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Digestive Disorders > Lower Abdomen

Intestinal flora: The basis for healthy digestion and a weak point in many diseases

Dr. med. André Sommer

Dr. med. André Sommer

The term “intestinal flora” refers to all bacteria in the gut. They contribute significantly to healthy digestion and protection against foreign and harmful bacteria. This article explains how the intestinal flora is composed, how it looks in healthy people and what changes there are with diseases.

What is intestinal flora?

In addition to the body's own cells, the human intestine also contains a considerable amount of foreign microorganisms that are only visible under the microscope. The entirety of the microorganisms in the intestine is called the intestinal flora or intestinal microbiota. Another commonly used synonym is gut microbiome, but some scientists use this term specifically to refer to the entire genome of the microorganisms.

The intestinal flora consists largely of bacteria. Intestinal bacteria and humans live in a symbiotic relationship, which means that both partners benefit from each other: The intestinal bacteria perform numerous metabolic and protective functions for the human organism, while the human intestine offers a protected, nutrient-rich habitat for the microorganisms.

The intestine is home to the majority of all microorganisms. It is assumed that 200 grams of the intestinal weight are due to bacteria. The number of genes of the microorganisms in the intestine clearly exceeds that of their host.

What does intestinal flora do?

1. Intestinal flora supports the metabolism

Thanks to the enormous genetic diversity of the different types of bacteria, the intestinal flora can take on numerous functions that human cells cannot perform or only perform to a very limited extent:

  • Production (synthesis) of vitamins B1, B2, B6, B12, K
  • Synthesis of all essential and non-essential amino acids (the body can also produce non-essential amino acids itself, essential amino acids must be ingested with food)
  • Dismantling and disposal of toxic substances
  • Breakdown of carbohydrates that human cells cannot digest

The intestinal flora generally improves the nutrient supply to the human body. In some cases, however, an impaired function of the intestinal flora can also be the cause of indigestion. With lactose intolerance, for example, the milk sugar (lactose) in milk products is not broken down by the enzyme lactase in the small intestine of the host, as is otherwise the case, but by the intestinal flora in the large intestine. This can create gases and can lead to bloating, abdominal cramps and diarrhea.

2. The intestinal flora protects its host and its immune system

Similar to the animal world, bacteria compete against each other in the intestine for limited food. The intestinal flora located in the intestine often has a survival advantage over new, harmful (pathogenic) types of bacteria. As a result, the natural intestinal flora displaces harmful germs and can effectively prevent re-colonization by pathogenic bacteria. In ecology this is called the “exclusion of competition principle.”

The intestinal mucosa has a much larger surface area than the skin, so the intestinal system in the intestine has to protect particularly against harmful external influences. The intestinal wall, as the largest interface between the body and the outside world, therefore plays an important role in the development of the human immune system. The continuous interaction between intestinal flora and immune cells can have a major impact on the immune system.

It is believed that the composition of the intestinal flora in early childhood in particular has a far-reaching effect into adulthood. For example, there seems to be a connection between early childhood intestinal flora and the development of allergies: Children with an improperly developed intestinal flora are more likely to develop an insufficiently trained immune system that overreacts when in contact with substances that are actually harmless (allergy).

3. The gut flora and our nervous system - the microbiome-gut-brain axis

The so-called microbiome-gut-brain axis is a communication system that mediates hormonal and immunological signals and nerve signals between the microbiome, gut and brain.

This system enables the brain to control important intestinal functions (e.g. intestinal mobility, mucus production and immune defense), which also affects the survival of the different types of bacteria. For example, it is known that the chemical environment of the bacteria and thus the composition of the intestinal flora can change under stressful situations. This system may also work the other way around and bacterial products can enter the brain.

There is also evidence that the intestinal flora, via the microbiome-gut-brain axis, could play a major role in the development of diseases of the nervous system (e.g. Alzheimer's, Parkinson's). This applies, for example, to experiments in which rats were used as a model to study the disease. It was shown here that a protein that is typically increasingly deposited in the brain of Parkinson's patients (alpha-synuclein) can migrate into certain areas of the brain via nerve fibers if it is injected into the intestinal wall of the rats.

Another mechanism through which intestinal bacteria could act on the brain is mediated by the serotonin level in the blood. Serotonin is a messenger substance in the nervous system. If there is insufficient serotonin in relation to the need, depression can occur.

Serotonin is produced both in the brain and outside the brain (peripherally). The majority of the peripherally produced serotonin comes from the intestine and the intestinal flora could influence the amount of serotonin in the blood and ultimately the signal processing of the brain by changing the serotonin secretion of the intestine. However, there is a barrier between the brain and blood (the so-called blood-brain barrier) that protects the brain from being immediately affected by blood components. It is therefore not entirely clear to what extent the serotonin produced in the intestine can actually work in the brain.

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How is the intestinal flora composed?

There is a very uneven distribution of the bacterial flora within the digestive tract. Mainly because of the strong acidic gastric acid, which limits the survival of bacteria, the stomach and the subsequent small intestine are almost bacteria-free. On the other hand, there are many microorganisms in the colon.

