How Diet Shapes the Gut Microbiome

The gut microbiome plays a vital role in human health, impacting everything from our metabolism and immune system to our mental health. As such, scientists are increasingly focused on finding new ways to support the microbiome to improve human health. Among the various factors that shape the gut microbiome, diet stands out as one of the most powerful and accessible tools at our disposal.

Why does having a healthy microbiome matter?

The gut microbiome is made up of trillions of bacteria, viruses, fungi and other microorganisms that each contribute to the delicate balance of this ecosystem. While the definition of a ‘healthy’ microbiome continues to evolve with ongoing research, scientists generally agree that microbial diversity—both in the number of different species present and the functions they perform—is a key indicator of gut health. Disruptions to this microbial balance have been linked to a wide range of health conditions, including inflammatory bowel disease, obesity and diabetes.

Diet and the gut microbiome

Your microbiome is influenced by many factors, such as where you live, the medications you take and whether you own pets. However, diet is one of the largest contributing factors. The relationship between diet and the microbiome is highly individualised—no two people (or their microbiomes) will respond the same way to the same foods. This is because our gut microbes work together to break down various dietary components, producing a wide array of compounds in the process. The unique composition of an individual’s microbiome will determine what compounds are produced from the foods they consume^1,2.

While scientists continue to explore how specific foods interact with our gut microbes, several dietary patterns have shown distinct influences on the microbiome:

• Western diet: The typical Western diet is characterised by high levels of animal protein, saturated fats and ultra-processed foods. Compared to other dietary patterns, this diet is associated with lower microbial diversity and a lower production of beneficial compounds, such as short-chain fatty acids (SCFA)³. Ultra-processed foods often contain preservatives, emulsifiers or other additives that may also negatively impact gut health⁴.
• High-fibre diets: Dietary fibres are superfoods for your gut bacteria, helping to support SCFA production and maintain gut barrier integrity (more on this below). High-fibre diets are also associated with an increased abundance of beneficial microbes, such as species of Lactobacillus and Bifidobacterium³.
• Mediterranean diet: The Mediterranean diet has long been recommended for its health benefits. This dietary pattern prioritises a high intake of diverse fruits, vegetables, whole grains, nuts, seeds, legumes, and healthy fats, such as olive oil. The benefits of the Mediterranean diet (and similar whole-food dietary patterns) on body weight and heart health may be mediated in part by the gut microbiome^5-8. Studies show that the Mediterranean diet increases the abundance of health-promoting microbes, such as Faecalibacterium prausnitzii and Roseburia species. Furthermore, microbiome changes observed with the Mediterranean diet are associated with improved cognitive function, reduced inflammation and an increased production of SCFA⁵.

Key examples of how diet-microbiome interactions influence human health

Dietary fibre plays a crucial role in gut health, with significant implications for overall well-being. Research shows that diets high in fibre are associated with positive health outcomes, including a reduced risk of colon cancer, type 2 diabetes, and other metabolic conditions⁹.

The health-promoting effects of dietary fibre are thought to occur largely through its interactions with the microbiome. Dietary fibres cannot be broken down by human cells. Instead, they reach the lower gut, where they are fermented by gut bacteria. The major products of microbial fermentation are SCFAs, which offer a range of health-promoting functions^3,9. For example, SCFAs stimulate cells in the gut to produce the hormones glucagon-like peptide 1 (GLP-1) and peptide YY, which help regulate appetite and blood sugar levels. They also play a critical role in regulating our immune cells, maintaining a healthy gut barrier, and regulating the pH of the gut, which helps prevent the growth of unwanted pathogens. A diet rich in diverse dietary fibres will support the gut microbiome’s ability to perform these critical functions.

Polyphenols, which are abundant in plant foods such as fruits, vegetables, whole grain cereals, cacao, wine, tea and coffee provide another compelling example of how dietary compounds interact with the gut microbiome^10-12. Polyphenols nourish beneficial bacteria in our gut, such as Bifidobacterium, Akkermansia and Lactobacillus species, which are important for reducing inflammation, maintaining a healthy gut barrier, and regulating the immune system. Polyphenols also possess antimicrobial properties that help combat potential pathogens, further supporting overall gut health. The relationship between polyphenols and the microbiome is a two-way street: while polyphenols directly influence the composition and function of the microbiome, gut microbes may also metabolise these compounds to enhance their bioavailability. This allows polyphenols to be more easily absorbed so they can exert beneficial effects throughout the body.

