What is the microbiome and why should we know about it

Man is constantly confronted with microorganisms that live around us, on us, inside us. The role of various bacteria, viruses and fungi in the pathogenesis of many diseases has been established, among them a far from complete list includes: plague, rheumatism, tuberculosis, whooping cough, anthrax, Lyme disease and many other dangerous diseases caused by bacteria. That is, a person has many reasons to negatively perceive bacteria. But we live in an amazing time when, with the advent of new technologies, our ideas about health and disease are changing. Today, a completely new understanding of the need for microorganisms inside and outside our body and their importance not only for our digestion, but also for well-being in general has been established.

Microbiome: what it is

Microbiome is the micro-organisms such as bacteria, archaea, fungi and viruses that live in a particular ecosystem or organism.

Microorganisms are ubiquitous throughout, including the human body, soil, fossils, seas, fresh water, the atmosphere, and even in hydrothermal vents and subglacial lakes.

The term “microbiome” has replaced the outdated definition of microflora, since “flora” is translated as the plant world. It was first introduced in 2001 to refer to pooled microbiota genomes. Microbiota - used to characterize the microbiocenosis of individual organs and systems. For example, intestinal microbiota, skin microbiota, placenta microbiota, breast milk microbiota, etc. Thanks to modern scientific research in the field of genetics, scientists have been able to identify and quantify the microorganisms living in the human body. With the help of the latest scientific developments, it was possible to establish that there are more than 1,100 types of microorganisms, most of which are anaerobes. It has been proven that the more diverse the gut micro-organisms, the better the human health, and low diversity is associated with various diseases. The introduction of molecular genetic technologies into the practice of microbiological research has made it possible to obtain new information about the composition and properties of the intestinal microbiota in people of different ages.

All microbiomes have a few things in common, but it is a dynamic community that can change depending on various factors, whether it be climate change, in terms of the groups that inhabit the planet, or dietary changes, in terms of human microbiome. But in any case, the microbiome is always closely related to its host.

Microbiome prevalence

Microbiome of the oceans

Oceans cover almost 70% of our planet, therefore, research is constantly being carried out on microorganisms that inhabit water spaces. These tiny "residents" are the "building blocks" for the larger life forms on the planet, they produce almost half of the oxygen we breathe, recycle about the same percentage of carbon dioxide, and remove more than half of the methane in the world's oceans.

Soil microbiome

Soil and fossils are inhabited by a huge number of microorganisms. According to rough estimates, each gram of soil contains about 40 thousand species of microscopic inhabitants. They are necessary to support many of the processes that ensure the growth of vegetation. Also, the soil microbiome is responsible for the breakdown of pollutants, for the cycle of nitrogen and carbon.

Atmospheric microbiome

Microorganisms are known to be present everywhere in the atmosphere, but vary from place to place and over time. Microorganisms with dust particles migrate freely around the globe. The atmospheric microbiome can influence the spread of infectious diseases, general human health, agriculture, cloud formation and precipitation.

The human microbiome

According to the US National Institutes of Health, only 10% of the cells that make up the human body are actually human cells, and the remaining 90% belong to the bacteria inhabiting various human microbiota. Thus, homo sapiens is a "superorganism" in which a large number of different organisms coexist. In 2008, the global project "Human Microbiome" was launched, which aimed to decipher the genome of bacteria inhabiting the human body. The European consortium MetaHIT is engaged in deciphering the genome of bacteria that inhabit the gastrointestinal tract. About 3 million genes have already been deciphered, which is about 150 times the human gene set. The results of the project will allow to establish the relationship of these genes with human health, disease development and phenotype. According to the journal Science, the decoding of the human metagenome is one of the greatest scientific discoveries of the last decade.

The human microbiome includes about a thousand varieties of bacteria that live on a person's skin, mouth, intestines and vagina.

In different parts of the body, colonies of microbes differ from each other. The differences between the gut and oral microbiomes are comparable to the differences between bacterial colonies found on soil and in the oceans.

The peculiarity of the microbiome of each person is in its uniqueness. It is assumed that the formation of an individual microbiome is influenced by such factors as dietary habits, the environment, genetic factors, and the impact of microbes on a person at a very early age. Therefore, the presence of a certain microbiota will make it possible to predict the characteristics of metabolism and indicate a predisposition to certain diseases.

It is noted that in individuals with serious chronic diseases, for example, with diabetes, the diversity of the microbiome is simplified. Also, a decrease in the diversity of microorganisms is observed in patients with intestinal dysfunction, with autoimmune diseases, obesity, heart disease, as well as in the elderly. This is due to the fact that the normal intestinal microbiota is involved in a variety of physiological functions of the body: protective, digestive, detoxifying and anticarcinogenic, synthetic, genetic, immunogenic, in the regulation of cholesterol and oxalate metabolism.

