What Does a Healthy Gut Microbiome Look Like?

Microbiome by EpicTop10.com is licensed under CC BY 2.0.

By Dale Mayo, Sept. 14, 2023

What is the microbiome?

According to the National Institutes of Health, National Human Genome Research Institute, “The microbiome is the community of microorganisms (such as fungi, bacteria and viruses) that exists in a particular environment.” We used to think of bacteria that colonized humans as bad, now we know that there are also microbes that benefit humans. In your gut, there are trillions of bacteria that are vital for keeping you healthy, microbes that help in digestion of food, and that protect you by keeping pathogens out.(1,2) In a healthy person, the microbes are symbiotic, benefiting the human host and the microbiota. A disturbance in the balance of pathogenic and symbiotic microbiota from infection or prolonged use of antibiotics may put you at greater risk of disease.(3)

Recently, the gut microbiome has been a primary focus of specialized research and of general interest to the public. We know is that an individual’s microbiome is unique – your microbiota is first determined by DNA; first exposure to microorganisms as an infant during delivery; and through breast milk.(4) From that point on, there are many things that can modify your microbiome: where you live and travel, what you eat, how you exercise, how old you are, what medications you take, and many other internal and external factors.

The figure below shows factors that influence a healthy microbiome and external factors that can change its balance.(5)

https://www.gastrojournal.org/article/S0016-5085(20)35508-6/fulltext

Why a healthy gut microbiome is important

While we can’t yet define what a healthy gut is, we do know how your gut microbiome affects your health.

• Chronic disease. Many large studies have investigated the relevance of the gut microbiome in gastrointestinal disorders (e.g., intestinal bowel diseases [IBD], irritable bowel syndrome [IBS], colorectal cancer) which include severe intestinal inflammation. Gut microbes also play an important role in the regulation of aspects of metabolic disorders.(6) Patients with chronic illnesses including type 2 diabetes, obesity and cardiovascular disease exhibit a hyperactive immune system that fails to recognize a harmless stimulus and is linked to an altered gut microbiome.(7) The microbiota in the large intestine help to break down complex carbohydrates (fiber) with their digestive enzymes. The fermentation of indigestible fibers causes the production of short chain fatty acids (SCFA) that can be used by the body as a nutrient source but also play an important role in muscle function and possibly the prevention of chronic diseases, including certain cancers and bowel disorders.(8)
• Immune defenses. Gut bacteria help prime our immune system defenses to combat infections. Early studies found that mice treated with antibiotics that eliminate bacteria in the gut exhibited an impaired immune response. They had low counts of virus-fighting white blood cells, weak antibody responses and poor production of a protein that is vital for combating viral infection and modulating the immune response.(9) Microbiota stimulate the immune system, break down potentially toxic food compounds, and synthesize certain vitamins and amino acids, including the B vitamins and vitamin K. For example, the key enzymes needed to form vitamin B12 are only found in bacteria, not in plants and animals.(10)
• Body Mass Index (BMI). The link between the gut microbiome and obesity is not clear, but studies have suggested the gut microbiome plays a role in our weight and body composition. People with obesity have less bacterial diversity in their guts and other differences in their microbiomes compared to lean people. One potential reason for this is diet: the energy from ultra-processed foods that are low in fiber (as in a Western diet) is absorbed in the upper gastrointestinal tract; fiber-rich foods aren’t absorbed easily and travel all the way through the digestive tract, where it feeds both you and your microbiome, which effectively lowers your calorie intake.(11) Another possible reason is lack of aerobic exercise, which has been shown to enhance microbial variation.(12)
• Brain/mood. New research suggests that major depressive disorder is linked to disruptions in energy and lipid metabolism, possibly caused by the interplay of the gut microbiome and blood metabolome, however no causal role can be identified.(13) While research is now looking at diet and probiotics for treating anxiety and depression, new theories and models are needed to predict how those strains will affect the individual's particular microbiome community.(14)

How diet affects your microbiome

Of the factors that determine the makeup of your microbiota, diet is the easiest to control (easier than genes, environment, and medication use). But knowing what food is best for your microbiome might prove difficult. Even though scientists may find a link between one food and an improvement in gut bacteria, it doesn't mean that food has caused the change in the microbiome.(15)

A western diet contains foods typically found in an American diet: white bread, ground beef, sugary snacks, French fries, chips, processed meats, and fruit juices.

"Fast Food" by Christian Cable is licensed under CC BY 2.0.

A high-fiber diet contains foods like oats, beans, lentils, nuts, fruits, vegetables, brown rice, quinoa, and other whole grains.

"k3839-3" by USDAgov is licensed under CC BY 2.0.

