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Microbiome -

your 100 trillion friends

Compiled from sources by Sandra Tamm





Planet Earth has nearly 7 billion people, but about 5 non-million bacteria (10). They are everywhere - on the floor, on the table, in the sink, in the coffee cup, inside and on you. Most of our microbes live in the gut, but their “host” is also our skin,  mouth, lungs, urinary tract, genitals and stomach.


We currently know that there are ten times more microbes in the human intestinal tract than eukaryotic (one of the two main cell types found in living organisms ) cells (4,10,15). 3194-bb3b-136bad5cf58d_According to Marika Mikelsaare, emeritus professor of microbiology at the University of Tartu, until the beginning of the 2000s, it was thought that  there were about 500 different types of microbes living in the intestine. Since the middle of the new century - thanks to the introduction of molecular methodologies - the figure has been presented from one thousand to two thousand. "The intestinal microbial community is always depicted as an iceberg, the visible part of which, i.e. the identified species, is only up to 10 percent of the total number. So close to people and still such an unknown and interesting area!" he noted (9). All this considered, we are more colonies of bacteria than people.

Our body is a complex ecosystem that needs to be balanced and cared for in order for us to be healthy. This ecosystem consists of bacteria, fungi, viruses, and protozoa (1,12). Its exact composition differs from person to person, depending on his menu, factors affecting his health during his life (infections, medications, etc.), place of residence and also ancestors.


The community of microbes inhabiting our body is called microbiome or microflora or "second genome" (11).


According to the study of the international scientific project MetaHIT (Metagenomics of the Human Intestinal Tract), published in the journal Nature, the microbes living in the human intestine have 3.3 million genes, which far eclipses the number of human genes: there are 23 000 genes in the human genome. Thus, the number of genes of bacteria living in the human body exceeds more than a hundred times the number of human genes. According to researchers, knowing the genetic background of the intestinal microflora is at least as important as studying the human genome, and it also allows diseases to be prevented and treated better (9).


This powerful "army" has a greater impact on our health than we can imagine, and unfortunately its importance to our health is underestimated. Constantly rinsing your mouth with all kinds of "bacteria-free" products is far from a wise thing to do. 


These tiny microorganisms perform several important functions in our body, of which the list below is only a part of them (1,8,12):


  • help digest food

  • contribute to the absorption of nutrients

  • synthesize hormones

  • act as a cleaning machine for the body - they can neutralize many poisons found in food, so they can be seen as a "second liver". Therefore, if the proportion of good bacteria in the gut decreases, a greater burden falls on the liver.

  • produce nutrients necessary for the body (sh vitamins K and B12, B9 or folate, short-chain fatty acids)

  • "train" our immune system

  • affect body weight

  • play a role in the development of various diseases

  • affect our brain chemistry and mental health, including our mood and emotions.

  • affect the sleep-wake rhythm


Kathrine Pollard, professor of biostatistics at the University of California and her colleagues are of the opinion that the same species of bacteria behave differently in different people, but most studies do not go that deep._cc781905-5cde -3194-bb3b-136bad5cf58d_Pollard's research suggests that it is not so much the type of bacteria that is important as what the bacteria produces in the body. For example, some bacteria produce anti-inflammatory molecules or vitamins like B12 and K, while others speed up the conversion of calories into body fat. Moreover, it was found that one species of bacteria can have genetic differences (7).


"A wide variety of bacteria are used as probiotics, but not all of them have equal therapeutic properties, and the fact that one is suitable for one and another for another is not insignificant."

Dr. Kaja Julge, pediatrician-allergist, children's clinic of Tartu University Clinic




The intestinal microflora, the brain, the immune and hormonal systems are very closely related.

More than a century ago, microbiologists established that the gut microflora of healthy and diseased people is different (4).


Human microflora begins to form at birth. The intestine of a newborn is sterile, which, passing through the birth canal, comes into contact with its first very necessary bacteria.

The first colonization takes place at birth and it is extremely important what kind of microorganisms the child is exposed to at the moment of birth, in very early infancy, and it is greatly influenced by the way of feeding and the use of antibiotics (3,4).


Babies born by caesarean section have different microbial communities than those born naturally. Also, a baby on mircoflora bottle feeding is radically different from a baby on breast milk. The importance of breast milk in the development of the microflora of babies has been very thoroughly studied, and studies confirm that it is breast milk that promotes the normal development of the baby's intestinal microflora, which in turn lays the foundation for a strong immune system and better absorption of nutrients (2).


The microflora of the intestinal tract plays an important role in the development of balanced immune reactions. Intestinal flora affects both innate and acquired immune mechanisms, both humoral and cellular immunity. In recent decades, a lot of attention has been paid to probiotics, their ability to prevent and treat several diseases. A wide variety of bacteria are used as probiotics, but not all of them have equal therapeutic properties, and the fact that one is suitable for one and another for another is not insignificant (4).