So far, around 50 different strains of bacteria have been identified in the human gut. However, the intestinal flora essentially consists of the following two strains of bacteria:

  • Firmicutes
  • Bacteroidetes

How does the intestinal flora form in newborns?

Newborns hardly have any bacteria in their intestines. The human intestine is colonized by bacteria for the first time during the birth process. The initial intestinal flora differs in natural births (bacteria from the maternal vaginal flora) and Caesarean section births (bacteria from the maternal skin flora).

The nutrition of the newborn also plays a particularly important role. The higher percentage of so-called bifidobacteria in the intestine of breastfed children compared to children with formula food (artificial milk) is just one example. One possible explanation for this is that breast milk contains bacteria that also influence the colonization behavior of other bacteria.

With the transition to solid food, the composition of the intestinal flora changes significantly: the lactose-decomposing bacteria, which previously had a central function, are replaced by other types of bacteria. These bacteria can utilize carbohydrates, proteins and fats and also form vitamins. It is also known today that certain diets such as the low-FODMAP diet change the intestinal flora.

FODMAP stands for “Fermentable Oligo-,** Di-, **Monosaccharides and Polyols”. These are carbohydrate building blocks that are poorly absorbed through the intestinal wall and thus remain in the intestine and are metabolized by bacteria.

Even in adulthood, the microbiome can be changed drastically by diet. For example, an increased proportion of firmicutes has been observed in obese people, whereas a diet high in fiber and low in fat appears to reduce their proportion.

The fact that the composition of the intestinal flora can differ even in healthy people can be explained by the fact that many functions are performed by several types of bacteria. A reduced proportion of one species can thus be compensated for by the increased proportion of another species.

What do intestinal flora have to do with IBS?

A more or less stable balance between the gut microbiome and the host organism that settles in adulthood is called eubiosis. Under certain circumstances, this balance can be disturbed in terms of the number and composition of the bacteria (dysbiosis, improper colonization). This is the case, for example, if a wide range of bacterial species is killed in the course of long-term treatment with an antibiotic. Even with severe diarrhea, there is often a shift in the intestinal flora, which can favor post-infectious irritable bowel syndrome.

Such drastic dysregulation is often accompanied by acute side effects. It is believed that a strongly disturbed intestinal flora can favor a number of diseases. These diseases include, for example, obesity, type 2 diabetes, Alzheimer's, Parkinson's and chronic inflammatory bowel diseases such as ulcerative colitis and Crohn's disease, in which the immune system attacks its own intestine. This also applies to irritable bowel syndrome.

Various mechanisms contribute to dysbiosis in irritable bowel syndrome. On the one hand, the altered balance of the intestinal flora can result in a change in the bacterial metabolism. On the other hand, due to the weakening of the resident microbiome, pathogenic bacteria can more easily settle on the intestinal wall or even penetrate into it. In addition, the small intestine can be colonized incorrectly. This means that bacteria from the colon migrate into the small intestine. As already mentioned, the small intestine in healthy people is largely free of bacteria.

What role do intestinal flora have in treating IBS?

Since the intestinal flora plays a crucial role in the development of irritable bowel syndrome, it also represents a possible target for treatments.


These are preparations of useful bacterial cultures that are then supposed to colonize the intestine. Probiotics are available in various dosage forms, such as in tablets or yogurts. So far, however, there has been no precise scientific understanding of the effectiveness of probiotics on irritable bowel syndrome.

Stool transplant

With a stool transplant, the stool of a healthy donor is inserted (implanted) into the intestine of a sick recipient. This is usually done as part of a colonoscopy. The donor has to meet certain conditions, the stool is examined (for example for pathogenic bacteria) and then purified. Only then will the recipient be treated with it.

With clostridium difficile-associated diarrhea_ (a diarrhea caused by the bacterium _clostridium difficile), this method is sometimes successfully used as the last resort. “Last resort” means that all other therapy options have been tried first. This diarrheal disease can develop after therapy with antibiotics if as a side effect many of the beneficial intestinal bacteria have been killed and therefore the harmful bacterium clostridium difficile can take over in the intestine.

The benefits of stool transplantation for chronic inflammatory diseases and irritable bowel syndrome have not yet been demonstrated and is the subject of current research. So far, however, only a few people have benefited from a stool transplant as part of these studies.

What is certain is that the side effects and long-term consequences of stool transplantation cannot yet be estimated with certainty. Especially in the case of an injured bowel (e.g. in the context of an inflammatory bowel disease), bacteria in the transplanted stool can get into the blood of the recipient. This has already resulted in deaths from blood poisoning.

At the moment, several drugs are in the test phase, which synthetically replicate parts of the stool transplant in order to have a more controlled and positive effect on the intestinal flora in other ways (e.g. via tablets).

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Dr. med. André Sommer

Dr. med. André Sommer

I’m André, a medical doctor from Berlin. Together with a team of medical doctors, nutritionists and data scientists we empower people to understand digestive issues with our app Cara Care.

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