Your Gut Microbes Make Medicine: The Healing Compounds Made by Healthy Gut Bacteria
In root cause medicine, we often say: “You are not just what you eat — you are what your microbes make.”
Research to decode the role of the many healthy microbes that reside in our gut is a new frontier that has taught us more about the importance of gut health awareness. Your gut microbes are not passive passengers. They are active metabolic partners that transform the foods you eat into powerful healing compounds that greatly influence inflammation, hormone balance, blood sugar regulation, immune function, mitochondrial health, brain chemistry and longevity.
When your gut ecosystem is diverse and well-fed, it produces compounds that protect and repair you. When it is disrupted, production of these beneficial metabolites drops — and inflammation and metabolic dysfunction can rise.
Below is a review of some of the most important compounds your healthy gut bacteria make and how to support them.
Short-Chain Fatty Acids (SCFAs): The Foundation of Gut Healing
When you eat fiber (especially from vegetables, legumes, nuts, seeds, and whole plants), your gut bacteria ferment it and produce short-chain fatty acids (SCFAs):
- Butyrate
- Propionate
- Acetate
Why Short Chain Fatty Acids (SCFAs) Matter So Much
Butyrate is one of the most important healing compounds in the body.
Functions of the fatty acid butyrate that is produced by the healthy bacteria in the gut include:
- Feeding the cells lining your colon
- Strengthening the integrity of the gut barrier (“leaky gut” protection)
- Lowering inflammation
- Supporting immune balance
- Influencing gene expression
- Butyrate may improve insulin sensitivity
Low fiber intake does not support butyrate producing bacteria in the gut, resulting in low butyrate production. The standard American diet is known to be low in fiber and increasing fiber intake is a common goal people need to work on to optimize their health.
Research by Koh et al. (2016) in Cell shows SCFAs act as signaling molecules that influence metabolism and immune regulation throughout the body.
When butyrate production is low, we often see increased gut permeability, which allows molecules to seep through the gut lining into our circulation, increasing systemic inflammation and causing metabolic dysfunction, as well as increasing food sensitivities. When low SCFAs are identified on a stool test, a butyrate supplement is usually recommended while the patient works on the dietary changes needed to improve the microbial balance in the gut.
Certain gut bacteria and their metabolites — especially short-chain fatty acids (SCFAs) like butyrate — stimulate gut cells to increase serotonin production. About 90–95% of the body’s serotonin is produced in the gastrointestinal tract, not the brain. Dysbiosis, or an unhealthy balance of gut microbes can reduce the amount of serotonin in your body which is needed for many bodily functions, from regulating bowel movements to modulating the immune system.
Microbiome-Made Vitamins
Did you know that certain gut bacteria produce vitamins we need for energy and metabolism? Our gut bacteria produce small amounts of important nutrients when you consume sufficient fiber and a whole foods diet. Some of the vitamins produced in our gut include:
| Vitamins Produced by the Microbiome | |
| Vitamin K2 | Biotin (B7) |
| Pyridoxine (B6) | Riboflavin (B2) |
| Folate (B9) | Thiamin (B1) |
| Cobalamin (B12) | |
These nutrients are important for proper blood clotting, energy production, DNA repair, and supporting nervous system function.
Tryptophan Metabolites: Gut-Brain and Immune Support
Your gut bacteria also transform the amino acid tryptophan into beneficial compounds such as Indole-3-propionic acid (IPA) and Indole-3-aldehyde.
These compounds actually strengthen the gut lining, help regulate immune tolerance, act as antioxidants and even influence brain health.
Agus et al. (2018) demonstrated how microbial tryptophan metabolism helps regulate inflammation and barrier function.
This is one reason gut health is so connected to mood, resilience, and brain clarity.
Polyphenol Metabolites: Where Plants and Microbes Work Together
Many plant compounds (polyphenols) are poorly absorbed on their own. Instead, your gut bacteria convert them into more powerful, bioactive forms. One example is a molecule called Urolithin A that has been shown to boost mitochondria, which produce energy in our cells throughout our body including the brain.
Eating plant foods that contain a precursor polyphenols called ellagitannins such as pomegranates, berries and walnuts allow gut bacteria to make urolithin A. Your gut bacteria convert ellagitannins into urolithin A which has been shown stimulate mitophagy (clearing out damaged mitochondria), improve mitochondrial efficiency, enhance muscle endurance, and support healthy aging pathways. Urolithin A is sold as a supplement and marketed for brain health but it may be more beneficial to incorporate berries, walnuts and pomegranates to make your own urolithin A and benefit from the other medicinal aspects of these foods which often work synergistically with other systems in the body.
