Bacteria in the gut: the most important questions and answers

Bakterien im Darm: Die wichtigsten Fragen und Antworten

The topic of bacteria in the intestine is becoming more and more present in research. Many different studies and works deal with this area. However, the research is still in its infancy. It is anticipated that many aspects of the gut remain unexplored. Not all assumptions are absolutely clear. Many connections and elements have not yet been sufficiently investigated.

This article aims to help clarify significant facts and questions about the bacteria in your gut. The most important points are answered here. This should help you to better understand the intestine and the intestinal bacteria it contains, their functions and tasks.

the essentials in brief

  • The gut contributes to your immune system. 70 to 80% of all immune defense cells are located in the intestine. A healthy intestinal flora therefore contributes to your health.
  • There are different types of food to strengthen your intestinal flora. Probiotic foods help to build up the intestinal flora. Prebiotic foods support the existing good bacteria in the gut.
  • Dangerous bacteria can be picked up by spoiled, bad food. But poor hygiene, especially after going to the toilet, can also lead to the ingestion of bad bacteria.

Bacteria in the gut: what you should know

Many things have not yet been clarified in connection with our intestines. Therefore, in the next section, we want to answer the most important, open questions as best we can. We try to weigh all important issues against each other and create clarity about this topic.

But a peculiarity at the beginning. The gut is a very important part of our body. He is not only responsible for digesting food. As you will see, it plays a huge role in our health. The largest part of our immune system is in it.

That's why you should always make sure that your intestines are doing well. The bacteria in the gut should be in balance. Eat a balanced, gut-friendly diet and drink enough fluids. This is the best way to support your intestines and the bacteria they contain.

Development of bacteria in the intestine

In infants who are just being born, the intestines are still largely sterile. This means that there are only a few bacteria in the intestines of a newborn. It has long been assumed that the intestinal bacteria only develop after birth.

However, researchers have discovered that the unborn child already comes into contact with bacteria in the mother's womb, which then find their way into the mother's intestines. These bacteria get into the intestines of the unborn child via the amniotic fluid or the umbilical cord, for example. During birth and throughout the life of every human being, the intestinal bacteria continue to develop. They multiply and the number of gut bacteria increases (6).

The resulting ecosystem consisting of the intestinal bacteria is also called the microbiome. It refers to all of the colonization of bacteria in your intestines. That is, all bacteria that are in the intestine. The microbiome is made up of many different bacteria; archeae, viruses, phages, yeasts and fungi can also be found in it.

Another important term that we should clarify is the intestinal flora. It represents the amount of all microorganisms that colonize the intestines. The intestinal flora, i.e. the bacterial ecosystem of our intestines, is composed differently in each person. It is as individual as a fingerprint(1).

Did you know that the intestinal surface is around 400 to 500 square meters? That's almost 2 tennis courts.

Which bacteria settle in an intestine also differs from person to person. It depends on various factors and life circumstances. For example, different bacteria are found in infants born vaginally than in infants born by cesarean section. Whether you were breastfed as a baby or not also plays a role.

The circumstances in which a person lives, where they come from or the environment in which they find themselves are also important. In addition, certain components of the colonization of the bacteria in the intestine can be linked to the genetic material (2).

In addition to the aspects already mentioned, diet is also a very important factor. It also influences the colonization of your intestines. The consumption of different foods contributes to the absorption or formation of different bacteria. That is why, for example, whether you eat vegan or vegetarian food, eat meat or eat very greasy food plays a role in the composition of the bacteria in the intestine (2).

What is the function of bacteria in the gut?

You now have an overview of the development and composition of intestinal bacteria. But what do intestinal bacteria do for your body and how do they work? The beneficial bacteria in your gut have a positive and important function. However, there are also gut bacteria that can harm your body. But more on that later.

human body with its vessels

Here you can see the human body with all its vascular and blood connections. Everything in the body is connected. The intestine plays a large and important role for humans. (Image Source: John Jackson / Unsplash)

On the one hand, intestinal bacteria are an important part of digestion. They help digest certain nutrients, such as whole grains, certain vegetables, and fiber. They also make the energy contained in food available to your body. He can then draw on this energy. In addition, the intestinal bacteria provide your body with vitamins, enzymes, as well as fatty and amino acids (7).

