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Intestinal Microbiota: Functions and Its Importance for Health

Intestinal Microbiota: Functions and Its Importance for Health

Published: 13 June, 2024 | 13'

As we have seen in previous articles, we know that the microbiota is the set of microorganisms that colonize our body and are present in both the skin and mucous membranes, be it in the gastrointestinal tract, respiratory system, genitourinary or vaginal area, among others. There are different bacterial communities or microbiotas, all relevant to our well-being and health.

One of them, perhaps the most widely known, is the intestinal microbiota. In this article, we explore with biologist and nutrition doctor, Rita Cava, the different functions of the intestinal microbiota and how to take care of it.

What is the intestinal microbiota?

The intestinal microbiota is considered the most important for maintaining our health, and it comprises the largest number of symbiotic or mutualistic microorganisms in the body.

As biologist and nutrition doctor, Rita Cava, explains: "The gastrointestinal mucosa can house up to 1014 bacteria in its 400 m2 of surface area, increasing bacterial colonization from the stomach to the colon"."

Composition of the intestinal microbiota

In general, the intestinal microbiota is composed of 6 bacterial groups: Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia, of which Firmicutes and Bacteroidetes are the main ones; fungi and some viruses are also present.

Intestinal bacteria perform functions such as food fermentation, protection against pathogens, stimulation of the immune response, and vitamin production.

"Any imbalance in the composition and/or functions of the intestinal microbiota causes what is called disbiosis, which directly affects general health", explains biologist and nutrition doctor, Rita Cava. On the other hand, if the microbiota shows stability, resistance, and symbiotic interaction in our intestines, it is called eubiosis ("healthy conditions").

Functions of the intestinal microbiota

The intestinal microbiota is closely involved in nutrient extraction, metabolism, and immunity. Let's take a detailed look at some of its functions.

Barrier against pathogens. Prevent colonization by other pathogenic microorganisms

One of the main functions of the microbiota is preventing the colonization of pathogenic microorganisms. It does this through a series of mechanisms at its disposal, as explained by Dr. Cava:

  • "Resistance to colonization or competitive exclusion: the intestinal microbiota can exclude pathogens due to competition for nutrients and/or stimulate the direct emission of antimicrobial substances."
  • Immunomodulation: the intestinal microbiota produces defensins and other antimicrobial substances that eliminate pathogens directly. It also stimulates the immune system, which recognizes the pathogen's antigens and initiates a cascade of immune responses for its destruction.
  • Coaggregation with pathogens: Some microorganisms in the intestinal microbiota can bind to the pathogen and prevent its adhesion to the intestinal mucosa.
  • Tissue integrity: the microbiota is associated with intestinal tissue cells (Paneth cells) that "monitor" the tissue structure and, in case of gaps, produce antimicrobial substances.

Digestion and nutrition: helping with food digestion

The intestinal microbiota plays a key role in the digestive process. "The ingested food is partly degraded by the enzymes of the gastrointestinal tract in order to facilitate its absorption; the other undigested part is substrate for the metabolic activity of the intestinal microbiota, especially in the colon," explains the specialist.

Here are some of the metabolic processes carried out by the intestinal microbiota:

  • Fermentation of complex carbohydrates (such as starch and fibers), which generates short-chain fatty acids (i.e. propionate, butyrate) that are used as an energy source by both the microbiota and intestinal cells and also enter the circulatory system where they are distributed to different organs.
  • Regulation of lipid storage, which is why its role in obesity and metabolic syndrome is currently of interest and under study.
  • Transformation of inactive dietary compounds into bioactive molecules; an example is the transformation of some soy isoflavones into compounds with estrogenic activity such as equol.

Regulation of metabolism: energy and microbiota

The intestinal microbiota plays a fundamental role in the path that nutrients take once they are absorbed in our body.

The products of the fermentation of the intestinal microbiota are varied, however, the most important ones are short-chain fatty acids (SCFAs), which provide at least 10% of our daily energy needs.