How many microbes we have

Back in the early 1970s, it was quite difficult for scientists to determine the number of microbes inhabiting our bodies, the data ranged from hundreds of billions to hundreds of trillions. Since 2016, based on genomic analysis, it has been established that the average adult human body consists of about 39 trillion microbial cells and about 30 trillion human cells. Moreover, these figures may vary depending on the weight, height, age and gender of the person. But in any case, the weight of all microorganisms can be from 1 to 3 percent of the total body weight of a person, and this is approximately from 900 g to 2.7 kg - almost the same weight as the brain.

The microbiome is considered another human organ

The human microbiome is represented by bacteria that reside inside and outside of our body. The vast majority of microorganisms are found in the human gastrointestinal tract. This is the intestinal microbiota, which includes up to a thousand species of microorganisms. The gut microbiomes of different people may contain similar types of microbes, but in most cases they will be different strains. In addition to the gut, the other most studied are the microbiota of the cavity, nose, eyes, lungs, skin, and vagina.

How the human microbiome is formed

The colonization of the intestines of the fetus with microorganisms is laid already in the second half of pregnancy from the mother (according to foreign and domestic studies, before the 22nd week of gestation of microbes in there is no fetus at all, and starting from the 24th week, single colonies of Escherichia coli and lactobacilli appear).

The development of the fetal gut microbiota is affected by diet, maternal lifestyle, and the fact that antibiotics are taken during pregnancy. The mother is the first source of colonization and infection of her child. The state of its microbiota is also determined by the method of delivery (natural, operative childbirth), the place of delivery - a maternity hospital or an apartment, when physiological births are carried out at home. The microbiota of the gastrointestinal tract of the infant depends on the condition of the skin, birth canal and intestines of the mother, as well as on whether antibiotic therapy was used in the mother and child. The time of attachment to the breast, the nature of feeding from birth is essential. Since the colonization of the mucous membranes of a newborn by microorganisms begins from the moment it passes through the birth canal, the natural method of delivery is one of the fundamental ones that influence the formation of the microbiota.

Today, we have reliable data on the composition of the microflora of the vagina of a woman in labor, which is more populated by lactobacilli (more than 60%), enterococci, staphylococci and the fungal bacterium candida, therefore, the microbiota of babies born naturally contains bacteria, close to the mother's vaginal microbiota with a predominance of lactobacilli, and those born by caesarean section - microorganisms similar to those inhabiting the mother's skin - more staphylococci and propionic bacteria.

In 2013, scientists at the University of Washington School of Medicine examined the placenta of 195 women giving birth and found bacteria that resemble the oral microbiota, and that microbes are also found in the amniotic fluid. Another study found that almost 30% of babies get the bacteria they need to build their gut microbiome, along with their mother's breast milk, which contains up to 700 different microorganisms. They enter the mother's milk from the intestines by bacterial translocation into the bloodstream, bypassing the lymph nodes.

The process of microbiome formation continues during the first 3 years of human life. During this time, the composition of the microbiome often changes, but by the age of 3, a mature individual microbiome is formed. By this time it becomes quite stable, though not static. That is, the composition of the microbial community throughout life remains quite plastic and variable. Research into the formation of the microbiome is ongoing, and it is believed 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 changes in the skin microbiome occur during puberty. In women, the composition and structure of the vaginal microbiome changes at least three times: during pregnancy, after childbirth, and during menopause.

It should be noted that the human microbiome consists of certain types of microorganisms that complement each other and even their host, performing important functions for maintaining human viability.

For example, intestinal bacteria are involved in the synthesis of vitamins and enzymes, digestion, strengthening the immune system, and may even affect brain activity.

Interestingly, the human microbiome can even be contained outside the body. Our germs can stay on any surface we come into contact with, and even be in the environment. It is enough for a person to simply enter the room to leave some of their own microbes in the air., the so-called "microbial cloud".

Role in the body

The symbiosis of microbes plays an important role for the human body, as it takes part in:

  • increase immunity;
  • infection prevention;
  • maintaining the functionality of the digestive system;
  • regulation of hormonal balance;
  • the functioning of the brain.

The state of the microbiome can even determine which diseases a person is prone to developing. In 2018, the British journal Nature, the most influential scientific publication in the field of biology and medicine, published the results of a large-scale study on the microbiome. Scientists, after analyzing the microbiome of more than 1000 healthy people, revealed a close relationship between the microbiota and changes in cholesterol, body weight, blood glucose levels and several other parameters. The experts who conducted the study concluded that using genetic data and a person's microbiome profile, it is much easier to determine its propensity for certain disorders. Changes in the microbiome have been proven to lead to allergies, autoimmune, cardiovascular, metabolic and psychiatric diseases.

