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The gastrointestinal microbiota

Your gastrointestinal microbiota consists of all of the microorganisms that populate your intestines.
The equilibrium between bacteria, yeasts, fungi, and other microorganisms is fundamental to your health.

The equilibrial composition of gastrointestinal microbiota


Knowledge about intestinal microbiota, or gut flora, has improved through the use of new identification techniques based on studying the genes (DNA) of the microorganisms that populate the intestines. It is now estimated that hundreds of species of bacteria make up the intestinal microbiota. They are divided between dominant species, more rare species, and transitory species that circulate throughout the digestive tract. The colon, also called the large intestine, can have up to ten thousand billion bacteria, or as many as the number of cells in your body. That means your colon is one of the most densely populated ecosystems in the world! Certain potentially dangerous bacteria can be present in small numbers without any illness arising. Bacteriophages—viruses that only infect bacteria—are also found in the intestine. There are ten to a hundred times more of them than the most represented bacteria. Yeasts, fungi, and even parasites also cohabit in this densely-packed area..

Composition regulated by diet

The dominant microbiota is a “signature” for each individual. Only a tiny fraction of the species are widely shared in the human population: around 60 bacterial species are carried by 50% of individuals in the same geographic area. Although it is still being debated, it is suggested that there are three different types of bacterial composition (enterotypes). These groups define your “intestinal ecology” and are related, at least in part, to your dietary habits: one of them is linked to a Western diet rich in sugar and animal fats and another is associated with a significant consumption of fruit and vegetables. As microbiota can be deliberately regulated, it is imperative that it be done intelligently to preserve symbiosis, i.e. a harmonious relationship between your bacteria and your intestine: your health depends on the diversity of your microbiota!

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From 0 to 3 years, children’s microbiota diversifies.


Until adult age, intestinal microbiota diversifies, then stabilizes.


As we age, microbiota becomes slightly impoverished.

The microorganisms in your intestines, primarily bacteria, form a “partnership” with them that starts right at birth. It takes around three years for gastrointestinal microbiota to build up, before a period of relative stability until old age when it undergoes profound changes again.

The digestive system of a newborn is quickly colonized by “simple” microbiota, originating from their mother’s vaginal and fecal bacteria. Breastfeeding provides favorable bacteria, such as bifidobacteria, but intestinal microbiota takes around three years to stabilize. This stabilization depends on numerous factors. For example, anaerobic bacteria, which don’t need oxygen to survive, are in the minority in infants but are dominant in adults. The development of these anaerobic bacteria is slower when birth is by caesarian section or premature and microbiota is less diverse than in infants born vaginally at full-term. The diversity of microbiota also depends on the early childhood environment: less diversity has been observed in Westernized countries, which may be linked to overactive hygiene. Gastrointestinal microbiota is enhanced over the years, but it always retains the imprint of the early childhood profile. Less microbial diversity can lead to potentially long-term illness.

A loss of diversity in the elderly

In adulthood, few factors can radically change the dominant microbiota aside from hormonal variations during puberty, pregnancy, and menopause. But it is in old-age that variations become more pronounced. Microbiota is impoverished by physiological changes, such as a reduction in immunity, a less varied diet, taking numerous medications including antibiotics, and especially lifestyle, when people become less independent. In fact, elderly people living in retirement homes have more impoverished microbiota than those living at home and continuing with their usual diet. This profound change in the equilibrium of the microbiota can lead to illness, such as intestinal inflammation and increased sensitivity to infection.

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Functions of the microbiota

The microbiota can be considered to be a functional organ in the human body. It works closely with your intestines and plays different important roles. 

Healthy microbiota creates a strong partnership with your intestines: symbiosis. It controls functions both on a local and a systemic scale, meaning your entire body.

GP - Le role du microbiote Intestinal - EN

In episode 2 of MICROREVEAL, Julie is suffering from diarrhea. To help shed light on this issue, Louise Ekland asked Dr. Alexis Mosca – a pediatric gastroenterologist – about intestinal microbiota, an indispensable ally for our health.

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Role in intestinal metabolism

Intestinal microbiota executes metabolic functions that are essential to digestion. A small fraction of food is not digested when it leaves the small intestine and is fermented by microbiota in the colon. These fermentation processes produce gas and numerous metabolites, including short-chain fatty acids, a real “fuel” for the cells in your colon.

Defensive role

  • Barrier effect:
    Your intestine is confronted with a significant challenge: tolerating microbiota bacteria, which are beneficial, while, at the same time, effectively preventing dangerous bacteria, called pathogens, from colonizing. Microbiota acts as a barrier against pathogens. The “good” bacteria of the microbiota fight directly against pathogens by competing for the same nutrients. Furthermore, some bacteria release antimicrobial molecules against the pathogenic bacteria while others stimulate the production of mucus to protect intestinal cells from attacks and avoid harmful effects on your body.
  • Stimulation of the immune system:Bacteria of the intestinal flora are involved in the maturation and activation of cells in the intestinal immune system, which protects you from attacks by pathogenic agents like bacteria and viruses. The intestine is the primary reservoir for immune cells in your body. For its part, the immune system influences the composition and diversity of microbiota. 

Dysbiosis can disrupt this defensive role and lead to the development of disease.

Role of intestinal mucosa

Intestinal microbiota plays an important role in the maturation of the digestive tract, and in particular on the size and thickness of the intestinal mucosa, the production of mucus, the irrigation of intestinal cells, and the enzymatic activity of the mucosa.

Emerging functions

Recent studies have identified other roles for the microbiota. Some bacteria of the intestinal flora may protect against inflammatory and metabolic diseases while others may actually induce these diseases or even behavioral and neurological problems. Much more work is necessary to identify the mechanisms.


Disruption of the intestinal microbiota can cause disruptions affecting various areas of the human body.

Affecting the microbiota

There are five ways to affect the equilibrium of microbiota. Each of them has its own specific features.