Nourish Your Microbiome for Gut Health and Whole-Body Wellness
The food you eat fuels your body and supports trillions of gut microbes vital for digestion, immunity, and mental health. Learn how a diet rich in prebiotics, probiotics, and plants can boost your gut and overall health.
by Lori A Smolin, PhD and
What we eat nourishes our bodies. Food provides energy and nutrients to fuel our activity, builds and maintains our muscles, bones, and other structures, and regulates body processes. But the food we eat also nourishes the community of microorganisms that live in our gut. This microbiome includes over one thousand species of microbes and contains more genes than the entire human genome.[1] The numbers and species of organisms in this microscopic world depend in part on what we feed them. In turn, they affect our gastrointestinal (GI) tract and overall health. What should you eat to promote a healthy microbiome?
What is the Gut Microbiome?
The gut microbiome includes all the microorganisms that live in our GI tracts, as well as the metabolites they produce, and the environment in which they live. [2] We have long known that the gut microbiome benefits our health. It facilitates the absorption of nutrients and synthesizes vitamins, including vitamin B12 and vitamin K. It metabolizes phytochemicals, increasing their bioavailability and health-promoting effects.[3] It digests food components, such as fiber, which cannot be broken down by human enzymes, producing important metabolites, and protects us from pathogens and toxins. We now understand that the microbiome also has effects that extend beyond the GI tract, impacting functions throughout the body and protecting against conditions ranging from depression to obesity. [4,5]
How Do Microbes in Our Gut Impact Overall Health?
Many of the health effects of the microbiome are believed to be mediated through the metabolites and other molecules produced by the microbes.[6] Some of these have their effect at the intestinal epithelium, while others travel via the lymph and blood to other parts of the body. Molecules that remain in the gut have local effects as well as far-reaching consequences. For example, short chain fatty acids, produced by the breakdown of dietary fiber, are used for energy by epithelial cells in the colon and make the colon contents more acidic, preventing harmful microbes from growing.[4] Short chain fatty acids in the gut also have widespread effects. They influence the maturation of immune cells, which then migrate to other parts of the body, [6] and they bind to endocrine cells in the gut epithelium causing the release of peptides that affect food intake and glucose metabolism.[7] Likewise, neurotransmitters produced by the microbiome generate local effects, and distant ones by signaling the central nervous system. [6,8]
Molecules that leave the gut can impact systems throughout the body by directly signaling neural, endocrine, immunological, and metabolic pathways and by triggering the release of signaling molecules such as neurotransmitters and metabolic factors. [4,6] For example, substances produced by gut bacteria affect levels of neurotransmitters in the brain and thus impact brain function and cognition, [8] and trimethylamine N-oxide (TMAO), a molecule produced by the microbiome, can alter metabolic pathways, increasing the risk of cardiovascular disease.[9] Compounds produced by phytochemical metabolism in the gut provide antioxidant, anti-inflammatory, and anti-cancer effects throughout the body.[3] Through these varied interactions, the microbiome plays an important role in regulating metabolic health, and has the potential to decrease or increase the risk of diseases such as diabetes, cardiovascular disease, and cancer. [4, 5]
A Healthy Microbiome
There is no single definition of a healthy microbiome and no single microbiome configuration that is consistent with overall health, [10] but in general a healthy microbiome is a diverse, balanced community of microorganisms that promotes the health of the host in a variety of ways.[11] The microbiome stimulates the immune response, protects the host from pathogens, limits inflammation, and supports the nervous system.[5]
