The Gut Microbiome: We Are Ecosystems, Not Individuals
Written By Kevin Wallace.
Each of us carries tens of trillions of microbes, most of them in the gut. They help digest food, train the immune system, make vitamins and anti-inflammatory compounds, and send signals that reach the brain. Diet shapes this inner ecosystem more than almost anything else. Fiber and a wide variety of plants feed it. Fermented foods can add to it. Ultra-processed foods and unnecessary antibiotics damage it.
I have touched the microbiome in earlier articles. It deserves one of its own. We are not single organisms living alone in our bodies. We are walking ecosystems. Caring for the life inside us is the same kind of work as caring for the land around us.
None of this is a treatment plan. A serious gut infection, inflammatory bowel disease, or a drug you already take belongs with the clinician who knows your chart.
1. We are ecosystems
You may have heard that bacteria outnumber our own cells ten to one. That figure was a back-of-the-envelope guess. A 2016 recount from the Weizmann Institute estimated about 38 trillion bacteria and about 30 trillion human cells in a typical adult man, roughly one to one (1). Nearly all of those bacteria live in the colon. Add fungi, viruses, and archaea, and each of us is home to a community of hundreds of species. That community, and the genes it carries, is the microbiome.
One to one is still remarkable. Cell for cell, we are about as much microbe as human. Those microbes carry far more genes than we do, and they do chemistry we cannot do alone.
As a permaculturist, I think of the gut the way I think of soil. Healthy soil is not one organism. It is diversity: a web in which species feed each other, compete, and keep pests in check. Strip the diversity and problems take hold. The gut works the same way.
2. What our gut microbes do for us
| Job | How it works |
|---|---|
| Digest fiber | Our enzymes cannot break down most dietary fiber. Gut bacteria ferment it into short-chain fatty acids: butyrate, acetate, and propionate. Butyrate is the main fuel for the cells lining the colon. |
| Calm inflammation | Those fatty acids help regulate immune cells and dampen inflammation. |
| Protect the gut barrier | A healthy community helps keep the mucus layer and the tight seal of the lining, so bacterial products stay out of the blood. |
| Train the immune system | A large share of immune tissue sits along the gut and learns, from the microbes it meets, what to tolerate and what to fight. |
| Make vitamins | Gut bacteria make vitamin K and several B vitamins. Colon bacteria also make B12, but that B12 is produced too far down the tract to be absorbed. It does not replace a B12 supplement on a plant-based diet. |
| Crowd out invaders | A dense community leaves less room and less food for organisms that cause disease. |
| Process bile acids, drugs, and plant compounds | Microbes transform bile acids, polyphenols, and many medicines. That is one reason two people can eat the same meal, or take the same drug, and respond differently. |
The bargain is old. We give them a warm home and a steady food supply. They return the favor in dozens of ways. The bargain fails when the food supply is fiber-poor, or when a drug wipes the community out.
3. The gut-brain axis
The gut and the brain talk all day. The microbiome is part of the conversation.
The vagus nerve runs from the brainstem to the gut and carries signals both ways. Most of the body’s serotonin is made in the gut, and microbes influence that production. Gut serotonin does not cross into the brain. It affects gut movement and sends signals up the nerve. Inflammation that starts in the gut can reach the brain. Short-chain fatty acids and other microbial products enter the blood and can influence it too.
In animals, changing the microbiome changes anxiety-like behavior and stress responses. A harmless soil bacterium, Mycobacterium vaccae, activated serotonin-producing neurons in mice and produced effects similar to antidepressants (2). That is early animal work, not a prescription. Human studies are mostly associations. Mood and digestion travel together often enough that the connection is worth respecting, and not worth a supplement claim.
4. When the ecosystem goes wrong
Dysbiosis means a gut community that has lost diversity or balance. It has been linked with obesity, type 2 diabetes, inflammatory bowel disease, allergies, and heart disease. For most of those, we still cannot say whether the microbiome is a cause, a consequence, or both. Two examples show the connection can be real.
Heart disease and TMAO. Choline and carnitine, found mostly in red meat, egg yolks, and other animal foods, are converted by some gut bacteria into a compound the liver turns into trimethylamine N-oxide, TMAO. In a Cleveland Clinic study of 4,007 people undergoing elective heart catheterization, those in the highest TMAO quartile had about 2.5 times the risk of heart attack, stroke, or death over three years compared with the lowest quartile. The unadjusted hazard ratio was 2.54 (3). Antibiotics in the related feeding studies knocked TMAO down, which is evidence the microbes were doing the converting. The same group found that long-term vegans and vegetarians produced far less TMAO after a carnitine challenge than meat eaters, because their gut communities were different (4). Diet, microbes, and risk are tied together. TMAO is a marker with a mechanism. It is not a reason to buy a TMAO test from a wellness site.
