Antibiotics and the microbiome: consequences for the gut and health

The infection is over, the antibiotic has worked – everything should be fine now. But sometimes the body doesn’t feel back in balance afterwards: Digestion goes crazy, the immune system seems to react more sensitively or the psyche also feels stressed. This is where the interplay between antibiotics and the microbiome becomes important: can antibiotic therapy change our microbial balance – and what consequences can this have?

Antibiotics can save lives in an emergency because they can treat bacterial infections that can become life-threatening without treatment. However, this effect also has a downside: antibiotics do not distinguish between dangerous pathogens and the bacteria that play an important role in our health as part of our microbiome. So what happens when antibiotic therapy not only fights the infection, but also changes our microbial balance? What is the interaction between antibiotics and the microbiome? Sometimes the consequences are immediate. Sometimes they remain as subtle traces – and only become visible many years later: in the gut, the immune system, the metabolism or even in the psyche.

It is therefore easy to see antibiotics as a medical miracle cure. But how do they actually achieve this?

How do antibiotics work?

The short answer is: against bacteria. This narrowing down is important because it explains why we sometimes drag ourselves to the doctor completely exhausted and still don’t get a prescription for antibiotics. This is usually due to a viral infection. Antibiotics can do nothing against it.

A distinction is made between broad-spectrum and narrow-spectrum antibiotics. Broad-spectrum antibiotics are effective against many different types of bacteria. They are often used when the exact pathogen is not yet known or needs to be treated quickly. Narrow-spectrum antibiotics have a more targeted effect against certain groups of bacteria and are mainly used when the pathogen can be narrowed down more precisely.

The mode of action of antibiotics can basically be divided into two groups: bactericidal (bacteria-killing) and bacteriostatic (inhibiting the growth of bacteria) antibiotics. Depending on the active ingredient, they attack different structures or processes that are specific to bacterial cells. As a result, bacteria can be specifically targeted, while human cells are hardly affected:

• They disrupt the replication of DNA and thus the division of bacteria.
• They inhibit the formation of RNA or proteins so that important building blocks are missing.
• They disrupt the structure of the cell wall and thus prevent the bacteria from continuing to grow stably.

In a nutshell: Antibiotics interfere with the vital mechanisms of bacteria! This makes them an effective weapon against bacterial pathogens – but does their effect end there, or do they also have consequences that we may have paid too little attention to for too long?

When antibiotics affect the microbiome

For a long time, the intensive use of antibiotics focused research on one problem in particular: the increase in resistance genes. In recent decades, however, another concern has become increasingly pressing – one that could have insidious and previously overlooked consequences for us humans: the question of what antibiotics do to our microbiome. This is because antibiotics not only act against pathogens. Because they attack basic bacterial structures, they often also affect the bacteria that perform important tasks in our bodies.

Our microbiome is the entirety of all microorganisms that live in and on our body and their genetic information. It comprises around 38 trillion bacteria, over 95% of which are found in the large intestine. For a long time, the microbiome was primarily attributed a role in digestion. Today, however, it is clear that this view has vastly underestimated the importance of our microbiome. The bacteria are in constant communication with our body: they help to keep pathogens at bay, support the stability of the intestinal barrier, influence our immune system and produce metabolic products that are relevant for both our physical and mental health. If this delicate balance is disturbed, it can therefore have far-reaching consequences .

Antibiotics upset this balance. And even in the long term. A very recent study from 2026 examined the gut microbiome of almost 15,000 people and showed that the bacterial composition can be altered even years after antibiotics have been administered and that the microbial diversity is sometimes lower. Other studies also indicate that individual bacterial species do not always fully recover after antibiotic therapy and can therefore leave scars in the microbiome.

But what impact do these changes actually have on our health?

Consequences of antibiotic-associated dysbiosis

If the composition of our body’s own bacteria is disturbed, this can have various consequences. Some of these become apparent immediately after antibiotic therapy and are already well documented scientifically. Others only become visible in the long term and are therefore somewhat more difficult to record scientifically. Nevertheless, the evidence is piling up here too!

Antibiotics and the microbiome: Acute consequences

The major change in our microbiome is particularly relevant because it plays an important role in protecting us from opportunistic pathogens. This is particularly important because few areas of our body come into contact with as many potential pathogens as our digestive tract. With every sip of water and every bite of food, microorganisms are constantly entering our bodies.

Normally, this is of relatively little concern to us because our body is well protected . Especially in the gut, our microbiome is an important part of this protective function – in several ways:

1. Competition for space and nutrients
2. Production of antimicrobial substances such as bacteriocins
3. Strengthening the intestinal barrier
4. Training the body’s own immune system

All of a sudden, this protective system is shaken – and pathogens can take advantage of this. Probably the best known of these is C. difficile, which is responsible for around 15-20% of antibiotic-associated diarrheal diseases. If left untreated, an infection can become life-threatening in severe cases.

