The Diet Myth that I want to share:

For 10 days, his son consumed only fast food meals. At the end of the experiment, the percentage of Bacteroids (types of bacteria that would seem to facilitate weight gain because they have the ability to extract as many calories as possible from food) increased from 25 to 58%. The population of Firmicutes has decreased from 72 to 28%. But most interesting: the diversity of the microbiota was decimated by 40% in less than 3 days!


In short, it shows that the diet impacts directly and quickly on our microbiota, and that an unbalanced diet is harmful.
Each species has a preference for certain foods because it allows them to feed and reproduce. They will do everything in their power to ensure their survival, to the point of making the host want to consume the same source of food, no matter how harmful it may be to him. They can even kill other bacteria, like Enterobacter, which produces an endotoxin that attacks the cells of its competitors under certain conditions.


To know: the more diverse your microbiota, the better! There are no “good” or “bad” bacteria, it’s all about balance!


Now that we saw what could trigger a dysbiosis, let’s see:

The leaky gut symptoms
  • Digestive disorders: bloating, pain…
  • Abdominal pain
  • Many food intolerances or sensitivities, or even allergies

Consequence: Chronic inflammation that induces an imbalance of the:

Endocrino system (disturbed hormonal system)

Immune system. Our immunity cells are in charge of detecting and destroying anything that is not recognized as a mere nutrient or self. Our microbiota is the first line of defense in our body. If it is not able to protect us, we are more likely to be infected.

Nervous system. We have more neurons in our intestines than in our brains! People in coma cannot breathe without medical help, but their intestines continue to function.  Opportunistic bacteria (not-very-sympathetic bacteria which are only there for free meals), produce toxins that paralyze our muscle nerve cells in our intestines causing discomfort, abdominal distension and sometimes constipation. Moreover, when these opportunistic bacteria are close to each other, they form a biofilm, a kind of small cocoon. They become difficult to eliminate, especially as minerals and metals will accumulate there.


Chronic inflammation causes chronic diseases



Dysbiosis consequences

They are numerous and do not only affect the digestive tract. They can affect the ENT sphere, cause skin symptoms, allergies, weight gain or even obesity, a depressive state…


How to avoid dysbiosis?

No, it’s not enough to feed on probiotics to make everything look beautiful and pretty again. If your microbiota is overcrowded with a type of bacteria that becomes harmful, you don’t want to encourage their growth! Here are some actions to take:

    • Learning to manage stress

    • Physical activity. An experiment conducted on rats showed that those who ran the most produced more butyrate, our super fatty acid benefits for our intestine wall.
    • Change your diet: plant-rich, diversified, balanced in sugars, proteins and fats rich in omega-3 and polyphenols. These encourage the growth of certain bacteria and thus, prevent the non-colonization of less sympathetic bacteria in our intestines, such as Escherichia coli. (one culpit of diarrhea).
    • Avoid medications when not necessary, and do have a probiotic treatment following antibiotic treatment. Medications may be helpful, but they are often used to calm the symptoms and not cause it. In Clean Gut, Ph Junger explains the phenomenon very well: it’s like painting the leaves of a sick tree instead of looking after its roots.
    • Favour breastfeeding and natural Birth.  It has been proven that children born by C-section, and therefore not enjoying the bacteria of the vaginal flora of the mother, had more fragile intestines. Breast milk is rich in natural probiotics, beneficial to the child, and contains lactoferrin, a protein that accelerates the maturation of intestinal cells.


Remember : our microbiota matures at the age of three. The first few years of life are important, but keeping a diet beneficial to our microbiota in the long term is even more important.


Some foods are natural protectors such as foods rich in glutamine. L-glutamine is an amino acid that our bacteria love. It contributes to the health of our epithelial cells. It is found in oilseeds and legumes.

Fermented beverages, kefir, vegetables such as Jerusalem artichokes and onions can also probiotic food. We should not forget garlic, spices and herbs.


What about genes?

Oh, genetics! “I’m like that but it’s not my fault, my whole family is the same!” No, no, no, no !!! Of course we have genetic predispositions, but genes are only expressed in a certain environment. This is the principle of epigenetics.



If you have the same lifestyle as our father who has diabetes, then yes, the expression of this gene is more likely to express itself. On the other hand, if you set up a healthy lifestyle, this gene will not necessarily be expressed.
In addition, as seen previously, we have 10 times more bacteria than cells in our body. These bacteria also have genes that communicate with ours.

The microbiota of real twins shares about 50% of the main families of microbes, while the population of the same environment shares 40%.

Genetics plays a role, but does not explain everything.


Keys points to remember

If you were to remember only one thing from this article, remember that the majority of chronic diseases today are the cause of dysbiosis and inflammation of the intestines due to an intestinal permeability, itself generated by a unbalanced diet, and bad lifestyle habits.


Think of your microbiota as a garden for which you are responsible. You need to be careful that the soil (your intestines) is rich in nutrients so that plants (microorganisms) grow. You need to be careful of weeds (ultra-processed foods) and toxics that can impair growth and cause disease. You want to grow a wide variety of possible plants, diversity is the key!




I hope you enjoyed this article and made you understand more the importance of nutrition in your health.


To go further

Here some books which :





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