Early in life the gut microbiome contributes to the development and maturation of the immune system. The GI tract is host to a large number of immune cells, which are in constant communication with the gut microbiome. [5] This interaction helps to train and modulate the immune response, ensuring it is strong enough to fight infection, but not so strong that it damages the host. The immune system must protect against infection by pathogens but allow the growth of beneficial bacteria, while not permitting them to overgrow or cross the intestinal epithelium.[12] A healthy gut microbiome helps maintain the mucosal barrier, which prevents the entry of pathogens and toxins into the body. The gut microbiome also helps support and protect the nervous system through its communication with the brain via nerves in the gut, molecules carried in the blood, and its effect on the immune system. [13]
Dysbiosis: When Bad Bacteria Prevail
Dysbiosis occurs when there is an imbalance in the microbiota; this could be a decrease in the number of beneficial bacteria, an overgrowth of harmful bacteria, or a decrease in overall microbiome diversity. Individuals with dysbiosis may experience GI symptoms such as gas, diarrhea, bloating, and food intolerances; dysbiosis has also been proposed to have far reaching health implications.[14] Products produced by “bad” bacteria harm health by disrupting the epithelial barrier, triggering inflammation, and potentially driving the initiation and progression of colorectal cancer.[5] Interactions between the microbiome and the immune system have been implicated in inflammatory bowel diseases such as Crohn’s disease and ulcerative colitis. An unhealthy microbiome has also been linked to extra-intestinal autoimmune diseases such as rheumatoid arthritis, and diseases linked to chronic inflammation such as diabetes, obesity, cardiovascular disease, and cancers. [5,12,14] The gut-brain connection has also led to research that links disturbances in the gut microbiota to mental illnesses such as anxiety, depression, and neurodegenerative diseases. [13,14]
Eating to Boost the Health of Your Microbiome
The composition of the intestinal microbiota is unique to each person. It is shaped by a variety of factors including diet, age, gender, medications, body weight, exercise, socio-economic conditions, sleep, stress, smoking, and alcohol use. About half of the variability between individuals’ microbiomes can be attributed to diet.[15] Studies show that consuming a Mediterranean dietary pattern based on vegetables, fruits, whole grains, legumes, and nuts with moderate intake of fish, poultry, eggs, and dairy products has a beneficial effect on the microbiome when compared to a Western dietary pattern more reliant on red and processed meats and other processed foods. [15]
Choosing a diet based on the plant foods – vegetables, fruits, whole grains, legumes, and nuts – that are the foundation of the Mediterranean diet promotes a healthy microbiome by providing an abundance of prebiotics and phytochemicals. Prebiotics are high-fiber foods that serve as nourishment for beneficial gut bacteria, stimulating their growth and activity. Foods high in prebiotics include bananas, garlic, barley, wheat bran, oats, apples, onions, chickpeas, avocados, and almonds. The phytochemicals found in these plant foods pass into the colon where they function as prebiotics, modifying the composition of the microbiota by stimulating or inhibiting the growth of certain types of microbes. [3]
A diet containing probiotics also supports a healthy microbiome. Probiotics are living microorganisms found in fermented dairy and plant-based foods such as yogurt, kefir, miso, tempeh, sauerkraut, pickles, kombucha, and kimchi. When consumed these bacteria add to the existing microbiota, but only live temporarily in the gut, so to be of benefit they need to be consumed regularly. Probiotics are also available as supplements, but there is little information on which strains and doses are beneficial and safe for specific health conditions.[16] Food sources of probiotics are likely a better option because they are less expensive, have a history of safe use, provide a greater number and variety of microbes, and bring with them essential nutrients.
In contrast, choosing a diet high in red and processed meats, and the saturated fats they contain, can negatively alter the composition of the microbiome. For example, diets high in animal protein and saturated fat have been found to decrease the number of beneficial bacteria and reduce microbial diversity. [17,18] The breakdown of red and processed meats also produces metabolites that increase inflammation.[17] These changes are associated with an increased risk of metabolic diseases such as obesity and diabetes.
