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Microbiome, the medicine of the future

Updated: Jun 7, 2023

They are known as the defenses of our body, protection begins at birth, unfortunately the indiscriminate use of antibiotics and other aggressors has left us very unprotected. Find out how the knowledge in this new field is advancing.


Research and knowledge regarding the microbiome are rapidly advancing, representing the latest step towards personalized medicine. It is like a unique fingerprint that each individual has in their microbiome.

The microbiome consists mostly of beneficial microorganisms such as bacteria, viruses, and protozoa, which inhabit our bodies and perform a wide range of essential functions for our survival and health.

The microbiome varies depending on the body part it inhabits: skin, feces, vagina, mouth. It is influenced by factors such as the individual's location, age, and diet.

Around 70% of the cells in our body are microbes, while the remaining 30% are human cells. Microbes contribute to 2 million genes, whereas humans only have about 2% of the total genes.

The nasal cavity contains 10 g of microbiome, the mouth 20 g, the vagina 20 g, the skin 200 g, and the intestines 1,000 g.

Among its functions are:

  • They control appetite and satiety.

  • The immune system.

  • Mood and emotions.

  • Anxiety.

  • Learning and memory capacity.

  • Where the protection of the microbiome begins.

It starts from birth. Kjersti Aagaard Tillery from Baylor College of Medicine in Houston, Texas, found that the composition of microorganisms residing in the vagina changes during pregnancy: Lactobacillus johnsonii, a bacteria that produces digestive enzymes and is normally found in the intestines, begins to proliferate. Thus, during a normal delivery, the baby will be exposed to this and other microbes that prepare them to digest breast milk, which harbors over 600 species of bacteria, as confirmed in another study by Khaterine M. Hunt from the University of Idaho, United States.

The bacteria we acquire at birth form communities that stay with us throughout our lives; they change as they adapt to the development of our bodies and the conditions we encounter, such as humidity, temperature, what we eat, and the medications we take.

Children born by cesarean section will obtain a microbiome from their mother's skin and will be more prone to diseases such as asthma, allergies, and even obesity. All other mammals are born through the normal birth canal.


It is within the scope of the Human Microbiome Project (HMP), which revealed over 5,000,000 bacterial genes that were mixed with human genes. The HMP is a research program that started in 2007 with the aim of constructing a genetic catalog or map of microorganisms.

That is why the composition of the microbiome is unique to each individual. When the results of the HMP were announced, Curtis Huttenhower, one of the researchers on the project, stated that they were able to establish that "each person's microbial signature is unique, much like how an individual's genome is unique."

The findings of the HMP are changing the understanding of health, how we view diseases, and how we conceive of the human body. Health depends on the balance of these ecosystems and, therefore, on the diversity of our microbes.

This new medical ecology suggests that preserving the biological diversity of the microbiota is as important for human health as conserving the diversity of macroscopic organisms is for environmental health.

How to take care of our Microbiome?

  • Avoid sugar and refined carbohydrates.

  • Avoid antibiotics as much as possible, as they deplete biodiversity and weaken the immune system.

  • Eliminate the use of mouthwash (Listerine), as bad breath is often related to poor digestion.

  • Vaginal douching disrupts the natural pH balance.

  • It is advised to take probiotics after receiving antibiotic treatment. López Munguía believes that the side effects of indiscriminate antibiotic use, such as the development of antibiotic-resistant pathogens, are as serious as the direct effect of destroying the microbiota. "If people knew all the beneficial functions these bacteria have in our bodies," says the researcher, "they would think twice before taking an antibiotic."

Functions of the Microbiome

Benefits for the Skin:

Benign microorganisms feed on the greasy secretions of skin cells and produce a moisturizing layer that keeps the skin flexible and prevents it from cracking. This way, many pathogenic microbes that could invade us through skin cracks cannot penetrate the body. Lazcano from UNAM adds that without the beneficial microorganisms we carry in our bodies, we would also die "due to infections in the mucous membranes, in the skin, or from pathogens that normally cannot proliferate thanks to the presence of the hosts we always carry."

