Gut Health & the Microbiome: What Research Shows

An Entire Ecosystem in Your Gut

Our digestive tract is home to approximately 38 trillion bacteria (estimate for a man weighing 70 kg). That is roughly the same number of cells as the human body itself contains (Sender et al., 2016). This community is known as the gut microbiome. In a study of 124 people from Europe, between 1,000 and 1,150 common bacterial species were present across the group as a whole, with at least 160 in each individual (Qin et al., 2010). Together, they weigh around 200 grams 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, studied the microbial diversity of healthy people at various body sites, in what was then the largest group of participants. 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. In experiments in mice, certain gut bacteria promoted serotonin production in cells of the colonic lining (Yano et al., 2015).

A study of ten volunteers showed that just five days of an exclusively animal-based or exclusively plant-based diet measurably changed the composition of the gut microbiome (David et al., 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	Live microorganisms that, when taken in adequate amounts, confer a health benefit on the body (definition by FAO and WHO)	Lactobacillus, Bifidobacterium (found in yoghurt, kefir, sauerkraut, kimchi, miso)
Postbiotics	Preparations of inactivated microorganisms and/or their components that confer a health benefit (definition by the scientific association ISAPP, 2021)	Inactivated microorganisms or cell components, with or without metabolites

Butyrate in particular is a focus of current research. This short-chain fatty acid is produced by gut bacteria from dietary fibre. Its role in the gut is being actively researched.

Fibre Diversity as the Key

The American Gut Project (McDonald et al., 2018) analysed stool samples from over 10,000 participants across 45 countries and territories, most of them from the USA, the United Kingdom, and Australia. 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)

Alongside the amount of fibre (guideline: 30 g per day), the variety of fibre types likely also supports a more diverse bacterial community (McDonald et al., 2018). Different types of fibre nourish different bacterial strains. Legumes, nuts, and seeds have a high fibre content, as do whole grains (DGE).

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 showed that the number of different plants in the diet was associated with microbiome diversity, whereas diet types such as vegan or omnivorous explained hardly anything (McDonald et al., 2018).

What Can Change the Microbiome

Various factors can change the composition of the microbiome:

• Antibiotics: Necessary for bacterial infections, but they also reduce beneficial gut bacteria. In twelve healthy men who took three antibiotics for four days, the microbiome largely recovered within about one and a half months. However, nine common bacterial species were still undetectable in most of them after six months (Palleja et al., 2018).
• Stress: In animal experiments, various stressors changed the composition of the gut microbiome. In humans, the data so far are sparse (Karl et al., 2018).

Practical Recommendations

A few simple principles for everyday life:

• 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.
• 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 links a diverse, fibre-rich diet with plenty of plant-based foods to a more diverse microbiome. What stands out: the number of different plants was associated with microbiome diversity, whereas the type of diet hardly was.

Learn more about dietary fibre, its effects, and practical tips: Dietary Fiber: The Underrated Nutrient.

---

Sources:

• Sender R, Fuchs S, Milo R (2016). Revised estimates for the number of human and bacteria cells in the body. PLOS Biology, 14(8), e1002533. DOI: 10.1371/journal.pbio.1002533
• Qin J, Li R, Raes J et al. (2010). A human gut microbial gene catalogue established by metagenomic sequencing. Nature, 464(7285), 59-65. DOI: 10.1038/nature08821
• Human Microbiome Project Consortium (2012). Structure, function and diversity of the healthy human microbiome. Nature, 486(7402), 207-214. DOI: 10.1038/nature11234
• Yano JM, Yu K, Donaldson GP, Shastri GG, Ann P, Ma L, Nagler CR, Ismagilov RF, Mazmanian SK, Hsiao EY (2015). Indigenous bacteria from the gut microbiota regulate host serotonin biosynthesis. Cell, 161(2), 264-276. DOI: 10.1016/j.cell.2015.02.047
• David LA, Maurice CF, Carmody RN et al. (2014). Diet rapidly and reproducibly alters the human gut microbiome. Nature, 505(7484), 559-563. DOI: 10.1038/nature12820
• Hill C, Guarner F, Reid G, Gibson GR, Merenstein DJ et al. (2014). The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic. Nature Reviews Gastroenterology & Hepatology, 11(8), 506-514. DOI: 10.1038/nrgastro.2014.66
• Salminen S, Collado MC, Endo A, Hill C, Lebeer S et al. (2021). The International Scientific Association of Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of postbiotics. Nature Reviews Gastroenterology & Hepatology, 18(9), 649-667. DOI: 10.1038/s41575-021-00440-6
• Sonnenburg ED, Sonnenburg JL (2014). Starving our microbial self: the deleterious consequences of a diet deficient in microbiota-accessible carbohydrates. Cell Metabolism, 20(5), 779-786. DOI: 10.1016/j.cmet.2014.07.003
• McDonald D, Hyde E, Debelius JW, Morton JT, Gonzalez A et al. (2018). American Gut: an Open Platform for Citizen Science Microbiome Research. mSystems, 3(3), e00031-18. DOI: 10.1128/mSystems.00031-18
• Deutsche Gesellschaft für Ernährung (DGE). Selected questions and answers on dietary fibre (in German). dge.de
• Palleja A, Mikkelsen KH, Forslund SK et al. (2018). Recovery of gut microbiota of healthy adults following antibiotic exposure. Nature Microbiology, 3(11), 1255-1265. DOI: 10.1038/s41564-018-0257-9
• Karl JP, Hatch AM, Arcidiacono SM, Pearce SC, Pantoja-Feliciano IG, Doherty LA, Soares JW (2018). Effects of Psychological, Environmental and Physical Stressors on the Gut Microbiota. Frontiers in Microbiology, 9, 2013. DOI: 10.3389/fmicb.2018.02013