"Playing" with the intestinal microflora can lead to very serious consequences. If we talk about the disturbed microflora, it is worth knowing that in some people the microflora recovers in weeks, in others in months, and in others in a year. However, in some people, the imbalance of the microflora persists throughout life (10). The imbalance of microflora is calleddysbiosis, where in this case there is an insufficient amount of so-called "good bacteria" in the intestine and an excess of  "bad bacteria". Dysbiosis is believed to be the root cause of many health problems. Problems such as yeast infections, irritable bowel syndrome, chronic fatigue syndrome, rheumatoid arthritis, type II diabetes. The most common symptoms that may indicate an imbalance of the intestinal microflora are flatulence, heartburn, abdominal cramps, bad breath, constipation and diarrhea. Dysbiosis can also be indicated by unusually high fatigue, joint pain, headaches, depression, anxiety and weakened immunity (6,8).


In recent years, scientists have made great strides in studying the impact of the microbiome on human health more broadly. When it comes to obesity, scientists have said that the gut is one of the forgotten organs that actually plays a central role in the problem. Studies have found that the microflora of the stomach affects the absorption of fat, glucose and cholesterol in the small intestine, and also whether the body rather burns fat or "stores" it (12). Therefore, the problems with weight go much further than just "eat less - move more". 

Among other things, it has been found that the microbiome can also play an important role in the development of autoimmune diseases (5,13).


It has also been studied that during pregnancy, the microflora of a woman's gut changes drastically - major changes occur in the third month of pregnancy.  Here, the changes did not depend on the initial weight, nutrition, or the woman's general health._cc781905-5cde-3194-bb3b -136bad5cf58d_ Similar changes occur in diabetes (insulin resistance syndrome) - a person's weight increases, insulin sensitivity decreases, and blood sugar  levels increase. Sometimes these changes are severe enough to be diagnosed as gestational diabetes. However, it remains unclear why exactly the microbiome changes so dramatically during pregnancy. It is thought to be initiated by a change in the female immune system (13,14).





Studies have shown that the effect of a change in the menu on the microflora can be manifested within 24 hours (8). 


Among other things, they have a harmful effect (6,8):


  • stress - both physical and psychological

  • chronic infections

  • environmental toxins

  • antibiotics, NSAIDs (nonsteroidal anti-inflammatory painkillers such as diclofenac, aspirin, ibuprofen, etc.)

  • sugar, refined carbohydrates and processed foods

  • protein-rich food and a low proportion of fiber in the menu

  • gluten

  • plant protection products

  • alcohol


Among other things, they support:


  • enough fiber in food (add fruits and vegetables, berries to the menu)

  • prebiotic foods: flaxseeds, oatmeal, legumes (chickpeas, lentils, beans), fruits and vegetables (especially bananas, onions, leeks, potatoes)

  • probiotic foods: acidified foods such as yogurt, sour milk, kefir, acidified sauerkraut (and other acidified vegetables), acidified saladkimchi, fermented soy. However, it is important to know that acidified foods are not suitable for everyone, precisely because of the biogenic amines they contain, which can cause health problems for some people, especially those who are sensitiveto histamine;

  • drinking clean water daily

  • moderate physical activity and daily exposure to fresh air






The well-being of our microbiome depends on our food and lifestyle choices.  If the intestinal microflora is out of balance, it is a favorable ground for the development of various diseases (both acute and chronic).


Of course, not all bacteria are good for our health, but it is important to keep the good and bad bacteria in balance, and we can do this by consciously watching our diet and lifestyle. It is clear that with a conscious choice of food we can influence the microflora of our intestines and it is known that the change can take place within 24 hours.


As Jeroen Raes PhD, one of the leading researchers in the study of the human microbiome, says that knowledge of the human microbiome is still in its infancy. Scientists have already discovered a great deal about the community of microbes and their genes in the human microbiome, but much remains to be discovered.



Take care of your health by taking care of your friends!




Used sources:


1. Chutkan, R., MD. The Microbiome Solution. 2015 Mon. 3-5

2. Duke University Medical Center. Breast milk promotes a different gut flora growth than infant formulas. ScienceDaily, 27 August 2012. <>.

3. Benno Y, Mitsuoka T. Development of intestinal microflora in humans and animals. Bifidobacteria Microflora 1986;5:13–25.

4. Julge, K. "The role of intestinal microflora in influencing immunity and the importance of probiotics in disease prevention and treatment" Eesti Arst 2007; 86 (4): 282–286

5. Mathis, D; Benoist, C. Microbiota and autoimmune disease: The Hosted Self.  Cell Host & Microbe, Volume 10, Issue 4, p297–301, 20 October 2011, /cell-host-microbe/abstract/S1931-3128(11)00292-7

6. Mercola, J. How your microbiome controls your health, 2014,

7. Mercola, J. You Are What Your Microbes Eat, 2015

8. Muller, A., MSc. Can gut bugs make you fat?, Optimum Nutrition Magazine, p. 16-18, Autumn Issue 2012

9. Päärt, V. "Who live in our stomach", Novaator 2010,

10. Raes, J, PhD. The gut flora: You and your 100 trillion friends, 2012

11. Siigur, U., "Digestive tract microflora and obesity".







Strober, W “Inside the microbial and immune labyrinth: Gut microbes: friends or fiends”, Nature Medicine VOL 11/2010 (Impact Factor: 27.36). 11/2010; 16(11):1195-7. DOI: 10.1038/nm1110-1195




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