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What is a microbiome and why know about it

A person is constantly confronted with bacteria. They are everywhere: around us, on us, inside us. After many years of scientific research, mankind has learned well the relationship between bacteria and disease. And I must say, for fear of health in contact with many microbes, there are reasons. Plague, rheumatism, whooping cough, anthrax, Lyme disease and many other dangerous diseases begin due to the entry of bacteria. That is, a person has many reasons to perceive bacteria as the worst enemies. But in recent decades, scientists have changed their view of microorganisms. It turns out that not all of them are dangerous and not all should be avoided.

Microbiome: what is it

Microbiomes are a community of microorganisms, such as bacteria, archaea, fungi, and viruses that live in a particular ecosystem or organism.

Microorganisms are everywhere, including the human body, soil, deposits of land, sea, fresh water, atmosphere. Scientists find them even in extreme conditions, for example, in hydrothermal vents and subglacial lakes.

By the way, often the word "microbiota" is used instead of the term "microbiome". As a rule, both terms are used interchangeably, although experts say that there is a definite difference in the meaning of words. The microbiota is a dynamic community of trillions of microbes that live in harmony with human cells. But the microbiome is the collective name of the genes that live inside these microbes. By the way, the number of genes of all microbes living in the microbiome of one person is about 150 times the number of genes in the human genome.

All microbiomes have several features in common. Their "inhabitants" are always very numerous and diverse, although their qualitative composition is always different. Microbiome is a very dynamic community that can change depending on various factors, be it climate change, if we talk about the groups inhabiting the planet, or diet changes, if we talk about the human microbiome. But in any case, the microbiome is always closely connected with its owner.

Microbiome Habitats

Microbiome of the Oceans

Oceans cover almost 70% of our planet, but scientists are only beginning to find out about microorganisms inhabiting the Earth’s waters. These tiny inhabitants of the waters are the “building blocks” for the larger forms of life on the planet, they produce almost half of the oxygen we breathe, process about the same percentage of carbon dioxide, and remove more than half of the methane in the world's oceans.

Earth microbiome

Soil and land deposits contain a huge number of microbial communities. According to rough estimates, each gram of soil contains about 40 thousand species of microscopic inhabitants. They are necessary to maintain hundreds of processes, without which no plant can grow on such soil. Also, the microbiome of the earth is responsible for the splitting of pollutants, as well as for the nitrogen and carbon cycle.

Atmosphere microbiome

It is also difficult to research. So far, scientists know that microbes in the atmosphere are everywhere. Their set can vary from place to place, as well as over time. Microbes move freely through the atmosphere around the globe, clinging to dust particles. Atmospheric microbiome can influence the spread of infectious diseases, general health of people, agriculture, clouds and precipitation.

Human microbiome

A human microbiome is a collection of trillions of microbes living on the body and inside people. It consists of about a thousand species of bacteria that live on human skin, in the mouth, in its intestines and vagina.

These microbes and their genes, in fact, make us such a superorganism consisting of a symbiosis of human cells and microbes. Scientists suggest that the microbiome of one person may consist of about 8 million additional genes (for comparison, there are approximately 20-25 thousand genes in our genome itself).

In different parts of the body, colonies of microbes are very different from each other. The differences between the microbiomes of the intestine and the oral cavity are comparable to the difference in the colonies of bacteria found on the soil and in the oceans.

The peculiarity of the microbiome is that it is unique on the body of each person. Scientists cannot yet explain exactly how microbial diversity is created. Presumably, the formation of the microbiome is influenced by such factors as dietary habits, the environment, genetic factors and the effect of microbes on a person at a very early age.

But there is an interesting point. Scientists cannot yet explain why this is happening, but for people with serious chronic diseases, such as diabetes, the diversity of the microbiome is simplified. Also, a decrease in the diversity of microbes is observed in humans with intestinal dysfunction, in autoimmune diseases, obesity, heart diseases, as well as in the elderly.

How many microbes are in us

As early as the beginning of the 1970s, it was quite difficult for a scientist to determine the number of microbes that inhabit our organisms. In those days, data ranged from hundreds of billions to hundreds of trillions. In 2016, scientists conducted an analysis and it turned out that the body of an average adult person is 39 trillion microbial cells and 30 trillion actual human cells. Moreover, these figures can vary depending on the weight, height, age and sex of the person. But in any case, the weight of all microbes can be from 1 to 3 percent of the total weight of the human body, and this is from about 900 g to 2.7 kg - almost as much the brain weighs.

Where to look for a microbiome on a person

Microbes live on the human body everywhere. Although there are areas on which their concentration is higher. The vast majority of germs are found in the human gastrointestinal tract. Previously, they were called intestinal microflora, now - intestinal microbiota. Up to a thousand species of microorganisms live here. Intestinal microbiomes of different people may contain similar types of microbes, but in most cases they will differ in their strain. In addition to the intestines, the other most studied areas of the microbiome are the mouth, nasal cavity, eyes, lungs, skin, and vagina.