Acute consequences of antibiotic therapy are therefore not just an abstract change in the microbiome. They can directly weaken the natural protective function of the intestine and thus increase susceptibility to further complaints and infections. This is precisely why it is important to be aware of this temporary weakening and to take reactions of the body such as severe diarrhea, blood in the stool or fever particularly seriously.

Antibiotics and the microbiome: long-term consequences

1. consequences for the intestine

Over 95% of our bacteria are found in our intestines, more precisely in our large intestine. It is therefore not surprising that antibiotic treatment can lead to intestinal diseases.

Every year, around 10,000 people are newly diagnosed with chronic inflammatory bowel disease (IBD), mostly ulcerative colitis or Crohn’s disease. These diseases are particularly common in industrialized countries. The development of IBD is usually due to a combination of genetic susceptibility, environmental factors and microbial dysbiosis, which ultimately leads to a misdirected immune response in the intestine.

One of these environmental factors is the administration of antibiotics. It has not yet been conclusively clarified how antibiotics are linked to the development of IBD. This is probably because antibiotics weaken the intestinal microbiome and thus trigger processes that can promote IBD – such as an impaired nutrient supply, a weakened mucosal barrier, altered metabolic products and a misdirected immune response.

Irritable bowel syndrome is a functional bowel disease with recurring symptoms such as abdominal pain, flatulence, diarrhea or constipation, without a clearly identifiable cause. Microbial dysbiosis is considered an important possible factor in the development of irritable bowel syndrome. It is therefore not surprising that antibiotic therapies are associated with later irritable bowel syndrome. On the other hand, there are also cases of irritable bowel syndrome, especially irritable bowel syndrome with diarrhea, in which the symptoms can improve significantly after treatment with rifaximin, an antibiotic. This is presumably due to the fact that rifaximin has a positive effect on an existing microbial overgrowth and possibly also reduces bacteria that are present in excessive quantities in the small intestine.

2. consequences for the metabolism

Metabolic diseases are also repeatedly associated with antibiotic-related changes in the microbiome. Studies suggest that antibiotic use, especially repeated use in early childhood, may be associated with an increased risk of obesity later in life.

Associations have also been described for type 2 diabetes in large observational studies. For example, a systematic review from 2021, which included data from more than 3.9 million people, showed that antibiotic exposure was associated with an increased risk of type 2 diabetes. The effect was rather moderate, but still clearly measurable.
However, a causal relationship has not yet been clearly proven. One possible mechanism being discussed is that antibiotics could alter the intestinal microbiome and thus reduce the formation of short-chain fatty acids such as butyrate. As a result, the intestinal barrier could be weakened, making it easier for bacterial components such as LPS to pass through the intestinal wall. This could promote low-grade inflammatory processes, which in turn could impair insulin action.

3. consequences for the immune system

The microbiome is a kind of training partner for the immune system. Especially in the first years of life, both systems develop closely together: the immune system learns to differentiate between harmless companions and real invaders, and the microbiome helps it to control its reactions in a meaningful way.
If antibiotics change this microbial training environment, the communication between the microbiome and the immune system can also shift.

In particular, studies have linked antibiotic use in the first few years of life to an increased risk of allergies and asthma later in life.
A connection between antibiotic use and subsequent microbiome changes is also being discussed for autoimmune diseases such as rheumatoidarthritis, multiple sclerosis or type 1 diabetes – the study situation here is less clear to date.
A study from 2025 is also interesting in this context: it showed that newborns who had received antibiotics immediately after birth later showed a lower immune response to certain vaccinations. Their immune system did react, but less strongly – due to changes in the early microbiome.

4. consequences for the psyche and brain

Our gut bacteria are in constant communication with our brain via the so-called microbiota-gut-brain axis.
It is therefore not surprising that mental illnesses such as depression and anxiety disorders are also associated with a dysbiotic microbiome .
A study from 2024 examined almost 200,000 people from South Korea who had received antibiotics in the previous 1 to 9 years and was able to show that antibiotics are associated with an increased risk of developing depression. The broader the effect of the antibiotic, i.e. the more bacteria it affected, the more pronounced the link was.

Conscious use of antibiotics

Antibiotics have revolutionized medicine – and they are still saving lives today. Nevertheless, we can also view them with a critical eye. After all, antibiotics do not work in an empty space. They come into contact with a body that is co-inhabited by trillions of microorganisms. And we should bear these consequences in mind when deciding on antibiotic therapy.

The good news is that even though antibiotics affect our microbiome, we are not completely at the mercy of these changes. Diet, lifestyle and a sensible approach to antibiotics can play a role in strengthening the resilience of the microbiome and creating favorable conditions for its recovery.

The key message is therefore not to be afraid of antibiotics. Rather: understand their effect – and deal with them consciously.

Bibliography and further reading

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