Bottom Line
A healthy microbiome is essential to a healthy body and what you eat can affect your microbiome. Adopting a dietary pattern that is based on whole plant-based foods such as fruits, vegetables, and whole grains, which provide prebiotics and phytochemicals, and includes fermented foods such as yogurt and pickled vegetables, which provide probiotics, while limiting red and processed meats, can bolster your microbiome and promote your overall wellbeing. [15, 19]
References
[1] Rajilić-Stojanović M, de Vos WM. The first 1000 cultured species of the human gastrointestinal microbiota. FEMS Microbiology Reviews. 2014;38(5):996-1047. doi:https://doi.org/10.1111/1574-6976.12075
[2] Berg G, Rybakova D, Fischer D, et al. Microbiome definition re-visited: old concepts and new challenges. Microbiome. 2020;8(1). doi:https://doi.org/10.1186/s40168-020-00875-0
[3] 1.Santhiravel S, Bekhit AEDA, Mendis E, et al. The Impact of Plant Phytochemicals on the Gut Microbiota of Humans for a Balanced Life. International Journal of Molecular Sciences. 2022;23(15):8124. doi:https://doi.org/10.3390/ijms23158124
[4] Afzaal M, Saeed F, Shah YA, et al. Human gut microbiota in health and disease: Unveiling the relationship. Frontiers in Microbiology. 2022;13. doi:https://doi.org/10.3389/fmicb.2022.999001
[5] Hou K, Wu ZX, Chen XY, et al. Microbiota in Health and Diseases. Signal Transduction and Targeted Therapy. 2022;7. doi:https://doi.org/10.1038/s41392-022-00974-4
[6] Kuziel GA, Rakoff-Nahoum S. The gut microbiome. Current Biology. 2022;32(6):R257-R264. doi:https://doi.org/10.1016/j.cub.2022.02.023
[7] Cani PD. Human gut microbiome: hopes, threats and promises. Gut. 2018;67(9):1716-1725. doi:10.1136/gutjnl-2018-316723.
[8] Miri S, Yeo J, Abubaker S, Riadh Hammami. Neuromicrobiology, an emerging neurometabolic facet of the gut microbiome? 2023;14. doi:https://doi.org/10.3389/fmicb.2023.1098412
[9] Zhen J, Zhou Z, He M, et al. The gut microbial metabolite trimethylamine N-oxide and cardiovascular diseases. Frontiers in Endocrinology. 2023;14. doi:https://doi.org/10.3389/fendo.2023.1085041
[10] Shanahan F, Ghosh TS, O’Toole PW. The Healthy Microbiome (What is the definition of a healthy gut microbiome?). Gastroenterology. 2020;160(2). doi:https://doi.org/10.1053/j.gastro.2020.09.057
[11] Van Hul M, Cani PD, Petitfils C, De Vos, WM, Tilg, H, El-Omar, EM.
What defines a healthy gut microbiome? Gut 2024;73:1893-1908.
[12] Zheng, D., Liwinski, T. & Elinav, E. Interaction between microbiota and immunity in health and disease. Cell Res 30, 492–506 (2020). https://doi.org/10.1038/s41422-020-0332-7
[13] Loh JS, Mak WQ, Tan LKS, et al. Microbiota–gut–brain axis and its therapeutic applications in neurodegenerative diseases. Signal Transduction and Targeted Therapy. 2024;9(1):1-53. doi:https://doi.org/10.1038/s41392-024-01743-1
[14] United Stated Department of Agriculture. Agricultural Research Service. Keeping a Healthy Gut.
https://www.ars.usda.gov/oc/utm/keeping-a-healthy-gut/. Accessed December 9, 2024.
[15] Merra G, Noce A, Marrone G, et al. Influence of Mediterranean Diet on Human Gut Microbiota. Nutrients. 2021;13(1):7. doi:https://doi.org/10.3390/nu13010007
[16] NCCIH. Probiotics: Usefulness and Safety. NCCIH. Published 2016. https://www.nccih.nih.gov/health/probiotics-usefulness-and-safety
[17] Beam A, Clinger E, Hao L. Effect of Diet and Dietary Components on the Composition of the Gut Microbiota. Nutrients. 2021 Aug 15;13(8):2795. doi:10.3390/nu13082795.
[18] Wolters M, Ahrens J, Romaní-Pérez M, et al. Dietary fat, the gut microbiota, and metabolic health – A systematic review conducted within the MyNewGut project. Clinical Nutrition. 2019;38(6):2504-2520. doi:https://doi.org/10.1016/j.clnu.2018.12.024
[19] Armet AM, Deehan EC, O’Sullivan AF, et al. Rethinking healthy eating in light of the gut microbiome. Cell Host & Microbe. 2022;30(6):764-785. doi:https://doi.org/10.1016/j.chom.2022.04.016
Commentaires