These fatty acids (acetate, propionate, and butyrate) perform actions that directly influence the main metabolic processes of our body:

  • Acetate is the most abundant of the three and is an essential metabolite for bacterial growth. As mentioned before, it is distributed to organs in our body where it is used in the metabolism of cholesterol and lipogenesis (production of fatty acids), as well as in gluconeogenesis (production of sugars), and it may play a role in the central regulation of appetite. Several clinical studies have established a clear correlation between acetate concentration and reduced diet-induced obesity and decreased insulin resistance.
  • Propionate is transferred to the liver, where it regulates sugar production and satiety through a complex system of signals that interact with the fatty acid content in the intestine and the associated microbiota. Propionate, along with butyrate, can also regulate intestinal and immune function.
  • Butyrate is the main energy source for the cells that form the large intestine (colonocytes). This fatty acid not only regulates cellular regenerative cycle, but also activates sugar production within the intestine (gluconeogenesis), which has beneficial effects on glucose levels and energy balance. Butyrate also participates in the regulation of the oxygen level within the intestinal environment and proinflammatory factors, serving as a preventative mechanism against dysbiosis of the intestinal microbiota. Both butyrate and propionate appear to control intestinal hormones and reduce appetite and food intake.

Production of B and K vitamins

In addition to SCFA production, the intestinal microbiota produces other micronutrients such as vitamins, which provide countless benefits to both human metabolism and the microorganisms themselves.

The intestinal microbiota is a source of B-group vitamins, especially biotin (B7), pantothenic acid (B5), folic acid (B9), and vitamin B12.

They are primarily produced in the large intestine by bifidobacteria. "Although the microbiota produces B vitamins, the amounts produced are not enough to meet daily requirements, so it is recommended to obtain them through food," notes Dr. Cava.

Vitamin K (menaquinone) is another vitamin produced by the microbiota in the large intestine, specifically by genera such as Bacteroides, Eubacterium, Enterobacter, among others. "Although it has been shown that significant amounts of menaquinones are produced in the intestine, absorption from this source is not sufficient to meet the quantities necessary for all the metabolic processes of our body," the specialist points out.

The intestinal microbiota is also capable of generating amino acids from substances such as ammonia and urea.

Maintenance of the immune system: microscopic allies

The immune system consists of two systems of interactive responses: innate immunity (present from birth) and adaptive immunity (acquired through previous exposure), and it has been demonstrated that both interact extensively with the microbiota.

"This interaction is bidirectional," explains Cava: "this means that immune system signals can affect the intestinal microbiota, and vice versa, the intestinal microbiota can also affect the immune system."

Let's see how the intestinal microbiota interacts with both immune responses.

  • Innate immune response: the effects of the microbiota on the innate immune response are mediated by modulation of the immune tissue of the intestine (lymphoid tissue) and the inflammatory process, the release of immunoglobulins (such as IgA), and other immune cells, and the secretion of metabolites (tryptophan, indoles, butyrate). These stimuli activate both the barrier functions previously described and the production of other mediators that regulate and coordinate the response of immune cells to prevent pathogen invasion. Specifically, the microbiota ensures the structure of the intestinal tissue, preventing the penetration of pathogenic agents, as well as excessive immune activation and general inflammation, which can cause what is known as intestinal permeability.
  • Adaptive immune response: the microbiota regulates the adaptive immune response by differentiating and maturing B and T cells (types of white blood cells), their relocation to the site of infection, and also modulates associated inflammatory activity, preserving intestinal barrier function. The actions of the immune cells of the adaptive response vary significantly, as they directly depend on the type of bacterial species that originated them.

Neuroendocrine regulation

The metabolic activity of the intestinal microbiota generates endocrine and nervous signals that act on the nervous system, where it can modulate cognitive functions, mood, and behavior.

This axis of action of the intestinal microbiota is called the microbiota-gut-brain axis. Some examples include:

  • The intestinal microbiota stimulates the production, activity, and turnover of neurotransmitters such as serotonin, GABA, and catecholamines (adrenaline and noradrenaline), which in turn can regulate intestinal activity. An example of this interaction is the production by intestinal microorganisms of the amino acid tryptophan, a precursor to serotonin, which is involved in mood regulation; in turn, the action of serotonin contributes to the integrity of the intestinal barrier, regulating intestinal permeability and mucosal immune response.


  • Intestinal production of short-chain fatty acids (SCFAs) stimulates the production of a type of metabolites (intestinal endocrine hormones) that modulate glucose metabolism, insulin sensitivity, thermogenesis, and appetite, and these effects are exerted on the liver, adipose tissue, and nervous system.
  • The microbiota also regulates the secretion by intestinal cells of glucocorticoids, which participate in anti-inflammatory activity, cholesterol metabolism and modulate insulin uptake by cells.

