What is the microbiota ?

Who is it, how is it constructed and how does it evolve ?

Today, we know that the human being is made up of as many cells as micro-organisms. These micro-organisms are bacteria, viruses, fungi, parasites and constitute what is called the microbiota. 1013 micro-organisms are present in our body, and play a major role in our physiological imbalances, in many pathologies, and in particular in inflammatory diseases.

Most of these microorganisms are non-pathogenic (not dangerous), and when the balance is there, they live with us in a kind of symbiosis; whether it is in the skin, the mouth, the vagina, the lungs… The most important microbiota in terms of quantity is the intestinal microbiota, which is located mainly in the colon. It is implanted on the digestive wall and interacts permanently with it: it is the intestinal flora.

When the microbiota malfunctions, in quality and/or quantity, we speak of . It is this dysbiosis that causes the appearance of various symptoms and the inflammation found in so-called inflammatory diseases.

Each individual has his or her own microbiota, like a genetic fingerprint. The microbiota begins to form at fertilisation (of the oocyte by the spermatozoon) and stabilises at around the age of 2.

Throughout a human being’s life, the microbiota will be influenced by different factors that it is essential to know.

These different factors are :

  • the mode of birth (childbirth or vaginal delivery),
  • the mother’s microbiota,
  • the genetic background,
  • diet (breastfeeding or not, dietary diversification, diets…),
  • stress (emotional and physical),
  • hormonal variation (in relation to menstrual cycles, growth, puberty, pregnancy, menopause…),
  • infections (viral, bacterial, parasitic, fungal…),
  • synthetic allopathic treatments (antibiotics, painkillers, anti-inflammatories, antacids…),
  • the environment (pollution, endocrine disruptors…),
  • lifestyle (alcohol, tobacco, sport, sedentary lifestyle, place of living…).
  • The state of health of the microbiota, and therefore of the individual, depends on all these factors which it is important to understand and take into consideration in order to maintain a balanced health.

What are its roles ?

The micro-organisms present in each of our organs identify the pathogenic organisms (dangerous to humans) that arrive, by coming into contact with them, and then activating the pathways of our immune defences.

In addition to having, like the other microbiota (skin, lung, mouth…) this major role in our immunity, the intestinal microbiota, which we know best today, has a key role in our digestion. It draws from our food to feed itself. It allows the assimilation of nutrients, the fermentation of non-digestible residues, the synthesis of vitamins and amino acids as well as the elimination of stools via the contraction of the digestive tract.

At the same time, our intestine is closely linked to our central nervous system. This is known as the gut-brain axis. An imbalance in the intestinal microbiota could therefore modify the link with the brain and in return distort the information transmitted by the latter to the intestine, making both organs dysfunctional.

It is also known that the gut microbiota regulates inflammation, which is the cause of chronic diseases. The intestinal flora, when it is balanced and varied, regulates the body PH of the tissues and mucous membranes, via the digestive wall. This is known as the acid-base balance, which is one of the major keys to maintaining health.

Finally, some studies have shown that our intestinal microorganisms modify the metabolism of our hormones, and in particular oestrogens, via hormone absorption and production pathways, again modulated by diet, stress, lifestyle etc.

What happens when the microbiota malfunctions?

Links have been described and validated between chronic inflammatory bowel disease, cardiovascular disease, diabetes, obesity, neuropsychological disorders and gut dysbiosis.

It was found that everything is linked to the digestive wall, also called the intestinal barrier.

When this is damaged (due to several factors mentioned earlier in the article), the cells of the digestive wall (enterocytes), instead of being well attached and welded together to form a solid barrier, end up moving away from each other. The wall then becomes permeable (porous, full of holes) and can no longer properly perform its absorption function (which can lead to deficiencies in iron, B vitamins, hormones, neurotransmitters such as serotonin, etc.), or its protective barrier function (immunity).

It is this intestinal hyperpermeability that causes inflammation; first locally (causing abdominal pain, digestive problems etc.), then globally (causing fatigue, joint pain, migraines, menstrual cycle problems, sleep problems etc.). Once the inflammation has set in, a vicious circle begins, with a reduction in the immune system, malabsorption (causing deficiencies), a change in the body’s pH and then a dysbiosis. Pathogenic (pro-inflammatory) micro-organisms increase and non-pathogenic (anti-inflammatory) bacteria decrease. This is the beginning of the inflammatory disease which will then become chronic if nothing is done.

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How to preserve your microbiota and take care of it when it is dysfunctional ?

The first step in caring for your microbiota is to understand what has damaged it. It is essential to identify the factor(s) that have damaged the digestive tract so that it can be restored. Certain tests and analyses (blood and stool) exist to identify problems with the microbiota. Is it a problem related to diet, stress, sedentary lifestyle, hormonal regulation, infection? Depending on this, we set up a treatment adapted to the problem: anti-inflammatory diet, detection and then avoidance of food intolerances, treatment of pathogens, healing of the intestinal barrier (based on amino acids, pre- and post-biotics), management of stress and emotions, regulation of hormonal variations etc.

Many therapeutic options exist, particularly in alternative medicine. Health food, micronutrition, phytotherapy, aromatherapy… offer very effective solutions to soothe inflammation, and help the microbiota to restore itself.

However, as always in health, one of the keys lies not in therapy (treating diseases once they have set in), but in prevention. It is essential to put in place a global, holistic lifestyle beforehand, which would prevent the appearance of inflammation and therefore inflammatory pathologies.

Dr Marine Crest-GuilluySpecialist in micronutrition and in the management of disorders related to the intestinal microbiota


Written and scientifically validated by Dr Marine Crest-Guilluy

Editor-in-chief of the SNJMG magazine for several years, she has defended interns in general medicine and has written a book to testify to the conditions of their training.
A graduate in medical psychology, she is an expert in “burn-out” and is trying to have this pathology, to which doctors are particularly vulnerable, recognised.

Dr Marine Crest-Guilluy is also specialised in micronutrition and in the treatment of disorders related to the intestinal microbiota.

Having a global approach to the patient, she ensures a follow-up in integrative and functional medicine.

Dr Marine Crest-Guilly offers conventional allopathic treatment but also complementary therapies such as aromatherapy, phytotherapy, gemmotherapy and oligotherapy.


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