How is the human microbiome formed

A person begins to collect microbes in and on himself from the moment of birth. Infants are first exposed to the microbiota in the birth canal. And these microbes then help the baby to form its own intestinal microbiota. By the way, in infants born with caesarean section, the intestinal microflora forms much worse. Only after 6 months of age on these indicators, they catch up with children born in a natural way.

In addition, although this theory has yet to be proved, some scientists assume that a person is exposed to the first microbial effect even in the womb. If so, then the theory of the sterility of the environment of the female uterus will also be destroyed. In 2013, scientists from the University of Washington School of Medicine examined the placenta taken from 195 women. It turned out that a third of the placenta contains bacteria that resemble the microflora of the oral cavity. In addition, scientists have found that microbes are contained in the amniotic fluid. In another study, it turned out that almost 30% of babies get the bacteria that are necessary for the formation of the intestinal microbiome, along with the mother's breast milk.

The process of microbiome formation continues during the first 3 years of a person’s life. During this time, the composition of the microbiome often changes, but by the age of 3 a mature microbiome of a particular person is formed. By this time, it becomes quite stable, although not static. That is, the composition of the microbial community throughout life remains quite plastic and variable. How the microbiome is formed in each specific case is not completely clear to researchers. But experts suggest that this process depends on many factors, such as dietary habits, habitat, age, race, gender, hormonal changes, and even medication.

For example, it has been proven that during puberty, changes occur in the skin microbiome. In women, the composition and structure of the vaginal microbiome changes at least three times: during pregnancy, after childbirth and during menopause.

I must say that microbes do not colonize us randomly. A human microbiome consists of certain types of microorganisms that complement each other and even their host, performing important functions to maintain human vitality.

Take for example intestinal bacteria. Some of them are responsible for the synthesis of vitamins and enzymes. Others are necessary for proper digestion, and still others are responsible for strengthening the immune system. And some may affect the activity of the brain.

Interestingly, the human microbiome can be contained even outside the body. Our microbes can remain on any surface with which we come in contact, and even be in the environment. A person just needs to go into the room to throw into the air part of their own germs. Experts call this phenomenon a microbial cloud.

Role in the body

Scientists have studied microbiomes for almost 20 years before they came to the conclusion that this symbiosis of microbes plays an important role for the human body. It is important for:

  • enhance immunity;
  • infection prevention;
  • maintaining the functionality of the digestive system;
  • maintaining hormonal balance;
  • correct work of the brain.

The state of the microbiome can even determine the development of which diseases a person is prone to. In 2018, in the British journal Nature, which is the most influential scientific publication in the field of biology and medicine, the results of a large-scale study on the microbiome were published. Scientists, after analyzing the microbiome of more than 1000 healthy people, revealed a close relationship between the microbial community and changes in cholesterol, body weight, blood glucose and some other parameters. Experts who conducted the study, came to the conclusion that using genetic data and the profile of a human microbiome, it is much easier to determine its tendency to certain violations than in the case of using exclusively genetic material.

Many people probably know that vitamin B12 is one of those substances that is synthesized in the small intestine. But after studying the functions of the microbiome in the body, the scientists came to the conclusion that, nevertheless, this substance with a rather complex molecule is not produced by the human body itself, but by microorganisms contained in the intestine.

The relationship between microbiomes and health

The more scientists learn about the microbiome, the more evidence is obtained that an imbalance in the microbial community can be both a cause of illness and a cause of recovery.

There are close links between intestinal microbiomes and the occurrence of such diseases as type 2 diabetes, obesity, rheumatoid arthritis, cirrhosis, inflammatory bowel diseases, and metabolic syndrome. In addition, scientists suggest a relationship between the intestinal microbiome and the human propensity for anxiety, depression and autism.

Digestion and nutrition

The microbiota is a key factor affecting digestion. Without intestinal microflora, many popular products that a person uses would be inedible for him. For example, the same fiber contained in vegetables, fruits and nuts, without the intestinal microbiome, the body could not assimilate.

The human gastrointestinal tract copes well with the breakdown of monosaccharides (glucose) and disaccharides (lactose). But it is much more difficult for it to digest complex molecules and polysaccharides, and these are proteins, fats, starch and other complex carbohydrates obtained from vegetables and meat. And this is where intestinal microbes come to the rescue. They feed on the molecules of these products, by fermentation, break them down into metabolites, which the body is already able to assimilate and use in its own needs.