On the other hand, the bacteria in the intestine are an important part of your immune system . The intestinal bacteria prevent unwanted germs and pathogens from settling and multiplying. In addition, they fight toxins, so-called toxins, and promote the production of antibodies (3).

What types of bacteria are there in the gut?

It is normal for a large number of bacteria to settle in your intestines. You have already learned what the intestinal bacteria are useful for. However, not only positive bacteria can colonize your intestines, but dangerous bacteria can also invade. The following part shows the different types of bacteria in your body. This should give you an overview.

What are good bacteria in the gut?

Most gut bacteria are useful and helpful to your body. You need them for your health and your immune system . Beneficial bacteria in your gut include:

  • Lactobacillus
  • Bifidobacterium
  • Lactococcus
  • Lactobacillus bifidus

These bacteria contribute to a healthy intestinal flora.

What are bad or dangerous bacteria in the gut?

However, there are also bacteria that damage your intestines and thus your health.

Type Description
Aeromonas Also known as a hospital pathogen. It is commonly found in freshwater.
Bacillus cereus This is the typical causative agent of food poisoning.
Campylobacter jejuni/ coli These bacteria can be responsible for Guillan-Barreé syndrome, a nerve disease.
Clostridium difficile/perfringens May occur due to treatment with antibiotics.
EHEC EHEC means Enterohemorrhagic Escherichia coli. These toxic bacteria can damage kidney vessels.
EPEC Means Enterohemorrhagic Escherichia coli. This bacterium is common in infants.
salmonella This type of bacteria is common in rotten egg dishes, such as mayonnaise or tiramisu
shigella These bacteria are usually caught abroad in warmer areas.
Staphylococcus aureus These bacteria lead to poisoning by formed toxins. It leads to classic food poisoning, which usually only lasts 24 hours
Yersinia enterocolitica These bacteria are often found in children. They can be followed by diseases such as joint inflammation.
vibrios These bacteria are common in tropical climates. Especially in countries that are located by the sea.


So there are a variety of bacteria that can be dangerous for you and your intestines. That's why we want to show you later how you can best protect yourself against these unwanted intestinal bacteria and what options there are for preventing diseases.

How many types of bacteria colonize the gut?

Researchers have found around 1400 different types of microorganisms in the microbiome in our gut. Every single person has around 160 different types in their intestines. Overall, the composition of the gut bacteria is unique to each individual (2).

The colon is the most densely populated known ecosystem ever found.

Between 70 and 80% of all immune defense cells, i.e. cells that are responsible for the immune system, are located in the intestine. This is precisely why it is so important for your body and especially for your intestines that you pay attention to your intact, healthy and functioning intestinal flora (1).

What are the symptoms and causes of a disturbed intestinal flora?

The symptoms that occur most frequently when your intestinal flora is disturbed are: flu infections, diarrhea, changing bowel movements, abdominal pain, food intolerance, impure skin, flatulence and chronic inflammatory bowel diseases(1).

But before you worry too much about applicable symptoms, always check your health with your doctor first. Don't jump to conclusions and always get a professional opinion.

If there is reason to believe that your bacteria in the intestine are not balanced and your intestinal flora is disturbed, your doctor will examine you accordingly. A stool examination will probably be carried out for this purpose. Your feces will be examined for germs and dangerous bacteria.

A stool test will check your stool for pathogens.

There are many different causes for a disturbed intestinal flora. A number of factors can ensure that the bacteria in the intestine are no longer in balance. These factors include, for example (5):

  • Drugs that destroy parts of the gut bacteria.
  • advancing age
  • Incorrect, undiversified diet
  • stress, lack of sleep
  • Disease-Related Causes
  • Intoxication from environmental factors such as heavy metals

The causes of an imbalanced gut microbiome can be related to serious diseases. It can lead to secondary disorders such as obesity, asthma, allergies, neurodegenerative diseases, diabetes, irritable bowel syndrome and depression. This is just a small sample of the effects that can occur when there is an imbalance in the gut (1).