We do know that a fiber-rich diet is better for your gut microbiome (and your health) than a Western diet of highly processed. This is because while highly processed are handled in the upper digestive tract, dietary fiber moves on to the lower digestive tract, where it is broken down and fermented by enzymes from microbiota living in the colon. Fermentation releases short chain fatty acids (SCFA), which lowers the pH of the colon, which in turn determines the type of microbiota present that would survive in this acidic environment. The lower pH limits the growth of some harmful bacteria like Clostridium difficile. Growing research on SCFA explores their wide-ranging effects on health, including stimulating immune cell activity and maintaining normal blood levels of glucose and cholesterol.(16)

A small study comparing the effect of the two types of diet on microbiomes of healthy young research subjects suggested a number of benefits of a fiber-rich diet: fewer calories were absorbed, seemingly their gut microbes multiplied, they had higher circulating levels of SCFAs and increased levels of hormones such as GLP-1 (which promotes satiety), and they lost slightly more weigh and body fat.(17)

The use of probiotics and prebiotics as a prevention and treatment for different chronic diseases has largely increased in the last decade.(18) However, adding a few strains of bacteria to your healthy microbiome through taking a probiotic probably won't boost your gut health diversity all that much. In addition, taking prebiotics will add specific bacteria, but will not increase the diversity of the microbiome.(19)

Healthline has published nine science-based ways to improve your gut bacteria:(20)

• Eat a diverse range of foods.
• Eat lots of vegetables, legumes, beans, and fruit.
• Eat fermented foods (e.g., yogurt, kimchi, sauerkraut, kefir).
• Eat foods rich in polyphenols (e.g., cocoa and dark chocolate, red wine, grape skins, green tea, almonds, onions, blueberries, broccoli)
• Eat prebiotic foods (e.g., garlic, onions, leeks, asparagus, bananas, barley, oats, apples, chicory root, Jerusalem artichoke, dandelion greens, cocoa, flaxseeds, wheat bran, seaweed).(21)
• Increase your intake of probiotics (including fermented foods).
• Eat a plant-based diet.
• Eat whole grains.
• Finally, if you’re a new mother, breastfeed your baby for at least six months if you can.

https://www.sizzlefish.com/blogs/salmon/sheet-pan-baked-salmon

The future of research on the gut microbiome

Over the past 20 years, the field of gut microbiota and health has been pushing to move beyond observation and evolving to causal links. Many studies claim causality only correlations are demonstrated. Moving from correlation to causality is essential to finding interventions based on changing gut microbiota or by using specific active compounds.(22) Medical science is moving towards personalized medicine, which will be important in microbiome research and nutritional approaches to health.

References

1. Genome.gov - Microbiome
2. Maldonado-Contreras, A. (2021). A healthy microbiome builds a strong immune system that could help defeat COVID-19. UMass Chan Medical School News. Jan. 25, 2021.
3. Harvard School of Public Health - The Microbiome
4. Harvard School of Public Health - The Microbiome
5. Shanahan, F., Ghosh, T.S., and O’Toole, P.W. (2021). The healthy microbiome - what is the definition of a healthy gut microbiome? Gastroenterology, 160(2):483-494, Jan 2021.
6. de Vos, W.M., Tilg, H., Van Hul, M., and Cani, P.D. (2022). Gut microbiome and health: mechanistic insights. Gut 2022;71:1020-1032.
7. Maldonado-Contreras, A. (2021). A healthy microbiome builds a strong immune system that could help defeat COVID-19. UMass Chan Medical School News. Jan. 25, 2021.
8. Harvard School of Public Health - The Microbiome
9. Maldonado-Contreras, A. (2021). A healthy microbiome builds a strong immune system that could help defeat COVID-19. UMass Chan Medical School News. Jan. 25, 2021.
10. Harvard School of Public Health - The Microbiome
11. O’Connor, A. (2023). Are all calories created equal? Your gut microbes don’t think so. The Washington Post, June 13, 2023.
12. Aoun, A., Darwish, F., and Hamod, N. (2020). The influence of the gut microbiome on obesity in adults and the role of probiotics, prebiotics, and synbiotics for weight loss. Prev Nutr Food Sci. 2020 Jun 30;25(2):113-123.
13. Yasgur, B.S. (2023). Disrupted gut microbiome a key driver of major depression? Medscape Medical News, April 25, 2023.
14. Pennisi, E. (2020). Meet the psychobiome. Science, May 2020.
15. How to Eat Your Way to a Healthy Gut. BBC Future.
16. Harvard School of Public Health - The Microbiome
17. O’Connor, A. (2023). Are all calories created equal? Your gut microbes don’t think so. The Washington Post, June 13, 2023.
18. Aoun, A., Darwish, F., and Hamod, N. (2020). The influence of the gut microbiome on obesity in adults and the role of probiotics, prebiotics, and synbiotics for weight loss. Prev Nutr Food Sci. 2020 Jun 30;25(2):113-123.
19. How to Eat Your Way to a Healthy Gut. BBC Future.
20. Roberston, R. (2023). 9 ways to improve your gut bacteria, based on science. Healthline, Jan. 23, 2023.
21. Semeco, A. and Kelly, E. (2021). The 19 best prebiotic foods you should eat. Healthline, May 11, 2021.
22. de Vos, W.M., Tilg, H., Van Hul, M., and Cani, P.D. (2022). Gut microbiome and health: mechanistic insights. Gut 2022;71:1020-1032.