The microbiome is a type of "organ" that has been forgotten by modern medicine for many years. However, for over a dozen years, thanks to the development of biomedical sciences, a lot of research has been carried out, the results of which prove that the microbiome is more than just a group of microorganisms inhabiting our body. What is the microbiome? Why is it so important to our he alth? How to care for it?

Microbiome(microbiota, microflora) is a grouping of microorganisms characteristic for a given natural habitat. As a habitat, we should understand not only the sea or soil, but also the organism of humans and other animals. Therefore, in addition to the microbiome of the seas and soil, we distinguish the intestinal, skin, genital tract, ear and oral microbiome.

The composition of the microbiome varies depending on the habitat it occupies. Currently, the most research is carried out on the most numerous microbiome in our body, i.e. the digestive tract.

Microbiome, microbiota or microflora?

The term "microbiome" was first used in 2001 by Nobel laureate Joshua Lederberg, who used it to describe the genome set of all microbes inhabiting the human body. Therefore, the term is more often used in this sense.

When talking about the collection of all microorganisms as cells, the term "microbiota" should be used.

The term "microflora", on the other hand, is an old term that is used less frequently, and it dates back to the times when most microorganisms were classified into the plant kingdom (the term "flora" describes the totality of plant species found in a given area).

Microbiome - what does it consist of?

The microbiome consists of bacteria, yeast, fungi, protozoa, viruses and archaea. Remember that they do not always have to be "friendly" to their host. The microbiota may also include microorganisms potentially pathogenic for humans, e.g.Escherichia Coli .

Due to the abundance of microorganisms, the gastrointestinal microbiome deserves special attention, which mainly consists of bacteria from 4 subgroups:

  • Firmicutes(64%)
  • Bacteroides(23%)
  • Proteobacteria(8%)
  • Actinobacteria(3%)

In he althy people, individual sections of the digestive tract are characterized by a variable diversity of microorganisms. The stomach and duodenum are practically sterile,because the acidic pH of gastric juice creates an unfavorable environment for most microorganisms. In the small intestine, their number is greater, ranging from 10,000 to 100,000 in 1 gram of alimentary content.

Here, acidophilic bacteria of the genusLactobacillusandStreptococcusare predominant. The largest number of microorganisms is in the large intestine, and it is even a trillion cells in 1 gram of food content! The vast majority are oxygen-intolerant microorganisms (anaerobes), such asBifidobacteriumandClostridium .

It is estimated that there are 10 times more microorganisms in the digestive tract than cells in the human body (about 100 trillion cells weighing about 2 kg), and the number of genes in them is 3.3 million. For comparison, the human genome is only 21,000 genes.

Bacteria inhabiting the digestive tract can be divided according to the functions they perform in the body:

  • proteolytic (or putrefactive) bacteria are potentially pathogenic bacteria whose overgrowth in the intestine may adversely affect the body; they include, among others bacteria of the genusKlebsiella ,Enterobacter ,Serratia ,Citrobacter,Pseudomonas
  • protective (probiotic) bacteria are bacteria that inhibit the growth of pathogenic microorganisms, seal the intestinal epithelium and produce nutrients for the intestinal epithelium; they include, among others bacteria of the genusLactobacillusandBifidobacterium
  • immunostimulating bacteria stimulate the cells of the immune system, reduce the inflammatory response and stimulate the production of IgA antibodies through the mucosa; they include, among others bacteria of the genusEnterococcusiEscherichia coli . The latter is also potentially pathogenic under unfavorable conditions

Microbiome - what are its functions?

Gut microbes can metabolize food-derived substances - carbohydrates, proteins, fats, and those derived directly from humans such as dead cells and mucus. The microbiome uses them to support basic life activities.

Therefore, the functions of the microbiota can be compared to a type of bioreactor that produces countless amounts of bioactive substances during the fermentation process. The amount and nature of these substances will largely depend on the way we eat.

In addition to supporting digestive processes, the intestinal microbiome:

  • produces B vitamins and vitamin K
  • increases the absorption of minerals,such as magnesium and calcium
  • prevents colonization of the intestine by pathogenic bacteria
  • stimulates the maturation of the immune system cells and supports its work
  • calms inflammatory processes
  • influences the maturation and differentiation of intestinal epithelial cells
  • inactivates toxins and carcinogens
  • participates in the metabolism of cholesterol and bilirubin

Microbiome - what influences it?

  • genes

Although the composition of the gut microbiome is primarily influenced by environmental factors, the microbiome is also influenced to a lesser extent by the host's genotype. An example of such a relationship are variants of the FUT2 gene encoding the enzyme fucosyltransferase 2, responsible, inter alia, for the formation of antigens associated with blood groups.

