The microbiota

[Article updated on 19/09/2023]

Microbiota comes from the Greek micro-“small” and -biota “life”. We previously called it the intestinal flora, it’s a bit like our little inner secret garden.

Before reading on

I’m not an expert in this field, but I am passionate about nutrition and health.

The articles you’ll find on my site are the result of in-depth research that I’d like to share with you. However, I would like to stress that I am not a health professional and that my advice should in no way replace that of a qualified physician. I’m here to guide you, but it’s important that you consult a professional for specific questions or medical concerns. Your well-being is important. So be sure to consult the appropriate experts and take the best possible care of yourself.

100,000 billion bacteria live in our intestine, 10 times more than cells in our body. We are a real ecosystem, with many “species” that coexist and help each other.

Each individual has a specific microbiota, and it is not comparable to that of its neighbor. This one is fragile. We are going to talk about our intestine, which we call “the second brain” and then the microbiota itself: our bacteria!

The belly our second brain

Perhaps even the first brain… when we observe a newborn, it is not their brain development that informs them of their primary needs, but their belly! Hunger wakes him up, crying can reflect colic or belching… Many expressions in our French language are linked to this second brain. Like: Stomach in knots, fear in your stomach, stomach in your socks… all these expressions demonstrate the link between brain and intestine.

The intestine is an intelligent organ, equipped with neurons, just like the brain. There are 200 million neurons lining our digestive tract. This intestine is very large, 6.5m on average and 250m² if unfolded (the size of a tennis court!)

These two nervous systems are connected by the vagus nerve and use the same neurotransmitters, therefore the same language! The stomach is then in direct relationship with emotions. Serotonin, for example, causes a feeling of well-being for the brain, and in the stomach, it manages the immune system. 95% of this serotonin will be produced and released into the blood by the intestine to reach the hypothalamus, which manages our emotions. The bacteria in our microbiota communicate with our cells and therefore, the messages influence our mood.

Also when the communication between the two brains presents an anomaly, we observe digestive pathologies, such as irritable bowel syndrome for example. Without cause or organic pathology. A failure between nerves and mucous membranes is then highlighted, so the neurons are much more sensitive in these patients.


The microbiota

We are an ecosystem, we have more bacterial DNA than human DNA!!

You should know that the richer the microbiota, the healthier we are, and vice versa.

These “microbes” help us on a daily basis because they act on:

  • Digestion and absorption
  • The production of short-chain fatty acids, which are anti-inflammatory
  • The production of vitamins K and B vitamins
  • Immunity (80% of our immune defenses are directed by our bacteria and arise from the microbiota)
  • The brain secretes substances
  • Safety because they make it possible to determine what is toxic for our body

Every week new studies are published on this subject. Today, there is a decline in the diversity of our bacteria which is linked to increased risks of developing chronic pathologies such as cardiovascular diseases and diabetes. And the results show the influence of bacteria in these diseases.

INRA is studying the genome of the microbiota (meta-ic program) with the aim of detecting the role of bacteria in obesity, for example; the study concluded that obese subjects presented weakened microbiota, particularly in the Akkermansia muciniphila strain.

Our microbiota has changed over time due to several factors


The more food has been industrialized, the more the microbiota has become poorer, because we consume less and less fiber. While these fibers are the main substrate for our bacteria.

Also, the increasingly frequent presence of food additives weakens the diversity of our microbiota. Like E433 E466 (additives authorized on the market) widely used for its emulsifying qualities but which has destructive consequences on intestinal bacteria.

This deficit in bacterial diversity creates increased risks of developing chronic pathologies.


Of course, they are essential in certain cases, but be careful with our microbiota, taking antibiotics can cause us to lose strains of bacteria in our intestine forever. Antibiotics eradicate pathogenic bacteria as well as non-pathogenic ones. We just need to use antibiotics better without overusing them.

Caesarean sections

Caesarean sections are becoming more and more common, in Brazil or China for example, some cities have cesarean section rates of 80 to 90%. With this procedure, the child does not swallow the vaginal bacteria from the journey. Even if the baby will subsequently develop his microbiota, by breastfeeding, by being in contact with others… he will not be able to catch up with the constitution that he would have created vaginally. And that won’t make up for it.

It is currently being studied to smear the newborn with vaginal bacteria. He suckles a sample taken from the mother’s vagina in order to constitute her flora.

Projects and the future

Microbiota transplantation

We count 29,000 deaths in the USA each year of people affected by a resistant bacteria: Clostridium difficile. Often after antibiotic therapy, the clostridium takes advantage of the space freed up in the flora following the treatments to settle there.

When all antibiotic treatments fail, this fecal transplant technique is then proposed. Compatible human stools are collected to treat patients. They then act like a medicine, in 24 hours the patients are cured. And this with a success rate of 94% for carriers of clostridium difficile, which is spectacular (compared to 30% with antibiotics). Success rates impossible to achieve with any medication. The transplant is done rectally or nasally (nasogastric tube). This technique is currently only authorized for clostridium difficile.

Global scourge: obesity

As studies show, obese patients have a weakened microbiota. The test on mice attests that the transplantation of a microbiota from a healthy mouse causes weight loss in obese mice. This avenue looks very promising, the case is also valid for diabetes.