C. difficile and restoring a community. Clostridioides difficile often takes hold after antibiotics wipe out the normal community, and it tends to come back. The treatment that changed the field was restoring a screened donor community. FDA approved Rebyota, a rectal microbiota product, in November 2022, and Vowst, an oral capsule of purified fecal spores, in April 2023. Both are for preventing recurrence after antibiotics in adults, not for a general reset (5). This is the clearest proof that a microbial ecosystem can treat a disease. It is also a prescription product made from screened donor material. It is not a homemade transplant, and it is not a probiotic from a shelf.
Veterinarians have used the same idea longer than the FDA approvals. In cattle, the rumen is a fermentation vat, and the animal depends on its microbes to digest grass. When a rumen goes off, a classic treatment is rumen fluid from a healthy herd-mate. Fecal microbiota transfer is now used in dogs and other species for selected cases. The principle is restoration, not a daily capsule.
5. What feeds a healthy microbiome
Fiber, and enough of it. Fiber is the main food for gut bacteria. Most Americans eat far less than the recommended amount. Beans, lentils, whole grains, vegetables, fruits, nuts, and seeds are the sources. Different fibers feed different microbes, so variety matters as much as grams. Increase fiber slowly if you are not used to it. A sudden jump is how people decide fiber “doesn’t agree with them.”
Plant diversity. In the American Gut Project, people who ate more than 30 different plant foods a week had more diverse gut microbiomes than those who ate 10 or fewer (6). Herbs, spices, nuts, and seeds count. Thirty sounds like a lot until you count. Oatmeal with berries, walnuts, flax, and cinnamon is already five.
Fermented foods. In a Stanford randomized trial, 36 healthy adults were assigned to a high-fermented-food diet or a high-fiber diet for 17 weeks, 18 in each arm. The fermented-food group, aiming for about six servings a day, steadily increased gut microbial diversity and decreased inflammatory markers. The high-fiber group did not show the same diversity increase over that window. Their microbes did shift toward breaking fiber down. The cytokine score that was the primary outcome did not change overall (7). The study included yogurt and kefir. Plant-based eaters have other options: sauerkraut, kimchi, other fermented vegetables, miso, tempeh, kombucha, and vegetable brine. Look for refrigerated products that say live cultures. Shelf-stable pasteurized versions do not contain living microbes.
The practical reading is both, not one. Fiber and plant variety feed the microbes you have. Fermented foods can introduce new ones. Six servings a day was a study target, not a household rule. A daily serving that you will actually eat beats a protocol you abandon.
What we make. Thea and I ferment at home. Kimchi is the vegetable one: cabbage and seasonings, salt, time, and the microbes already on the leaves. We also make yogurt from soy milk. A plant milk will not set the way dairy does unless it has a culture that can work in it and, often, a thickener or a protein level high enough to gel. The point for this article is not a recipe. It is that a live ferment you make, kept cold and handled cleanly, is food. It is not a supplement, and it does not need a third-party seal. It does need clean jars, the right salt or culture, and the sense to throw out a batch that smells wrong. Mold that is not the expected surface yeast is a discard, not a dare.
6. What harms it
Unnecessary antibiotics. Antibiotics save lives. When you need one, take it as prescribed. Each course disrupts the gut community, sometimes for months, and some species may not fully return. Ask whether an antibiotic is needed. Do not take one for a cold or the flu.
Ultra-processed foods. Fiber-poor refined diets starve the community. Some additives may do direct harm. In a controlled feeding trial, the emulsifier carboxymethylcellulose reduced microbial diversity and the beneficial compounds microbes produce (8). That was one emulsifier, in a feeding study, not a ban on every packaged food. It is a reason to prefer food you can recognize.
Artificial sweeteners. In a randomized trial, two weeks of saccharin or sucralose altered the microbiome and, in some people, impaired blood sugar control. The effect depended on the person’s existing microbes (9). Not everyone responded. That is the finding, and it is why a blanket claim is too strong.
Other disruptors. Smoking, heavy drinking, chronic stress, short sleep, and very little movement are all associated with a less healthy microbiome. Association is not proof that fixing one of them will rewrite the stool test.
7. Probiotics, prebiotics, and microbiome tests
Probiotics are specific live microbes in a capsule or a food. Particular strains have helped with specific problems, including a lower risk of antibiotic-associated diarrhea in some studies. For healthy people, there is little evidence that a general probiotic improves health. Most supplement strains pass through without settling.
One trial surprised the field. After antibiotics, a multi-strain probiotic delayed the return of the person’s own gut community. Volunteers who received a transplant of their own stool, saved before the antibiotics, recovered within days (10). A few lab-grown strains are not an ecosystem. They can crowd recovery. I do not take a general probiotic. The ferments on the table are the microbes I am willing to eat.