People with an unfavorable variant of the FUT2 gene do not produce certain oligosaccharides, the lack of which predisposes them to deficiency of the protective bacteria of the genusBifidobacterium . About 20% of Europeans have an unfavorable variant of this gene.

  • age and delivery method

Before delivery in utero, our digestive tract is sterile. During natural childbirth, the gastrointestinal tract is populated by the mother's vaginal microbiome. Then, during breastfeeding with milk, prebiotic substances (human oligosaccharides) are passed on to the baby, which stimulate the growth of beneficial bacteria such asBifidobacterium .

Artificially fed babies may have less of these bacteria. It has been shown that childbirth and the way of feeding may be crucial in the proper development of the microbiome and the development of, for example, allergies. Significant differences in the composition of the microbiome have been noticed in naturally born infants compared to those delivered by caesarean section.

After the end of breastfeeding and the introduction of solid foods, the composition of the gut microbiome gradually resembles that of an adult. At the age of about 15, he becomes relatively stable (if the person is he althy and leads a proper lifestyle).

The next stage of human life, in which a change in the composition of the intestinal microbiome is observed, is the period after about 65 years of age. In the elderly, there is a decrease in the number of protective bacteria of the genusBifidobacteriumand an increase in the number of potentially pathogenic bacteria, such asClostridium .

The declineBifidobacterium , which reduce inflammation on the intestinal mucosa, may be one of the factors that exacerbate age-related disease processes. Why is this happening? This is largely a consequence of the fact that our body becomes less efficient with age,i.e. the condition of the dentition deteriorates, the amount of saliva secreted and the efficiency of organs, e.g. the pancreas, decreases.

  • Diet

Diet is one of the most influencing factors in the composition of the gut microbiome. If we provide our microbiome with the right amount of complex carbohydrates, microorganisms will produce substances such as short-chain fatty acids (SCFA), e.g. butyrate or lactic acid, which have a beneficial effect on the body, including by suppressing inflammatory responses.

It is estimated that 10-20% of consumed carbohydrates are resistant to digestion by human intestinal enzymes. These are non-digestible carbohydrates, such as resistant starch and non-starch polysaccharides (such as pectins and cellulose), which are ideal "nutrients" for the microbiome.

However, if our diet contains an excess of processed food, simple sugars, saturated fats and animal protein, the microorganisms will start to produce harmful substances such as biogenic amines (e.g. tyramine), skatole, indole or ammonia. These substances can damage the intestinal epithelial cells, induce inflammation and lead to disturbances in the permeability of the intestinal barrier.

A study was conducted in which the composition of the intestinal microbiome of children living in Italy and eating according to the Western diet model (rich in animal protein, fats and simple sugars) was compared with the diet of children living in rural Burkina Faso (rich in complex carbohydrates and low in animal protein). They showed that the composition of the microbiome in both groups differed dramatically.

The group of bacteria characteristic of obese people ( Firmicutes ) dominated in children from Italy, there was an overgrowth of putrefactive bacteria, and a reduced content of butyrate and other SCFA was found in the faeces. This has not been found in the children of Burkina Faso. This shows how improper eating habits affect the disturbance of the gut microbiome.

Diets low in complex carbohydrates (e.g., soluble fiber) reduce the diversity of the gut microbiome, especially protective bacteria of the genusBifidobacterium . An example of such a diet is the FODMAPs diet and an improperly balanced gluten-free diet.

The Mediterranean diet is the most favorable in the research, because in addition to a large amount of dietary fiber, it contains polyphenols. As recent studies show, 90-95% of polyphenols are accumulated in the large intestine, where they undergo various biochemical changes by the intestinal microbiome.

  • Psychological stress

In studies with mice and humans, it has been shown that psychological stress causesreducing the number of protective bacteria of the generaLactobacillusandBifidobacterium . In addition, stress stimulates the overgrowth of potentially pathogenic bacteria such asEscherichia Coli . This is probably due to the secretion of the stress hormone cortisol.

It has also been shown that polyphenols, such as resveratrol in grapes or catechins in tea, have a positive effect on the composition of the intestinal microbiota, acting as prebiotics.

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Microbiome and civilization diseases

The microbiome is often compared to an "organ" forgotten by modern medicine. Research clearly shows that the microbiome, like any other organ, is able to receive and respond to information from the environment - such as changes in pH, the presence of nutrients, immune cells, and hormones. This system is called quorum sensing and allows molecular dialogue between the microbiome and human cells and organs.

