How your diet shapes your gut microbiome

Deep within our gut lives a vast community of tiny microorganisms that have more influence on our health than we might think. They regulate digestion, control weight, strengthen the immune system, and provide energy. A healthy microbiome means greater well-being – read here to find out which microorganisms are involved and how the right diet can support them effectively!

Table of Contents

• What is the gut microbiome?
• Which foods promote a healthy gut microbiome?
• Which foods should be avoided to protect the gut microbiome?
• How quickly does the gut microbiome respond to dietary changes?
• Healthy diet – healthy microbiome – health benefits?
• Summary

What is the gut microbiome?

The term microbiome refers to the totality of all microorganisms that inhabit the human body. This includes bacteria, viruses, fungi, and other microbes found on the skin, in the oral cavity, in the gut, and in other areas of the body. The term gut microbiome refers specifically to the microorganisms that reside in the human intestines (NHI, 2025).

These gut-dwelling organisms play a central role in, for example: breaking down complex carbohydrates and dietary fiber; producing essential vitamins (B1, B9, B12, K) and short-chain fatty acids; nourishing intestinal cells and supporting fat digestion; strengthening the immune system by defending against harmful germs and regulating inflammation; and influencing the nervous system via the gut-brain axis, e.g., by producing serotonin, a neurotransmitter that stimulates the nervous system.

Source: Cleveland Clinic, 2023  

Which foods promote a healthy gut microbiome?

A healthy gut microbiome is supported by various nutrients. Probiotics, prebiotics, and polyphenol-rich foods play a key role by promoting the growth of beneficial bacteria and reducing harmful microorganisms:

Probiotics are foods or dietary supplements that contain live microorganisms intended to maintain or improve the "good" bacteria in the body. They are found in fermented products such as yogurt, kefir, sauerkraut, kimchi, miso, tempeh, kombucha, pickles, sourdough bread, and certain cheeses.

Prebiotics are foods (usually high-fiber foods) that serve as nourishment for human microflora. They are used to improve the balance of these microorganisms. Key prebiotics include asparagus, sugar beets, garlic, chicory, onions, Jerusalem artichokes, wheat, honey, bananas, barley, tomatoes, rye, soybeans, peas, and algae.

Polyphenol-rich foods promote beneficial gut bacteria like bifidobacteria and lactobacilli while reducing harmful germs such as E. coli and H. pylori. Examples include berries, green tea, dark chocolate, olives, grapes, walnuts, coffee, turmeric, and red cabbage.

Sources: Mayo Clinic, 2022; Plamada, D. et al., 2021

Which foods should be avoided to protect the gut microbiome?

The following foods can damage the gut microbiome:

• Sugar & sweeteners: Highly processed sugars like sodas, candies, and high-fructose syrup promote inflammation-causing bacteria and may inhibit the growth of healthy gut microbes.

• Highly processed foods: These are often low in fiber or micronutrients but high in additives or preservatives. Examples include fast food, ready meals, and chips.

• Unhealthy fats: Trans fats, found in margarine, fried foods, and industrially produced baked goods, promote inflammation and may foster the growth of harmful bacteria.

• Alcohol & preservatives: High-proof alcohol or preservatives such as nitrites can damage the gut barrier and negatively impact the microbiome.

• Tobacco smoke: Smoking also negatively affects the composition of the gut microbiome.

• Medications: Antibiotics kill not only harmful but also beneficial bacteria, which can disrupt the balance in the gut. Other medications, such as acid blockers, alter the pH level in the gut, which can negatively affect microbial diversity.

The gut microbiome can usually recover from temporary chemical exposure, such as short-term medication use needed for recovery. However, chronic stressors can change its composition.

Source: Cleveland Clinic, 2023 

How quickly does the gut microbiome respond to changes in diet?

Studies show that only a few bacterial strains undergo significant changes during a short-term dietary shift. In humans, the gut microbiome responds quickly to new foods, with the first changes appearing within 24 to 48 hours. However, these adjustments are usually temporary. Due to a lack of long-term dietary studies and interventions, knowledge about permanent effects remains limited. It is assumed that the gut microbiome can sustainably adapt over several weeks to months with a consistently healthy diet (Leeming, E. R. et al., 2019).

Healthy diet – healthy gut microbiome – health benefits?

A healthy diet promotes a diverse and stable gut microbiome with numerous health benefits:

• Improved digestion: The microbiome helps break down fiber and produces beneficial substances for the body.

• Healthy weight: A diverse microbiome supports a normal body weight and helps prevent obesity.

• Blood sugar control: A balanced microbiome reduces the risk of developing diabetes.

• More energy: The microbiome helps process food more efficiently and supplies the body with essential energy.

• Strong gut barrier: Protects the intestines from harmful substances and inflammation.

• Better satiety: Certain gut bacteria help regulate feelings of hunger.

• Heart health: A healthy microbiome can lower the risk of cardiovascular diseases.

• Stronger immune system: Helps the body defend against illnesses.

Source: Valdes A M et al., 2018

Summary

The gut microbiome consists of the microorganisms in the intestines. A healthy diet including probiotics (e.g., yogurt, sauerkraut), prebiotics (e.g., garlic, bananas), and polyphenol-rich foods (e.g., berries, green tea) supports a stable microbiome. Harmful influences include sugar, highly processed foods, unhealthy fats, alcohol, and antibiotics. Initial changes can be seen within 24–48 hours, while long-term adaptations may take weeks. A diverse microbiome aids digestion, weight management, blood sugar regulation, gut barrier function, satiety, heart health, and immune strength.