Equol: Hormone-Supportive Metabolite
Certain gut bacteria convert soy isoflavones into Equol, a compound that modulates estrogen receptors, acts as an antioxidant, may support cardiovascular health and may help reduce menopausal symptoms.
Other Polyphenol Metabolites
When gut bacteria metabolize flavonoids and catechins from foods like green tea, cocoa, berries and olive oil.
The gut bacteria use polyphenols in foods to produce phenolic acids that reduce oxidative stress, improve endothelial function and lower inflammation.
This helps explain why plant-rich diets are associated with better metabolic and cardiovascular outcomes.
Why Many People Are Unable to Produce these Healthy Microbial Byproducts
Several common modern exposures reduce microbial diversity and metabolite production.
Factors that reduce microbial diversity in the gut include low-fiber diets, ultra-processed foods, chronic stress, sleep deprivation, excessive alcohol or repeated antibiotic use. Toxic environmental exposures to pesticides, herbicides and molds are also examples of things that can negatively impact the microbial health of our guts.
A powerful study by Desai et al. (2016) showed that fiber deprivation causes gut bacteria to degrade the mucus barrier increasing your vulnerability to inflammation and infection. If there is no fiber for our gut bacteria to eat, they will consume the protective mucus layer of your gut, laying the groundwork for “leaky gut”.
When microbial diversity drops, so does production of these important molecules we need to stay healthy. Less microbial diversity = fewer beneficial metabolites.
How to Support Beneficial Metabolite Production
1. Aim to Eat 25–40g of Fiber Daily
Focus on diversity by choosing a variety of different plant foods. Each contains different compounds to nourish the gut microbes. Diversity drives microbial diversity.
- Leafy greens
- Cruciferous vegetables
- Root vegetables
- Legumes
- Nuts and seeds
- Berries
2. Prioritize Polyphenol-Rich Foods
Include the following polyphenol-rich foods in your diet regularly to provide substrates for beneficial metabolite production.
- Pomegranate
- Blueberries
- Blackberries
- Walnuts
- Extra virgin olive oil
- Green tea
- Dark cocoa
3. Include Fermented Foods
Yogurt, kefir, sauerkraut, kimchi, and other fermented foods are natural probiotics and have been consumed by humans for millennia. Fermented foods can support microbial diversity and resilience.
4. Use Antibiotics Only When Necessary
They are essential when truly needed — but repeated use can significantly reduce microbial diversity for months. Consider taking a probiotic and prebiotic supplement apart from antibiotics to support your gut when you are required to take an antibiotic medication.
5. Support Lifestyle Stability
Sleep, stress regulation, and regular movement, all improve microbial diversity and metabolic signaling. Avoid drinking excessive alcohol or relying on over-the-counter medications that may be contributing to a microbial imbalance in your gut.
Gut Health Goes Deeper than Digestion
Your gut microbiome is a metabolic organ. It transforms the fiber and polyphenols in the food we eat into vitamins and beneficial metabolites that help maintain our health. When your microbiome is diverse and nourished, it produces compounds that lower inflammation, improve mitochondrial health, support hormone balance, strengthen gut integrity and improve metabolic flexibility. When it’s disrupted, those protective compounds decline, which is why the gut is directly or indirectly in most disease states. Research on the microbiome and its function is still in its infancy, but what we have learned so far is fascinating and reinforces our need to eat whole foods including a variety of plants. Feed your microbes well, and they will feed your cells.