Due to the multi-level influence of the microbiome on our body, it should come as no surprise that the qualitative and quantitative disturbances of the microbome, called intestinal dysbiosis, can contribute to the emergence of many civilization diseases, such as:

  • obesity
  • diabetes
  • autoimmune diseases
  • allergies
  • depressive disorder
  • autism
  • Alzheimer's disease

A breakthrough in research on the relationship of the microbiome with human he alth was the project "Human Microbiome Project" initiated in 2007 by the American National Institute of He alth. It uses the most modern methods of molecular biology, which allowed to determine the differences in the composition of the human microbiome depending on latitude, genotype, age and diet.

Microbiome and obesity

The first studies pointing to the relationship of the gut microbiome with obesity were conducted in mice. It was noticed that obese mice have - compared to lean mice - disturbed proportions between bacteria from the groupFirmicutes(too much) andBacteroides(too little).

It is currently believed that the gut microbiome can influence the development of obesity in at least three mechanisms:

  • by producing extra calories (4-10% of the energy obtained from food is generated by the microbiome, it is about 80-200 kcal / day)
  • inducing inflammationlow intensity (so-called metabolic endotoxicemia, which may cause insulin resistance)
  • regulation of the hunger and satiety center (the microbiome influences, among others, the secretion of glucagon-like peptide-1 and peptide YY, and the time of intestinal transit)

The microbiome and the nervous system

Experimental studies in mice have shown that the gut microbiome influences the development of the nervous system, stress response and behavior. More and more studies also indicate a direct relationship between the gut microbiome and depressive disorders.

In this context, the so-called The gut-brain axis and the vagus nerve, which are responsible for transmitting signals from the gut to the brain.

Other mechanisms by which microorganisms can influence our behavior is their participation in the metabolism of tryptophan (it is a precursor to the synthesis of the "happiness hormone" - serotonin) or directly through the synthesis of neurotransmitters, e.g. bacteria of the type EscherichiaandEnterococcuscan produce serotonin, and of the typeLactobacillusGABA (neurotransmitter responsible for relaxing and relaxing).

In addition, research indicates the participation of the gut microbiome in the development of disorders such as:

  • autism
  • schizophrenia
  • ADHD
  • bipolar disorder
Worth knowing

SIBO, or bacterial overgrowth of the small intestine, is a type of intestinal dysbiosis, with excessive growth of bacteria in the small intestine, which are characteristic of the large intestine.

SIBO is the cause of digestive and absorption disorders. It coexists with many diseases, such as:

  • irritable bowel syndrome (84%)
  • celiac (66%)
  • gastroesophageal reflux disease (50%)
  • hypothyroidism (54%)
  • pancreatitis (35%)

The reason for SIBO may be:

  • intestinal motility disorders
  • antacids
  • stomach diseases
  • digestive enzyme deficiencies
  • old age
  • antibiotic therapy

The microbiome - how to care for it?

  • eat vegetables and fruits rich in polyphenols (blueberries, blueberries, raspberries) and prebiotic substances that are a "medium" for intestinal microorganisms (legumes, citrus fruits, Jerusalem artichoke, leek, onions, asparagus, bananas)
  • eat complex carbohydrates such as brown rice, oat bran, and oat bran, which contain soluble fiber that stimulates the production of butyrate
  • eat good quality fats, e.g. olive oil
  • drink greentea, because it contains polyphenols like catechins
  • increase the consumption of pickled vegetables, e.g. cabbage, cucumbers, beets and dairy products, e.g. yoghurt, kefir, as they are a source of probiotic microorganisms
  • avoid large amounts of alcohol, and if you already consume it, choose red wine that contains polyphenols such as resveratrol
  • eliminate junk food, sweetened drinks, cookies, and bars from your diet as they are a source of simple sugars and trans fats
  • avoid psychological stress, and if this is impossible, use relaxation techniques
  • get enough sleep
  • exercise regularly
About the authorKarolina Karabin, MD, PhD, molecular biologist, laboratory diagnostician, Cambridge Diagnostics Polska A biologist by profession, specializing in microbiology, and a laboratory diagnostician with over 10 years of experience in laboratory work. A graduate of the College of Molecular Medicine and a member of the Polish Society of Human Genetics. Head of research grants at the Laboratory of Molecular Diagnostics at the Department of Hematology, Oncology and Internal Diseases of the Medical University of Warsaw. She defended the title of doctor of medical sciences in the field of medical biology at the 1st Faculty of Medicine of the Medical University of Warsaw. Author of many scientific and popular science works in the field of laboratory diagnostics, molecular biology and nutrition. On a daily basis, as a specialist in the field of laboratory diagnostics, he runs the content department at Cambridge Diagnostics Polska and cooperates with a team of nutritionists at the CD Dietary Clinic. He shares his practical knowledge on diagnostics and diet therapy of diseases with specialists at conferences, training sessions, and in magazines and websites. She is particularly interested in the influence of modern lifestyle on molecular processes in the body.

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Gastrology