A disturbed intestinal flora could also be related to diseases that affect your psyche. Therefore, you should always make sure to maintain the balance in your intestines so that there is no disturbed bacterial ratio (8).

What throws the intestinal flora off balance?

Your diet affects the bacteria in your gut. Depending on what foods you eat, this can have positive or negative consequences. In addition, circumstances such as stress, travel, illnesses, especially those affecting the digestive tract, lack of sleep and certain medications can negatively affect the intestinal bacteria and thus the intestinal flora. This can throw the microbiome out of balance (1).

Dysbiosis refers to an imbalance in the intestinal flora.

If the intestinal flora is weakened, dysbiosis can occur. This means pathogens and dangerous bacteria can multiply and increase their accumulation. The settlement of beneficial bacteria is replaced (1).

How do dangerous bacteria get into the intestines?

Contaminated food is one way dangerous bacteria can get into your gut. If these have not been stored well or the food has spoiled, you can ingest dangerous bacteria. These then pass through your digestive tract into the intestines, settle there and multiply. Foods that you should be particularly careful about are meat, fish, raw eggs or milk. If these are no longer fresh, you should keep your hands off them (4).


This image shows a medical representation of drug-resistant, non-cyphoid Salmonella sp. Bacteria. (Image Source: CDC/Unsplash)

Another way dangerous bacteria can get into your gut is through the fecal-oral route. That means you're swallowing pathogens that someone else has passed in their stool. This can happen if you don't wash your hands after using the restroom, especially public restrooms. Therefore, always observe the hygiene measures (4,11).

Which home remedies can be used to strengthen the intestinal flora?

There are various ways to strengthen your intestinal flora. We would like to present two of them to you here.

You can use probiotic foods. These are foods that contain living microorganisms such as lactic acid bacteria or yeast. Probiotic foods support your immune system , help eliminate pathogens and thereby build up your intestinal flora. Probiotic foods include Yakult, Actimel, sauerkraut, and bread drink (10).

water glass

To support your intestinal flora, you should always drink enough liquid. (Image source: Thao Le Hoang / Unsplash)

The second way to strengthen your intestinal flora are prebiotic foods, such as psyllium, linseed, wheat bran, chicory, salsify, Jerusalem artichoke. A prebiotic diet can help your gut flora by supporting and strengthening the contained good bacteria in your gut (9).

In the following table we would like to clarify the exact difference between the two types.

kind For what is this good?
Probiotic Foods Build intestinal flora.
Prebiotic Foods Support bacteria that are already present in the intestinal flora.

In conclusion, it should be said that you should eat a varied diet. Drinking enough is also very important.


Although research into the gut has increased in recent years, much remains undiscovered. There are a multitude of studies that have uncovered some aspects, functions and workings of the gut. However, far from everything in the field of the human intestine has been sufficiently treated. Research is far from covering all the details.

The subject areas that have been researched to date have mostly provided well-founded and significant results for the elucidation of the functioning of the intestine and its bacteria. In any case, a lot of research still needs to be done in order to fully understand the entire intestine and all its special features.


  2. Prof. Michael Blaut (2015), We are colonized: Intestinal bacteria influence our health
  3. Patrice D Cani (2018), Human gut microbiome: hopes, threats and promises
  4. examined by Prof. Dr. re. of course Udo Reischl (2014), Stool examination for bacteria: Salmonella and Co.
  5. DocMedicus, imbalance of the intestinal flora (dysbiosis)
  6. dr re. of course Markus Brüngel (2017), The development of the intestinal flora - setting the course for life
  7. dr Fabian Frost, PD Dr. Georg Homuth, Prof. Dr. Markus M. Lerch (2020), Study by the University Medicine Greifswald clarifies which diseases damage the intestinal flora and the long-term stability of the bacterial intestinal microbiome
  8. Joachim Czichos (2019), study confirms possible influence of the intestinal flora on the psyche
  9. Hakan Öztürk (2003), In vitro studies on the influence of Jerusalem artichoke flour and Saccharomyces boulardii on the microbial forestomach metabolism
  10. Karin Stockert (2020), Allergy, microbiome and other epigenetic factors
  11. Prof. Dr. Ralf Bialek (2013), Gastrointestinal Infections
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