Maintenance and regeneration of the intestinal mucosa

The muconutritive microbiota plays a fundamental role in the maintenance of the integrity of the epithelial barrier, of the layer of mucin that lines the intestinal mucosa, as well as the mucous layer itself, which is essential for defense against pathogens, preventing the penetration of inflammatory components from the diet and serving as food for many other microorganisms in the microbiota.

What can alter the intestinal microbiota?

An imbalance in the intestinal microbiota leads to the so-called dysbiosis. External factors such as the use of antibiotics and other medications, stress, genetic factors, diet, and lifestyle have been implicated in the origin of dysbiosis.

In fact, Rita Cava points out: “this aspect is so important that dysbiosis in a pregnant woman can affect the type of microbiota transferred to the fetus, and thus the development of innate immunity, which can have possible short- and long-term consequences.

When the microbiota becomes imbalanced: implications for health

As we can see, dysbiosis or imbalances in the intestinal microbiota lead to the inappropriate selection of some microorganisms (i.e., overgrowth of the bacterial genus Clostridium) or promote the colonization of pathogens, negatively affecting the health of our body.

If the triggering factor is intense or persistent over time, the process can lead to disease, generally of a chronic or recurrent nature and with an inflammatory pattern”, says the expert.

Let's take a look at some cases:

  • Obesity: Data from studies conducted in obese individuals shows dysbiosis characterized by reduced microbial diversity in the intestinal microbiota (i.e., an increase in Firmicutes and a reduction in Bacteroidetes), which leads to an increase in adipose or fatty tissue due to increased energy extraction from a diet that is typically high in fats and sugars. Additionally, the intestinal barrier is affected, resulting in a high concentration of antigens that stimulate the immune system and the development of insulin resistance. Some studies also indicate that the metabolic activity of the "obese microbiota" sends specific markers to the nervous system, which appears to alter food preferences (i.e., altered taste receptors for fats and sweets).
  • Cardiovascular System: Modification of the intestinal microbiota leads to a disruption in its metabolic activity, reducing the production of SCFAs and generating an increase in non-beneficial metabolites (i.e., TMAO) that negatively affect cardiovascular function. Reduction in SCFA levels (acetate, butyrate, and propionate) causes imbalances in cholesterol metabolism, inflammation control, and intestinal barrier integrity, resulting in elevated blood lipids and dysfunctions in blood vessels that can raise blood pressure. Likewise, metabolites such as TMAO affect the regulation of the immune response, inflammation, and cholesterol, leading to
  • Gastrointestinal System: Dysbiosis of the intestinal microbiota is also implicated in the development of gastrointestinal diseases. One of the most common is Inflammatory Bowel Disease (IBD), in which the ratio between Bacteroidetes and Firmicutes decreases, causing local inflammation, dysregulation of the immune response, and impairment of intestinal barrier function caused by SCFA deficiency. The impairment of the intestinal mucosa barrier function (intestinal permeability) also leads to an increase in mucolytic intestinal microbial species (which alter tissue integrity and reduce mucous viscosity), further aggravating functionality and stimulating a severe inflammatory response.

How to care for and nurture your intestinal microbiota?

The quote from Hippocrates «let food be thy medicine and medicine be thy food», as well as the phrase from the German philosopher Feuerbach «we are what we eat», provide the perfect framework for understanding how diet influences our overall health.

Within the framework of maintaining a healthy intestinal system, "there are several dietary strategies that modulate the composition or metabolic and immunological activity of the intestinal microbiota, which can be useful with the help of a specialist," says the expert.

Let's take a look at some of the most well-known strategies.

Probiotics and prebiotics: reinforcing your flora

Probiotics and prebiotics are currently the most investigated and used functional ingredients for modulating the microbiota. They are frequently used as dietary supplements for oral intake, and differences in dosing and individual characteristics are the main factors that affect their effectiveness.

Now, let's see what each one is and how they benefit the health of the intestinal microbiota.

  • Prebiotics: defined by the FAO as "a non-viable food component that confers a health benefit on the host associated with modulation of the microbiota".

