Intestinal microbiota: what it is, how it affects health, what to eat to keep it healthy

Intestinal microbiota: what it is, how it affects health, what to eat to keep it healthy

The human intestinal mycorbiota is that complex of microorganisms that live in our intestines, which is therefore not a sterile environment. These are mainly bacteria and fungi belonging to different species, more or less numerous. Their relationship is essential to maintain good bowel regularity and proper functioning of our metabolism.

In fact, the intestinal microbiota performs numerous activities that help keep our intestines in good health. A healthy microbiota is useful, for example, to strengthen the immune system and protects against the action of pathogenic microorganisms. It is also needed to digest dietary fiber and its presence improves the absorption of some nutrients.

An unhealthy lifestyle and an unbalanced diet can affect the composition of the intestinal microbiota. This alteration is called dysbiosis and has negative consequences on the activity of our intestines and beyond. Hence, to help the metabolism it is important to keep it healthy. Let’s see in detail what is meant by intestinal microbiota and how to keep it healthy.

What is the intestinal microbiota for and where is it found?

The gut microbiota, also known as the intestinal flora, is the community of microorganisms that live in our intestinal tract. This microbial ecosystem includes a wide range of bacteria, viruses, fungi and other organisms, which interact with each other and with our body in complex ways. The whole human body, except the brain and the circulatory system, hosts microorganisms of various kinds, for a total of more than 38,000 billion species.

The digestive system, however, is the most populated district. This is because the intestine, from an anatomical point of view, constitutes a hollow tube, in communication with the outside.

It performs numerous tasks that are very important to our health and well-being. Here are some of its main functions:

  • Digestion and Metabolism: Gut bacteria help break down complex foods that our bodies cannot digest on their own. They produce enzymes that help break down fiber, carbohydrates and other substances, allowing us to extract nutrients and energy from the foods we eat.
  • Immune system support: the intestinal microbiota plays a fundamental role in maintaining the immune system. Intestinal bacteria interact with immune cells, helping to keep our defenses balanced. In fact, a healthy microbiota can help prevent autoimmune diseases and allergies.
  • Intestinal barrier and gut health: Helps maintain the protective barrier of the gut. In fact, beneficial bacteria produce substances that help maintain the integrity of the intestinal wall, preventing harmful substances from entering the bloodstream.
  • Production of vitamins and beneficial substances: some intestinal bacteria are able to synthesize vitamins that are important for our body, such as vitamin K and some B vitamins. Furthermore, they also produce very useful compounds, such as short-chain fatty acids, which can positively affect health.
  • Weight and metabolism regulation: The gut microbiota is involved in the regulation of body weight and metabolism. Some studies have highlighted a correlation between microbiota composition and obesity, suggesting a possible role of gut bacteria in weight gain or loss.
  • Gut-Brain Communication: According to studies, there is a two-way communication between the gut and the brain, known as the “gut-brain axis.” The gut microbiota is part of this communication by influencing neurotransmitters and the central nervous system, also having an effect on mood, stress and mental health.
  • Inflammation regulation: A healthy microbiota helps maintain controlled and balanced inflammation, protecting against the excessive inflammatory response that can lead to ailments such as colitis.
  • Metabolism of xenobiotics: The gut microbiota is involved in the metabolization of foreign substances called xenobiotics, including drugs, environmental toxins, and chemical compounds found in the diet. Gut bacteria can then transform these substances into less toxic or inactive compounds.

The gut microbiota is influenced by several factors, including age, diet, lifestyle, antibiotic use, stress, and genetics. Its balance is closely linked to our general state of health and can be achieved through a diet rich in dietary fiber, probiotic and prebiotic foods, as well as a healthy lifestyle.

Microbiota or microbiome?

Microbiota and microbiome are two terms that are often mistakenly used interchangeably.

There’s no need to get confused. In fact, although very similar, they contain a very different meaning. Let’s see it in summary.

  • The microbiota is the set of microorganisms. Identify the bacteria, yeasts, viruses, or parasites that coexist on surfaces or in the mucous membranes of our bodies. Based on the body district that they colonize, we can distinguish it into “intestinal microbiota”, “vaginal microbiota”, “skin microbiota”, etc.
  • The microbiome is instead the set of genetic material of microorganisms (microbiota). That is, it is formed by genes, molecules of DNA or RNA.

The microbiota therefore refers to organisms endowed with genetic material, capable of carrying out biological activity and reproducing. Instead, the microbiome only considers the presence of microbial genetic material. It is therefore indicative of the presence, or not, of a DNA or RNA molecule, but does not consider the interactions between microbial species.

What is the intestinal microbiota made up of?

Each of us has an intestinal microbiota with a different composition, in terms of number of microorganisms and species.

It is therefore said that everyone has a sort of microbial fingerprint, that is, a species profile different from that of other individuals. In fact, the microbiota is acquired at the time of delivery, by contact with the mother’s vaginal microbiota.

Later it changes thanks to environmental factors and individual habits. The organ mainly affected by the colonization of microorganisms is the large intestine. Here is settled a community that has more than a thousand species. These coexist with other microorganisms belonging to different taxonomic groups.


The dominant groups are predominantly the Bacteroidetes and the Firmicutes, which together constitute more than 90% of the species present in the human intestine. To these are added some exponents of the Proteobacteria and the Archaea. Everyone is almost “specialized” in precise tasks. For example, Bacteroidetes possess hydrolytic enzymes capable of digesting dietary fibers, simple sugars and alcohols, which otherwise we would not be able to dispose of.

Firmicutes, on the other hand, are mainly responsible for the production of butyrate, a molecule with anti-inflammatory activity for the intestine. Among the Proteobacteria, the best known is Escherichia coli, a bacterium beneficial for intestinal balance, of which there are also pathogenic subspecies. Finally, the Aarchea, which in our intestines contribute to the digestion of dietary fibers, with the production of methane.


Viruses, free in the environment, can reach our intestines. Those that actively participate in intestinal balance are mainly bacteriophages, i.e. viruses capable of attacking pathogenic bacteria. Thus, they help defend our body from infections.

Intestinal microbiota alterations: causes and consequences

There is no mathematical formula for the right ratio of species that should be present in the human intestine. The ratio of gut microbial species varies over time and depends largely on the maternal microbiota.

Indeed, during intrauterine life, the intestine of the fetus is completely sterile. With natural birth, the mother’s vaginal microbiota determines the makeup of the baby’s “starter” microbiota. Instead, with cesarean delivery, breastfeeding and other environmental factors have a lot of influence.

This first microbiota will be the one that will accompany the child in the growth stages. An imbalance in this phase of life can be responsible for conditions such as childhood obesity, as well as the onset of food allergies and intolerances in childhood.

Diagnosis: the intestinal microbiota test

Gut microbiota testing, also known as fecal microbiota analysis, is a test that evaluates the composition and diversity of bacteria and other microorganisms present in the intestinal tract. This type of test can provide useful information on intestinal health and the state of the microbiota.

It usually involves collecting a stool sample for laboratory testing. The analyzes can include different methodologies, such as DNA or RNA sequencing, which allow for the identification and quantification of the different bacterial strains and other microorganisms present in the faecal sample.

Through the test it is possible to obtain information on microbial diversity, on the presence of beneficial and pathogenic bacteria, on the balance between the different bacterial groups and on the presence of markers of inflammation or intestinal dysbiosis. This information may be useful for better understanding intestinal health and evaluating the need for therapeutic interventions or dietary and lifestyle modifications.

However, the intestinal microbiota test is a rather recent and constantly evolving analysis….