For many years, mankind has been convinced that body weight is determined solely by how much a person eats. But recently, scientists have made a revolutionary discovery. Experts, however, experts conducted only on mice, but the result is still impressive. It turned out that the tendency to corpulence is influenced by microbes living in our bodies. The scientists transplanted a microbiota from the intestines of a lean and obese person to experimental animals. As a result, the mice that got the germs from a more well-fed person gained extra weight. Whether this scheme works with the human body, scientists still need to study. But if so, then the microbiota can be a cure for obesity.

Immunity and inflammation

Experts say that the balance of the intestinal microbes largely depends on the balance of the immune system. The human intestine contains more immune cells than any other part of the body. That is, the intestinal microbiota and immunity cells are in constant contact. If this relationship is broken, there is a risk of developing complex diseases, including allergies, obesity, diabetes, depression and even cancer.

To confirm their theory, scientists again used mice. Experts in the laboratory raised animals whose intestines were completely devoid of microflora. They were very painful, they developed symptoms of pneumonia, asthma and inflammatory bowel disease. Then the scientists put microbes from healthy animals into sterile mice, and they quickly went on the mend. But the condition improved only in the smallest animals (at the age of 1-2 weeks), the “transplant” of the microbiota did not help the more adult. The results of the experiment were regarded by scientists as another confirmation of the importance of the microbiome for the survival of infants and strengthening their immunity.

In addition, studies have shown that the violation of the intestinal microbiome increases the risk of inflammatory diseases, including Crohn's disease and celiac disease, and also makes a person more prone to allergies.

Brain and nervous system

There is a close relationship between the gastrointestinal tract and the central nervous system. This connection is based on the vagus nerve, which sends signals from the intestines to the brain and vice versa. But the intestinal microbiome is able to produce a variety of neurotransmitters, including serotonin and GABA, which affect mood, appetite and thinking, and can also activate the vagus nerve.

In one study, scientists found that mice that had a strain of intestinal bacteria Lactobacillus rhamnosus introduced had less anxiety in stressful situations and they produced less stress hormone than animals that did not receive the bacterium. Then the scientists continued the experiment and cut the vagus nerve in animals, thus disturbing the relationship between the brain and the intestines. After this, the differences in the behavior of the mice disappeared, regardless of the state of their intestinal microbiome.

Other studies in mice also confirmed the relationship between intestinal microbes and depression, Parkinson's disease, autism, and mood disorders. It is also interesting that, according to the observations of specialists, almost 70% of children and adolescents suffering from autism have problems with the work of the gastrointestinal tract, which can also be evidence of the relationship between the microbiome and the work of the brain.

Who lives in us

This table provides a list of the most studied bacteria (genus and species) that inhabit human organisms.

Human bacteria
Genus of bacteriaKindsWhere livesMain functions
BacteroidetesB. acidifaciens

B. eggerthii

B. fragilis

B. helcogenes

B. intestinalis

B. thetaiotaomicron

IntestinesDevelops metabolites that prevent inflammation.
BifidobacteriumB. crudilactis

B. denticollis

B. gallicum

B. gallinarum

B. hapali

B. indicum

B. pullorum

B. reuteri

Intestines, oral cavity, vaginaPerforms a number of useful functions for the body, including serving for the prevention and treatment of ulcerative colitis
LactobacillusL. rhamnosus

L. casei

L. fermentum

L. gasseri

L. plantarum

L. acidophilus and L. ultunensis

Mouth, intestines, vaginaPrevention and treatment of diarrhea, as well as other digestive disorders
PrevotellaP. copri

P. dentalis

P. maculosa

P. marshii

P. oralis

P. oris

P. saliva

MouthRegulates metabolic processes
PseudomonasP. aeruginosa

P. maltophilia

P. aeruginosa

P. fluorescens

P. putida

P. cepacia

P. stutzeri

Skin, throat, mouth, intestines, urethra, vaginaCauses rashes and skin infections.
StreptococcusS. mitis

S. salivarius

S. mutans

S. pneumonia

S. pyogenes

Skin, eyes, nose, throat, mouth, guts, vaginaCauses various diseases, including pneumonia, pharyngitis, skin lesions, sepsis

The study of microbiomes is a relatively new trend in science. Although it should be noted that the Russian scientist Ilya Mechnikov, back in 1908, suggested that health could be improved and the body's aging slowed down if the intestinal microflora was corrected with the help of beneficial bacteria found in fermented milk products. Researchers have yet to learn a lot about the microbiota. But there is already an understanding that microbes are not always evil and danger.

Article author:
Izvozchikova Nina Vladislavovna

Specialty: infectious diseases specialist, gastroenterologist, pulmonologist.

Total experience: 35 years.

Education: 1975-1982, 1MMI, San gig, high qualification, infectious diseases doctor.

Science degree: doctor of the highest category, PhD.


  1. Infectious diseases.
  2. Parasitic diseases.
  3. Emergency conditions.
  4. Hiv
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Watch the video: 5 tips to keep your gut microbiome healthy. UCLA Health Newsroom (February 2020).