It is known that vitamin B12 is synthesized in the small intestine with the participation of microorganisms contained in the intestine.

The link between microbiomes and health

The more scientists learn about the microbiome, the more evidence they get that microbial imbalances can both cause disease and restore health.

There are strong links between the gut microbiome and the occurrence of diseases such as type 2 diabetes, obesity, rheumatoid arthritis, cirrhosis, inflammatory bowel disease, and metabolic syndrome. In addition, scientists suggest a relationship between the gut microbiome and a person's propensity for anxiety, depression and autism.

Digestion and nutrition

Microbiota is a key factor influencing digestion. Without intestinal microflora, many popular foods that a person consumes would be inedible for him. For example, the same fiber contained in vegetables, fruits and nuts, the body is not able to absorb without the intestinal microbiome.

In the human gastrointestinal tract, monosaccharides ( glucose ) and disaccharides ( lactose ) are easily broken down. But it is much more difficult for it to digest complex molecules and polysaccharides, and these are proteins, fats, starches and other complex carbohydrates derived from vegetables and meat. And this is where the intestinal microbiota comes to the rescue, bacteria that are broken down by fermentation of complex compounds into metabolites that 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 food a person eats. But recent experimental studies in mice have shown that the tendency to be overweight is influenced by microbes living in our bodies. After transplanting microbiota from the intestines of a lean and obese person into experimental animals, mice that received microbes from a more well-fed person gained excess weight. The question of whether this scheme also works with the human body requires further study. But if this is the case, then the microbiota could be an anti-obesity drug.

Immunity and inflammation

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

Experimental studies on mice whose intestines were as sterile as possible demonstrated that such animals were very sickly, they developed symptoms of pneumonia, asthma and inflammatory bowel disease. After replanting mice with bacteria from healthy animals, they quickly recovered, but the condition improved only in the smallest animals (at the age of 1-2 weeks), the “transplantation” of the microbiota did not help the older ones. The results of the experiment are regarded as another confirmation of the importance of the microbiome for the survival of infants and strengthening their immunity.

In addition, studies have shown that disruption of the gut microbiome increases the risk of inflammatory diseases, including Crohn's disease and celiac disease, and 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 gut to the brain and vice versa. The gut microbiome is capable of producing a range 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 injected with a strain of the intestinal bacterium Lactobacillus rhamnosus were less anxious and produced less stress hormone when under stress than control animals. When the vagus nerve was switched off in animals, differences in the behavior of mice disappeared, regardless of the state of their intestinal microbiome.

Other studies in mice have also confirmed the existence of a relationship between gut microbes and depression, Parkinson's disease, autism, mood disorders. Clinicians note that almost 70% of children and adolescents with autism have problems with the functioning of the gastrointestinal tract, which may also be evidence of the relationship between the microbiome and the work of the brain.

Identified microorganisms of the human microbiota

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

Bacteria of the human body
Genus of bacteria Species Where lives Main functions
Bacteroidetes B. acidi faciens

B. eggerthii

B. fragilis

B. helcogenes

B. intestinalis


Intestine Produces metabolites that prevent inflammation
Bifidobacterium B. crudilactis

B. denticollis

B. gallicum

B. gallinarum

B. hapali

B. indicum

B. pullorum

B. reuteri

Intestine, oral cavity, vagina Performs a number of useful functions for the body, including the prevention and treatment of ulcerative colitis
Lactobacillus L. rhamnosus

L. casei

L. fermentum

L. gasseri

L. plantarum

L. acidophilus and L. ultunensis

Mouth, intestines, vagina Prevention and treatment of diarrhea and other digestive disorders
Prevotella P. copri

P. dentalis

P maculosa

P. marshii

P. oralis

P. oris

P. saliva

Mouth Regulates metabolic processes
Pseudomonas P. aeruginosa

P. maltophilia

P. aeruginosa

P. fluorescens

) P. putida

P. cepacia

P. stutzeri

Skin, throat, mouth, intestines, urethra, vagina Causes rashes and skin infections
Streptococcus S. mitis

S. salivarius

S. mutans

S. pneumonia

S. pyogenes

Skin, eyes, nose, throat, mouth, intestines, vaginal search Causes 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 suggested back in 1908 that health can be improved and the aging of the body slowed down if the intestinal microflora is corrected with the help of beneficial bacteria found in fermented milk products. Researchers have much more to learn about the microbiota. But there is already an understanding that microbes are not always evil and danger.