The fermentation of carbohydrates is a fundamental activity of the intestinal microbiota, and prebiotics are a specific type of dietary fiber whose fermentation by the microbiota stimulates measurable changes in its composition. This usually leads to an increase in the relative abundance of beneficial bacteria (bifidobacteria or certain butyrate-producing bacteria), as well as a reduction in intestinal transit time, an increase in fecal bulk, and the number of bowel movements.

The most well-known prebiotics are inulin, fructooligosaccharides (FOS), lactulose, and galactooligosaccharides (GOS). Lactulose (a disaccharide of galactose and fructose) and lactitol (galactose and a glucose-derived polyalcohol) are also used. They are found in milk, vegetables, fruits, cereals, legumes, and nuts.

  • Probiotics: are defined, both by FAO and WHO, as "live microorganisms that, when consumed in appropriate amounts as part of a food, confer a health benefit on the host."

The most commonly used microorganisms as probiotics are yeasts (e.g., Saccharomyces) and bacteria from different genera (Lactobacillus, Enterococcus, Bifidobacterium, Propionibacterium, among others). Using probiotics has benefits such as the reversal of digestive symptoms (such as lactose intolerance) and the restoration of normal intestinal microbiota (e.g., diarrhea caused by rotavirus), among others.

Gut-friendly diets

The diet is one of the most crucial factors in the composition of the intestinal microbiota. By making modifications to the ingredients of the diet alone, changes in the composition of the microbiota can be achieved within 2 days.

In general, diets characterized by low fiber intake, high intake of saturated fats, high protein content, refined grains, sugar, salt, among others, result in a lower total amount of bacteria, specifically of beneficial species such as Lactobacillus spp. and Bifidobacterium spp.

As explained by specialist Rita Cava: "this promotes inflammation, causing intestinal permeability, the production of toxic metabolites, alterations in blood lipid and glucose levels, and immune responses."

What would be the most beneficial diets for maintaining or restoring the intestinal microbiota?

The Mediterranean diet is well-known as one of the healthiest dietary patterns due to its low intake of saturated fats and high intake of monounsaturated fats and polyunsaturated fatty acids (including olive oil and fish), the consumption of antioxidants from fruits and vegetables, a high intake of plant-based fiber (vegetables, whole grains, legumes, and nuts), and a low intake of protein from land animals, especially red meats. Under this dietary scheme, the intestinal microbiota is abundant in Lactobacillus spp., Bifidobacterium spp., and Prevotella spp., bacteria directly related to weight modulation and improvement of lipid and cholesterol profiles. In contrast, the presence of Clostridium spp. and certain enterobacteria is reduced, preventing inflammatory events.

This diet excludes foods that can negatively affect the diversity and quantity of the intestinal microbiota, increase intestinal permeability, and alter the mucous layer. These foods include high-fat and animal protein-containing foods, refined flours, and simple sugars typical of the Western diet (i.e., fast food and soft drinks). To avoid this, it recommends the intake of fruits and vegetables, resistant starches, certain proteins, omega-3 polyunsaturated fatty acids, among others, which promote a low-inflammatory environment, preserving the integrity of the intestinal structure and the stability of the intestinal microbiota.

These diets include plant-based foods (with the reduction or complete elimination of animal-based foods) with a high content of complex carbohydrates, which are the primary substrate for the metabolism of the intestinal microbiota. The abundance of fiber in these diets promotes the stability, maintenance, and diversity of intestinal bacteria. In addition, the inclusion of polyphenols (e.g., from tea, coffee, berries, and vegetables such as artichokes, olives, and asparagus) in this dietary strategy has been shown to have a beneficial effect on the presence of the following bacteria: Bifidobacterium spp. and Lactobacillus spp., which contribute to intestinal barrier function, and butyrate-producing bacteria such as Faecalibacterium prausnitzii and Bacteroides vulgatus, among others. This diet also regulates the bacterial populations of Escherichia coli and Enterobacter cloacae, which can induce inflammation.

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Content created by the specialists from the Scientific Information area of MARNYS in collaboration with Dr. Rita Cava. This article is informative and does not replace the consultation with a specialist.

Rita CavaAbout the Specialist

Dr. Rita Cava Roda, Biologist and PhD in Nutrition and Food Technology. University professor with over 20 years of experience in research and teaching, as well as a nutritionist and dietitian.