Everything you ever wanted to know about microbiota

You hardly spend a day without hearing about microbiota, but you still wonder what it is exactly and what it does for you?
Here you will find all the information you need to understand all this and learn how to take care of your microbiota.

What is microbiota?

The word “microbiota” defines the wide variety of microorganisms that lives in the same environment. Not to be confused with the “microbiome” which refers to the collective genome of the microorganisms in this same environment. Your microbiota includes all kinds of microorganisms: bacteria, viruses, fungi, yeasts, and protozoa. Humans host and cohabit with more than 100,000 billion1 of these microorganisms distributed within their different microbiota. They are located in the mouth, skin, lungs, vagina and gut. The latter, the intestinal microbiota, also called « intestinal flora », is not only the best known but also the richest.
What is microbiota?

Your intestinal microbiota in figures:

Everyone has its own combination of species among more than 1000 species, so it can be very different from one person to another. Therefore, remember that the composition of your gut microbiota is unique!

These variations can be explained by the fact that the microbiota of an individual evolves over time according to its lifestyle. Before birth, babies’ microbiota is not yet constituted3. The development phase of the intestinal microbiota takes place during the first 3 years of life.

Its diversification depends on several factors such as the type of delivery, breastfeeding, food diversification, etc. After this first phase, the composition of the microbiota stabilizes and remains relatively stable for the rest of its life.

The composition of the intestinal microbiota in adulthood is therefore strongly dependent on the diet and environment that the individual experienced during its early childhood. Certain events can nevertheless modify the composition of the adult microbiota, such as infections, the taking of medication such as antibiotics or a change in diet4.

With age, the microbiota tends to become slightly poorer and less diverse.

microbiota life
A diversified microbiota is essential for health throughout life. The influence of the intestinal microbiota on health has been widely demonstrated: maintaining its balance is essential. Maintaining both a diverse balance of different species and the microbiota that is right for the individual is essential for a healthy functioning. Links between the disruption of this balance, called dysbiosis, and certain diseases have also been demonstrated. Thus, taking care of your microbiota is key. Adopting a diverse and balanced diet is the best way to do so but taking “biotics” can be a great solution as well. Biotics (prebiotics, probiotics, synbiotics, postbiotics) are elements that are favorable to the life of the microbiota, they can be found directly in the food or in the form of supplements and drugs.

What does the gut microbiota do?

By definition, a SYMBIOSIS  refers to an interaction between two different organisms living in close physical association with mutual benefits5. Easy to understand that, we are in symbiosis with our microbiota. We serve as its support and provide it with food. But what does it do for us in return?


One of the main functions of the intestinal microbiota is its participation in digestion. On our own, we are not able to digest the insoluble fibers present in our food because we do not have the enzymes necessary to break them down. This is where the bacteria of our intestinal microbiota come to our aid.

They feed on these fibers and digest them by producing compounds called « short-chain fatty acids », nutrients that our cells use in turn as a source of energy and which would have beneficial effects on our health. The microbiota also participates in the proper absorption of certain nutrients and in the synthesis of some metabolites that are essential to the body.


The second essential function that the microbiota performs for its host: the role of a protective barrier. Whether it is the skin or intestinal microbiota, our microbiota forms an additional shield to fight against the invasion of pathogenic microorganisms.


The intestinal microbiota is also a key player in our immunity. At birth, the intestinal microbiota participates in the development of the intestinal immune system. Subsequently, together with the intestinal mucosa and the immune system, it constitutes the triptych of the intestinal immunity base. The microbiota colonizes the intestinal mucosa and prevents the installation of pathogenic bacteria by competing with them for access to nutrients. In brief, the microbiota helps to stimulate and develop the immune system.


Inflammation, which is directly linked to immunity, is also one of the areas in which our intestinal microbiota is involved. Inflammation is the defense reaction of our immune system to aggression. If the involvement of the microbiota in this phenomenon leaves little doubt but its exact role remains uncertain and is still under study. Just like inflammation, there is still a lot of uncertainty and things to discover about the influence of microbiota on our health. Research is now looking into the links it may have with some diseases such as diabetes, obesity, or even Alzheimer’s and the results never cease to amaze the scientists. Far from being restricted to digestive health, the microbiota is a key element of health in a very global way.

Why can our microbiota be unbalanced?

The health of the microbiota relies on maintaining a good balance between all the species that make it up. Indeed, within this ecosystem, some bacteria are considered « good » bacteria while others can have negative effects on health. Various factors can cause a temporary imbalance in the microbiota, but the microbiota has a resilient capacity that allows it to return to its original state of equilibrium within a few weeks. Problems arise when the imbalance persists and pathogenic bacteria take over the others, which is called dysbiosis.

Several factors can be at the origin of this state of imbalance:

An unbalanced diet,
too rich in sugars and fats

Infections, especially
digestive infections

Certain medications
such as antibiotics

Stress & anxiety


Alcohol and tobacco


Dysbiosis can manifest itself through:

No doubt about it, our microbiota influences our health at all levels!

How to balance your microbiota?

Here are some key tips for taking care of the balance of your gut microbiota:

1. Institut Pasteur, dossier : microbiote, vers une révolution thérapeutique, 2020
2. INSERM, Microbiote intestinal, 2016
3. Selma-Royo, Marta et al. “Shaping Microbiota During the First 1000 Days of Life.” Advances in experimental medicine and biology vol. 1125 (2019): 3-24. doi:10.1007/5584_2018_312
4. Mills, Susan et al. “Precision Nutrition and the Microbiome, Part I: Current State of the Science.” Nutrients vol. 11,4 923. 24 Apr. 2019, doi:10.3390/nu11040923
5. Oxford Languages. Symbiosis, 2020.
6. Pascal V, Pozuelo M, Borruel N, et al. A microbial signature for Crohn’s disease. Gut. 2017;66:813-22.
7. Liang S, Wu X, Hu X, Wang T, Jin F. Recognizing Depression from the Microbiota⁻Gut⁻Brain Axis. Int J Mol Sci. 2018 May 29;19(6):1592. doi: 10.3390/ijms19061592.
PMID: 29843470; PMCID: PMC6032096.