Gut Health & the Microbiome: What Research Shows

An Entire Ecosystem in Your Gut

Our digestive tract is home to approximately 38 trillion microorganisms. That is roughly the same number of cells as the human body itself contains (Sender et al., 2016). This community of over 1,000 different bacterial species is known as the gut microbiome. Together, they weigh 1.5 to 2 kilograms and form a complex ecosystem that does far more than simply aid digestion.

The Human Microbiome Project (2012), a large-scale initiative by the US National Institutes of Health, was the first to systematically map the microbial diversity of the human body. The findings show that the microbiome is as unique as a fingerprint. Every person carries a distinct combination of bacterial strains.

The Gut-Brain Axis

The gut and the brain communicate bidirectionally via the vagus nerve, hormones, and neurotransmitters. This communication system is known as the gut-brain axis.

A particularly striking example: approximately 90% of the body’s serotonin is produced in the gut (Yano et al., 2015). Serotonin is a neurotransmitter associated with mood, sleep, and well-being. This does not mean the gut alone controls mood. However, research suggests that the composition of the microbiome may influence neurotransmitter production.

Studies at Stanford University led by Justin and Erica Sonnenburg show that dietary changes can measurably alter the composition of the microbiome within just a few days (Sonnenburg & Sonnenburg, 2014).

Prebiotics, Probiotics, and Postbiotics

These three terms are frequently confused. Here are the differences:

Term	What is it?	Examples
Prebiotics	Indigestible fibres that serve as food for beneficial gut bacteria	Inulin, resistant starch, pectin (found in chicory, garlic, onions, bananas, oats)
Probiotics	Living microorganisms that may positively influence gut flora	Lactobacillus, Bifidobacterium (found in yoghurt, kefir, sauerkraut, kimchi, miso)
Postbiotics	Metabolic by-products of gut bacteria with health benefits	Short-chain fatty acids such as butyrate, propionate, and acetate

Butyrate in particular is a focus of current research. This short-chain fatty acid is produced by gut bacteria from dietary fibre and may strengthen the intestinal barrier and modulate inflammatory processes.

Fibre Diversity as the Key

The American Gut Project (McDonald et al., 2018) analysed stool samples from over 10,000 participants across 45 countries. A central finding: individuals who consumed more than 30 different plant species per week had significantly greater microbiome diversity than those consuming fewer than 10 plant species.

Plant species include:

• Vegetables and fruits
• Legumes (lentils, chickpeas, beans)
• Whole grains (oats, spelt, quinoa)
• Nuts and seeds
• Herbs and spices
• Grasses (e.g. barley grass, wheatgrass)

What matters is not just the amount of fibre (guideline: 30g per day), but above all the variety. Different types of fibre nourish different bacterial strains.

Plant-Based Eating and Microbiome Diversity

Research findings from Sonnenburg et al. suggest that a fibre-rich, plant-focused diet may promote microbial diversity in the gut. In contrast, a low-fibre diet has been associated with a reduction in certain bacterial species.

The American Gut Project confirmed this: the number of different plants in the diet was the strongest predictor of microbiome diversity. Stronger than any other factor examined, including whether someone followed a vegetarian or omnivorous diet.

What May Harm the Microbiome

Certain substances can negatively influence the composition of the microbiome:

• Emulsifiers (e.g. polysorbate 80, carboxymethylcellulose): Studies by Chassaing et al. (2015) show that these additives, commonly used in processed foods, may impair the mucus layer of the gut and alter the composition of gut flora.
• Artificial sweeteners: Suez et al. (2014) found that certain artificial sweeteners can alter the composition of the gut microbiome and affect glucose tolerance.
• Antibiotics: Necessary for bacterial infections, but they also eliminate beneficial bacteria. Studies show that the microbiome may take months to recover after antibiotic treatment.
• Chronic stress: Through the gut-brain axis, sustained stress can affect the intestinal barrier and microbial composition.

Practical Recommendations

Research suggests that several simple principles may support gut health:

• Increase plant variety: Aim for 30 different plant species per week. Herbs and spices count.
• Fermented foods: Regularly include yoghurt, kefir, sauerkraut, or kimchi in your diet.
• Eat fibre-rich foods: Legumes, whole grains, vegetables, and fruits form the foundation.
• Reduce processed foods: Especially those containing emulsifiers and artificial additives.
• Increase gradually: If your current fibre intake is low, increase it step by step to allow your gut to adapt.

Conclusion

The gut microbiome is a fascinating field of research that has made enormous progress in recent years. Research suggests that a diverse, fibre-rich diet with plenty of plant-based foods may positively influence the microbiome. The most important takeaway: variety over quantity. The more colourful and varied your diet, the better the conditions for a healthy gut ecosystem.

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Sources:

• Sender R, Fuchs S, Milo R (2016). Revised estimates for the number of human and bacteria cells in the body. Cell.
• Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature.
• Yano JM et al. (2015). Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell.
• Sonnenburg JL, Sonnenburg ED (2014). Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism.
• McDonald D et al. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems.
• Chassaing B et al. (2015). Dietary emulsifiers impact the mouse gut microbiota promoting colitis and metabolic syndrome. Nature.
• Suez J et al. (2014). Artificial sweeteners induce glucose intolerance by altering the gut microbiota. Nature.