References
Agus, A., Planchais, J., & Sokol, H. (2018). Gut microbiota regulation of tryptophan metabolism in health and disease. Cell Host & Microbe, 23(6), 716–724. https://doi.org/10.1016/j.chom.2018.05.003
Desai, M. S., Seekatz, A. M., Koropatkin, N. M., Kamada, N., Hickey, C. A., Wolter, M., Pudlo, N. A., Kitamoto, S., Terrapon, N., Muller, A., Young, V. B., Henrissat, B., Wilmes, P., Stappenbeck, T. S., Núñez, G., & Martens, E. C. (2016). A dietary fiber-deprived gut microbiota degrades the colonic mucus barrier and enhances pathogen susceptibility. Cell, 167(5), 1339–1353.e21. https://doi.org/10.1016/j.cell.2016.10.043
Koh, A., De Vadder, F., Kovatcheva-Datchary, P., & Bäckhed, F. (2016). From dietary fiber to host physiology: Short-chain fatty acids as key bacterial metabolites. Cell, 165(6), 1332–1345. https://doi.org/10.1016/j.cell.2016.05.041
LeBlanc, J. G., Milani, C., de Giori, G. S., Sesma, F., van Sinderen, D., & Ventura, M. (2013). Bacteria as vitamin suppliers to their host: A gut microbiota perspective. Current Opinion in Biotechnology, 24(2), 160–168. https://doi.org/10.1016/j.copbio.2012.08.005
Ridlon, J. M., Harris, S. C., Bhowmik, S., Kang, D. J., & Hylemon, P. B. (2014). Consequences of bile salt biotransformations by intestinal bacteria. Gut Microbes, 5(1), 22–39. https://doi.org/10.4161/gmic.28526
Ryu, D., Mouchiroud, L., Andreux, P. A., Katsyuba, E., Moullan, N., Nicolet-Dit-Félix, A. A., Williams, E. G., Jha, P., Lo Sasso, G., Huzard, D., Aebischer, P., Sandi, C., & Auwerx, J. (2016). Urolithin A induces mitophagy and prolongs lifespan in C. elegans and increases muscle function in rodents. Nature Medicine, 22(8), 879–888. https://doi.org/10.1038/nm.4132
Selma, M. V., Espín, J. C., & Tomás-Barberán, F. A. (2009). Interaction between phenolics and gut microbiota: Role in human health. Journal of Agricultural and Food Chemistry, 57(15), 6485–6501. https://doi.org/10.1021/jf902107d
Setchell, K. D. R., & Clerici, C. (2010). Equol: Pharmacokinetics and biological actions. The Journal of Nutrition, 140(7), 1363S–1368S. https://doi.org/10.3945/jn.109.119784
Singh, A., D’Amico, D., Andreux, P. A., Fouassier, A.-M., Blandel, F., Maniar, R., Nakamura, K., Shirasaka, Y., Gouspillou, G., & Auwerx, J. (2022). Urolithin A supplementation improves muscle endurance and mitochondrial health in humans: A randomized clinical trial. JAMA Network Open, 5(1), e2144279. https://doi.org/10.1001/jamanetworkopen.2021.44279
Homemade Fermented Pickle Recipe
Fermented pickles rely on good old-fashioned salt and beneficial bacteria to make the magic happen. The best part about a fermented pickle recipe? It’s easy to make as little (or as much) as you need, and they are packed-full of probiotic benefit.
* This recipe was adapted from author Jill Winger
Ingredients
- Small pickling cucumbers* (see notes)
- 1–2 cloves garlic
- 1 tablespoon mustard seed
- 10 peppercorns
- 1 bay leaf
- 1–2 heads of fresh dill (or 1 tablespoon dill seed, if you prefer)
- Sea salt and water to make 2% brine solution (instructions below)
Instructions
- How to Make 2% Brine:
Dissolve 1 tablespoon fine sea salt in 4 cups non-chlorinated water. If you don’t use all of the brine for this recipe, it will keep indefinitely in the fridge. I always use sea salt for my brines, but kosher salt or canning salt will work too. Just avoid iodized salts. The finer the salt, the less stirring you must to do to dissolve. - Start with very clean jars.
- Add the garlic, mustard seed, peppercorns, bay leaf, and dill to each jar.
- Wash your cucumbers thoroughly and discard any that are mushy or soft. Remove the blossom end from each cucumber, and pack them into the jars. I prefer to leave my cucumbers whole, as it seems to give a crunchier end result.
- Cover the cucumbers completely with the 2% brine solution.
- Add a weight to the jar to keep the cukes from floating to the top. (Fermenting glass weights are sold online but you can get creative with whatever you have on hand.)
- Add the air lock assembly (or regular lid if that’s what you’re using), and set aside to ferment at room temperature for 5-7 days. Keep in mind, the warmer your kitchen, the faster the fermenting process.
- After the initial fermenting process is over, remove the airlock, cover with a regular lid, and store at 32-50 degrees for up to six months. (I’m keeping mine in my fridge.) The pickles will continue to slowly ferment and improve in flavor during the storage process. After about six months, they will start to slowly degrade, but will absolutely still be edible.
Notes
It might be tempting to try to use the larger, slicing cucumbers to make pickles, but don’t. They are mostly water and will give you a mushy, limp result.
