Gut microbiome: facts and myths about your inner health

Imagine carrying a complex microcosm within you that influences your digestion, immune system, mood, and even your weight. Sounds like science fiction?
In reality, the microbiome—a unique network of organisms—determines far more than just your gut health. But what happens when this balance is disturbed? Can antibiotics destroy it? And are there really “good” and “bad” bacteria? In this article, you'll learn all about the facts and myths surrounding the gut microbiome!

Table of Contents

• What is the microbiome?
• All gut bacteria are good – fact or myth?
• Antibiotics destroy the gut microbiome – fact or myth?
• Probiotics and prebiotics heal all gut problems – fact or myth?
• The gut microbiome influences mental health – fact or myth?
• The gut microbiome determines our weight – fact or myth?
• A healthy gut microbiome strengthens the immune system – fact or myth?
• Summary

What is the microbiome?

The microbiome includes all microorganisms that inhabit the human body, including bacteria, viruses, and fungi. They are found on the skin, in the oral cavity, in the gut, and in other areas of the body. The gut microbiome specifically refers to the microbes that colonize the intestine (NHI, 2025).

All gut bacteria are good – fact or myth?

The gut contains a mix of “good” and “bad” bacteria.

Lactobacilli and bifidobacteria are among the most important “good” gut bacteria that play a central role in the health of the gut microbiome. Studies show that strains of bifidobacteria support gut health, promote anti-inflammatory processes, strengthen the immune system, and may relieve symptoms such as bloating and abdominal pain (Satish Kumar, L. et al, 2022; Zhang, Y. J. et al., 2015). Lactobacillus species produce lactic acid, which helps maintain an acidic environment in the gut (Wan, Z. et al., 2022). They also help maintain the intestinal mucosal barrier, defend against pathogens, and regulate immune responses (Huang, T. et al., 2023). These bacteria also contribute to the synthesis of essential vitamins such as B3, B6, and B9 (Hamzehlou, P. et al., 2018).

On the other hand, the gut may also contain “bad” bacteria, which can negatively affect health if they multiply excessively or produce harmful substances. For example, an infection with Clostridioides difficile can cause severe diarrhea, abdominal pain, and fever—especially when the balance of the gut microbiome has been disrupted by antibiotics (Mayo Clinic, 2023). Another example is Escherichia coli. In excessive amounts or in pathogenic forms, they can lead to diarrhea or mild fever (Cleveland Clinic, 2023).

A balanced gut microbiome with a diverse range of microorganisms is therefore essential for health.

Did you know that your gut microbiome is as unique as your fingerprint?

Every person has an individual composition of microorganisms influenced by genetics, diet, environment, and lifestyle. This unique bacterial community, in turn, affects our personal health—for example, our energy and performance levels, susceptibility to disease, or overall well-being (Williams, S., 2024). With personal initiative, a healthy lifestyle, and good nutritional habits, we can harness its potential.

Antibiotics destroy the gut microbiome – fact or myth?

Antibiotics have both short- and long-term effects on the gut microbiome. They impact the microbiome broadly and do not only target specific bacteria. This means that “good” gut bacteria are also killed along with the “bad” ones. The result is a reduced diversity and an altered composition of the gut microbiome (Labor Limbach, 2024).

The good news, however, is that the gut microbiome can recover after antibiotic therapy. Depending on the type of antibiotic, duration of intake, and individual factors such as diet and lifestyle, this recovery can take weeks to months (Ng, K. M., et al., 2019; UCLA Health, 2024).

Probiotics and prebiotics cure all gut problems – fact or myth?

• Probiotics are foods or dietary supplements that contain live microorganisms and are intended to maintain or improve the “good” bacteria (normal microflora) in the body. They are found in fermented foods such as yogurt, sauerkraut, and kefir.
  
• Prebiotics are foods (usually high-fiber foods) that serve as nourishment for the human microflora. They are used to improve the balance of these microorganisms. Key prebiotics include inulin and oligofructose, which are found in foods like onions, garlic, bananas, and chicory.
  

