The Human Microbiome

People and bacteria go hand in hand. Bacterial colonies protect the body against pathogens. Newborns receive their first bacteria from their mothers. 

There are about as many microorganisms on and in the body as there are human cells, estimated at 30 billion (3 x 1012) cells. Most of these microorganisms are bacteria, but fungi, viruses and prokaryotes (archaea, which are unicellular organisms without a nucleus) are also present. The body needs all of these microscopic beings to stay healthy. With the right combination, the body is protected against pathogens and allergies.

Microorganisms colonise the skin and mucous membranes. They are also found in the internal organs. All the microorganisms as a whole within one biological environment are referred to as the microbiome. Most microorganisms live in the gut microbiome.

A balance of bacteria and human cells

Even today, it is often claimed that people contain ten times more bacteria that human cells. This assumption is based on a nearly 50-year-old calculation made by an American chemist who quantified the human microbiome based on the entire surface of the alimentary tract and its bacterial density (Luckey 1972). What he did not know was that the environment in the upper gastrointestinal tract, i.e. from the mouth to the small intestine, is so acidic that very few bacteria can survive there. Microorganisms can only find optimal living conditions in the lower third of the small intestine and in the large intestine.

With this knowledge, researchers from the Weizmann Institute of Science in Rehovot, Israel, have recalculated the gut microbiome (Sender 2016). The resulting estimate is a balanced ratio of bacteria to human cells (Sender 2016).  An adult weighing 70 kilograms has about 38 trillion (3.8 x 1012) bacteria.

Microbiome starter kit from the mother

The scientists are currently still arguing whether children come into contact with their first bacteria in the womb or only at birth via the birth canal and contact with the outside world.

Previously, it was assumed that the uterus is ‘sterile’ ­– that it does not contain germs. However, several studies are now overturning this long-held dogma. “Recent studies have detected bacterial DNA in amniotic fluid and in newborns’ first bowel movement”, says Lisa Stinson of the University of Western Australia in Perth, Australia.

The microbiologist and her team discovered this in their own study (Stinson 2019): In all 50 newborns examined, they detected bacterial genetic material in the first bowel movement (meconium) and also in amniotic fluid in four out of five newborns. Critics say that this could also have been due to contamination at a later stage, and that the bacteria could have entered the samples when they were taken, transported or at some point in the laboratory. More studies will be needed to determine who is right.

The hunt for the perfect microbiome

Not everyone lives with the same microorganisms. The number and diversity of species varies from person to person and changes over the course of life. Researchers around the world are trying to understand why and to determine the optimal composition. But so far they have not succeeded. The system itself is complex, as is the way it interacts with the human body.

“Each individual has their own highly individual ‘bacterial profile’ at birth and in the initial months of life. Researchers compare it to the human fingerprint in terms of how difficult it is to change,” explains Angela Sommer from the editorial office of Quarks, the science programme of Westdeutscher Rundfunk in Cologne (Sommer 2019).

When the balance tilts

“A microbiome with the wrong composition can also harm us”, explains Samuel Huber of the University Medical Centre Hamburg-Eppendorf in the German pharmaceutical publication Deutsche Apotheker Zeitung (Gerlach 2019). According to the gastrointestinal specialist, the microbiome is influenced not only by our lifestyle and diet but also by the environment and the use of medications.

These varying factors make it difficult to determine which microbiome actually causes illness and how to counteract it.

For example, the use of probiotics to prevent allergies has not yet produced any convincing results (Wang 2019). One reason could be that the products do not yet contain the correct microorganisms and/or the dosage was too low.

Stool tests are expensive and inconclusive

A detailed analysis of the microbiome in the stool can cost up to 500 euros. Simple stool tests are available starting at 100 euros. But no matter which test you choose, the results are not terribly useful. “Microbiome research is still relatively new. Any bacterial shifts that may be revealed in these stool tests cannot be linked to an illness or chronic disease”, says Stefan Schreiber, director of the Institute of Clinical Molecular Biology at the University of Kiel and vice president of DePROM (German Society for Probiotic Medicine) (Giesselmann 2019).

The German Society of Gastroenterology, Digestive and Metabolic Diseases (DGVS) also considers microbiome analyses to be “expensive and pointless” (Pfeiffer 2018).

It will be some time yet before we understand the composition of the microbiome and how it affects us. Only then can procedures be developed and their results interpreted correctly.


Last updated: 1 July 2020



Gerlach A. Das Mikrobiom und die Darmflora (The microbiome and the gut bacteria)., 20 February 2020. (In German)


Giesselmann K. Probiotika: Nicht immer von Vorteil (Probiotics: not always beneficial). Dtsch Arztbl 2019;116(33-34):A-1484. (In German)


Luckey TD. Introduction to Intestinal Microecology. Am J Clin Nutr. 1972;25(12):1292-4.


Pfeiffer J. Teuer und sinnlos: DGVS rät von Stuhltests zur Analyse des Darm-Mikrobioms ab (Expensive and inconclusive: DGVS advises against stool tests for gut microbiome analysis). Press release from the German Society of Gastroenterology, Digestive and Metabolic Diseases (DGVS); press release dated 5 September 2020. (In German)


Sender R et al. Revised Estimates for the Number of Human and Bacteria Cells in the Body. PLoS Biol. 2016;14(8):e1002533.


Sommer A. Warum Probiotika ihr Geld (noch) nicht wert sind (Why probiotics are not worth it [yet]).; Westdeutscher Rundfunk Köln, 20 September 2019. (In German)


Stines LF et al. The Not-so-Sterile Womb: Evidence That the Human Fetus Is Exposed to Bacteria Prior to Birth. Front Microbiol. 2019;10:1124.


Wang HAT et al. The Role of Probiotics in Preventing Allergic Disease. Children (Basel). 2019;6(2):24.

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