The microbiome nourishes us

Our microscopic guests also generate vitamins and anti-inflammatory substances that our body cannot produce on its own. In the digestive tract, components of the intestinal microbiota (formerly known as "flora") help us assimilate nutrients and make certain compounds in food digestible. "Without the bacteria in the digestive tract, we would die from not absorbing the necessary amounts of vitamins," explains biologist Antonio Lazcano, professor at the Faculty of Sciences of UNAM. On the other hand, Agustín López Munguía, a researcher at the Institute of Biotechnology of UNAM, points out that "humans have only a few genes related to enzymes that allow us to digest complex carbohydrates.

With the microbiota, this capacity extends to more than 100 genes." In other words, the genes of the microbiome complement our own human genes (those of our cells). Moreover, these benign microbes that colonize us contribute more vital genes than our own genome: the DNA of a human consists of about 22,000 functional genes, while the organisms of the human microbiome contribute about 8,000,000 genes, which is 360 times more.

Immune System

A new wave of studies is investigating the relationship between certain health disorders and the composition of an individual's microbiome. For example, in recent decades, there has been a significant increase in allergies and obesity, among other conditions, especially in the United States. This increase coincides with the widespread use of antibiotics and other hygienic measures aimed at avoiding contact with microbes, particularly in early life. Several researchers suggest that these two factors are related.

In April of this year, an investigation was published in the journal Science that illustrates the effect of the microbiome on susceptibility to allergies, at least in mice. Richard S. Blumberg and his colleagues from Harvard University raised mice that were completely germ-free. These animals showed a pronounced tendency to develop allergic asthma and intestinal inflammation. "The immune system of mammals is widely stimulated with the initial contact with microorganisms in the neonatal stage," explain the researchers, citing previous studies. They further mention that this early contact with microbes in newborn mammals strengthens the immune system and has a lasting effect. For example, as mentioned by López Munguía, there is a strong relationship between early microbial exposure and resistance to asthma and inflammatory bowel disease.

The microbiome regulate weight

Other research has linked the composition of our microbiota to obesity and diabetes. Dr. López Munguía points out that the microbiota of different individuals, such as children, adults, thin people, and obese individuals, has been characterized, and it has been found that the profiles differ based on these factors. While human DNA is 99.9% similar, in terms of the microbiome, we are only about 10% similar compared to another person.

Microbiome studies can determine with 90% accuracy, using stool samples, whether a person is lean or obese, while genome studies can only determine this with 60% certainty.

If antibiotics are given to a baby in the first six months of life, they have a higher likelihood of becoming obese compared to those who do not receive antibiotics. This can also increase the risk of irritable bowel syndrome, heart diseases, certain types of cancer, among others.

A study in mice demonstrated that depending on the bacterial flora they have, they will absorb nutrients differently and it will control the mouse's appetite, which determines its weight. If the mice were given the microbiome of malnourished African children, they lost a significant amount of weight.

Anxiety, Mood, and Emotions

With a normal microbiome, there are balanced levels of bacteria that support cognitive and emotional capacities. However, when there is an imbalance and an overgrowth of bacteria, inflammation increases, leading to disturbances in emotional perceptions, as well as altered behavior and reasoning.

How does the gut flora affect the brain?

  • Through the Vagus Nerve, the intestine activates the vagus nerve that reaches up to the brainstem. Lactobacillus rhamnosus bacteria affects depressive behavior in mice.

  • Through the Immune System. 80% of immune cells reside in the intestine. Abnormalities here have an impact on neurological disorders. Bacteroides fragilis, when applied, becomes more resistant to multiple sclerosis, for example.

  • Through the Endocrine System, the intestine produces neuropeptides and neurotransmitters.

  • Through the metabolites produced in the intestines.

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