Source: Mayo Clinic, 2022. 

Probiotics and prebiotics are currently considered more as dietary supplements than medicinal products, which limits their clinical application. They support gut health but cannot cure all gut problems. Probiotics promote beneficial bacteria, reduce harmful substances, and produce health-promoting compounds. Prebiotics serve as food for good gut bacteria, promote their growth, and thereby contribute to maintaining health and treating certain conditions (Ji, J. et al., 2023). 

Pre- and probiotics can positively influence certain diseases. One study shows that probiotics, prebiotics, and synbiotics can help reduce intestinal inflammation and improve symptoms in inflammatory bowel diseases (Zhang, X. F., et al., 2021). However, in diseases such as Crohn’s disease and acute pancreatitis, they show no proven effect (Wilkins, T., & Sequoia, J., 2017).

The gut microbiome influences mental health – fact or myth?

The gut microbiome plays a crucial role in mental health. Dysbiosis—an imbalance of gut bacteria—is associated with conditions such as anxiety disorders, depression, bipolar disorder, and schizophrenia. Studies show that people with mental health issues often exhibit lower microbial diversity and a lack of health-promoting bacteria, while pro-inflammatory pathogens are more prevalent (Xiong, R. G. et al., 2023).

For example, a damaged intestinal barrier resulting from dysbiosis can allow bacteria to enter the bloodstream and trigger inflammation that affects the entire body and is linked to psychiatric disorders (Mhanna, A. et al, 2024). Furthermore, dysbiosis can interfere with the production of neurotransmitters that regulate mood, potentially leading to an imbalance in the brain and increased susceptibility to mental health disorders (Delanote, J. et al., 2024).

The gut microbiome determines our weight – fact or myth?

The gut microbiome plays a central role in weight management, as studies have shown. It influences energy production, fat storage, and inflammatory processes (Liu, B. N. et al., 2021).

Research indicates that people with a diverse gut microbiome tend to have healthier body weights, as a high diversity of gut bacteria helps regulate metabolism efficiently and optimizes energy extraction from food (Menni, C. et al., 2017).

Certain bacteria such as Christensenellaceae, Methanobacteriales, Lactobacillus, Bifidobacteria, and Akkermansia are found more frequently in lean individuals (Liu, B. N. et al., 2021). In contrast, studies show that obese individuals often exhibit an increased ratio of Firmicutes to Bacteroidetes at the phylum level—an important characteristic of the gut microbiome in obesity (Liu, B. N. et al., 2021).  

A healthy gut microbiome strengthens the immune system – fact or myth?

A healthy gut microbiome supports the immune system by defending against pathogens, strengthening the mucosal barrier, and regulating immune cells. Around 70–80% of immune cells are located in the gut, where a complex interaction occurs between the gut microbiome, intestinal epithelium, and mucosal immune system (Wiertsema, S. P. et al., 2021).

Studies show that signals from gut bacteria play a crucial role in the development of immune defenses (Wu, H. J. et al., 2021). Dysbiosis can disrupt immune tolerance, promote chronic inflammation, and contribute to diseases such as inflammatory bowel disease, autoimmune disorders, and colorectal cancer. It also increases intestinal permeability, which further weakens immune function (Toor, D. et al, 2019). 

Summary

• Are all gut bacteria good? → Myth. There are both beneficial and harmful bacteria. An imbalance can lead to digestive issues and infections.
• Do antibiotics destroy the gut microbiome? → Fact. They also kill good bacteria and weaken the microbiome. Recovery can take weeks to months.
• Do probiotics and prebiotics cure all gut problems? → Myth. They support the gut microbiome but are not a cure-all.
• Does the gut microbiome affect mental health? → Fact. An imbalance can trigger inflammation and increase the risk of conditions such as depression.
• Does the gut microbiome determine weight? → Fact. Certain bacteria promote a healthy metabolism, while others are linked to obesity.
• Does a healthy gut microbiome strengthen the immune system? → Fact. It protects against infections and regulates immune responses, while dysbiosis increases disease risk.