Leveraging diet to improve the health of your gut microbiome

Each day, we have an opportunity to nurture the health of our microbiome through the foods we eat. Current evidence strongly supports a diet rich in diverse plant foods for promoting a healthy and diverse microbiome. Large changes in diet can influence the microbiome in as little as 24 hours¹³, but maintaining healthy dietary patterns over the long-term will provide the most health benefits.

How the AHMB hopes to advance our understanding of diet-microbiome interactions

While we know that diet can have a profound impact on the gut microbiome, there are many questions that need to be addressed. Microbial biobanks such as the AHMB can play an important role in advancing research on diet-microbiome interactions. They will allow us to study how our gut microbes respond to different dietary components, and how this, in turn, affects our health. This deep understanding offers the potential for new microbiome-based therapies and personalised diet recommendations.

Click here to learn more about donating a sample to the AHMB!

References

1. Culp, E. J., Nelson, N. T., Verdegaal, A. A. & Goodman, A. L. Microbial transformation of dietary xenobiotics shapes gut microbiome composition. Cell 187, 6327-6345.e6320, doi:10.1016/j.cell.2024.08.038 (2024).
2. Johnson, A. J. et al. Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans. Cell Host Microbe 25, 789-802.e785, doi:10.1016/j.chom.2019.05.005 (2019).
3. Ross, F. C. et al. The interplay between diet and the gut microbiome: implications for health and disease. Nature Reviews Microbiology 22, 671-686, doi:10.1038/s41579-024-01068-4 (2024).
4. Whelan, K., Bancil, A. S., Lindsay, J. O. & Chassaing, B. Ultra-processed foods and food additives in gut health and disease. Nature Reviews Gastroenterology & Hepatology 21, 406-427, doi:10.1038/s41575-024-00893-5 (2024).
5. Rinott, E. et al. The effects of the Green-Mediterranean diet on cardiometabolic health are linked to gut microbiome modifications: a randomized controlled trial. Genome Med 14, doi:10.1186/s13073-022-01015-z (2022).
6. Meslier, V. et al. Mediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake. Gut 69, 1258-1268, doi:10.1136/gutjnl-2019-320438 (2020).
7. Ghosh, T. S. et al. Mediterranean diet intervention alters the gut microbiome in older people reducing frailty and improving health status: the NU-AGE 1-year dietary intervention across five European countries. Gut 69, 1218-1228, doi:10.1136/gutjnl-2019-319654 (2020).
8. Wang, D. D. et al. The gut microbiome modulates the protective association between a Mediterranean diet and cardiometabolic disease risk. Nature Medicine 27, 333-343, doi:10.1038/s41591-020-01223-3 (2021).
9. Delzenne, N. M., Bindels, L. B., Neyrinck, A. M. & Walter, J. The gut microbiome and dietary fibres: implications in obesity, cardiometabolic diseases and cancer. Nature Reviews Microbiology, doi:10.1038/s41579-024-01108-z (2024).
10. Corrêa, T. A. F., Rogero, M. M., Hassimotto, N. M. A. & Lajolo, F. M. The Two-Way Polyphenols-Microbiota Interactions and Their Effects on Obesity and Related Metabolic Diseases. Frontiers in Nutrition 6, doi:10.3389/fnut.2019.00188 (2019).
11. Cheng, H. et al. Interactions between gut microbiota and polyphenols: A mechanistic and metabolomic review. Phytomedicine 119, 154979, doi:10.1016/j.phymed.2023.154979 (2023).
12. Espín, J. C., González-Sarrías, A. & Tomás-Barberán, F. A. The gut microbiota: A key factor in the therapeutic effects of (poly)phenols. Biochemical Pharmacology 139, 82-93, doi:10.1016/j.bcp.2017.04.033 (2017).
13. David, L. A. et al. Diet rapidly and reproducibly alters the human gut microbiome. Nature 505, 559-563, doi:10.1038/nature12820 (2014).

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