Prebiotics are the fibers that feed beneficial microbes. Inulin in onions, garlic, leeks, asparagus, and chicory. Resistant starch in cooled potatoes, rice, and green bananas. Food covers this. A prebiotic powder is optional, and a large dose is a common cause of bloating.
Direct-to-consumer stool tests are not ready to guide dinner. There is no agreed definition of a healthy microbiome. Results vary from day to day. The reports have not been shown to improve health. I would spend the money on vegetables.
If you take a probiotic for a specific problem, pick a strain studied for that problem, use the third-party testing standard from the supplements article, and talk with your doctor if you are seriously ill or immunocompromised. A live microbe is the wrong experiment in a person with no immune reserve.
8. Soil, farms, and old friends
For most of human history, people lived close to soil, animals, and untreated water. The immune system evolved expecting that contact. The old-friends idea holds that losing those exposures leaves the immune system poorly trained and more prone to allergies and autoimmune disease. It is a hypothesis with some strong observations, not a settled law.
A striking comparison looked at Amish children, who live close to traditional farm animals, and Hutterite children, who share a similar genetic background and use industrialized farming. Amish children had far lower rates of asthma. Dust from Amish homes shaped innate immune responses in a protective direction. Mice exposed to that dust were protected against allergic airway disease (11). The study does not say a modern family should move into a barn. It says early, ordinary contact with a farm microbial world left a mark.
The soil bacterium in the mouse study fits something I have felt all my life. Putting my hands in the soil is therapy for me. Gardening, animals, woods, and produce from living soil are contact with a richer microbial world. The same rules that build soil, diversity, organic matter, little disturbance, and fewer chemicals that kill useful life, are the rules that build a gut.
9. Where we land
We are ecosystems. Roughly as many bacterial cells as human cells, mostly in the colon, doing work we cannot do alone.
Feed them fiber from beans, whole grains, vegetables, fruits, nuts, and seeds. Increase it slowly.
Aim for 30 different plant foods a week. Herbs, spices, nuts, and seeds count.
Add fermented foods with live cultures. Sauerkraut, kimchi, miso, tempeh, kombucha, and, in our kitchen, soy-milk yogurt. Pasteurized shelf-stable jars do not count.
Limit ultra-processed foods, and be wary of emulsifiers and artificial sweeteners. The human trials are small. The direction is consistent.
Use antibiotics when they are needed, and not for a virus.
Be skeptical of general probiotics and consumer stool tests. After antibiotics, a probiotic can delay recovery.
Gut bacteria do not cover B12. That supplement stays.
Get your hands dirty. Soil, animals, and outdoor time are part of the same story.
We are never truly alone. Each of us is a community. How we eat and live decides whether that community thrives.
10. References
Sender R, Fuchs S, Milo R. Revised estimates for the number of human and bacteria cells in the body. PLoS Biology. 2016;14(8):e1002533. The short Cell version is “Are we really vastly outnumbered?” Cell. 2016;164:337-340. cell.com
Lowry CA, et al. Identification of an immune-responsive mesolimbocortical serotonergic system: potential role in regulation of emotional behavior. Neuroscience. 2007;146:756-772. University of Bristol news summary. bristol.ac.uk
Tang WHW, Wang Z, Levison BS, et al. Intestinal microbial metabolism of phosphatidylcholine and cardiovascular risk. New England Journal of Medicine. 2013;368:1575-1584. nejm.org
Koeth RA, Wang Z, Levison BS, et al. Intestinal microbiota metabolism of L-carnitine, a nutrient in red meat, promotes atherosclerosis. Nature Medicine. 2013;19:576-585. nature.com
U.S. Food and Drug Administration. FDA approves first orally administered fecal microbiota product for the prevention of recurrence of Clostridioides difficile infection. April 26, 2023. Rebyota was approved November 30, 2022. fda.gov
McDonald D, Hyde E, Debelius JW, et al. American Gut: an open platform for citizen science microbiome research. mSystems. 2018;3(3):e00031-18. asm.org
Wastyk HC, Fragiadakis GK, Perelman D, et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021;184:4137-4153. cell.com
Chassaing B, Compher C, Bonhomme B, et al. Randomized controlled-feeding study of dietary emulsifier carboxymethylcellulose reveals detrimental impacts on the gut microbiota and metabolome. Gastroenterology. 2022;162:743-756. gastrojournal.org
Suez J, Cohen Y, Valdés-Mas R, et al. Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance. Cell. 2022;185:3307-3328. cell.com
Suez J, Zmora N, Zilberman-Schapira G, et al. Post-antibiotic gut mucosal microbiome reconstitution is impaired by probiotics and improved by autologous FMT. Cell. 2018;174:1406-1423. cell.com
Stein MM, Hrusch CL, Gozdz J, et al. Innate immunity and asthma risk in Amish and Hutterite farm children. New England Journal of Medicine. 2016;375:411-421. nejm.org
