The microbes in your gut are not a fixed inheritance. The trillions of bacteria, fungi and viruses living in your intestines, most of them in the colon, shift with what you eat, the medicines you take and the world around you, and they changed a great deal in your first few years of life. Nobody can change how they were born, but most people can change how much fiber they eat. (For what these microbes actually do, see what the gut microbiome is and what it does.)
It starts at birth
Everyone's mix of gut microbes is different. Harvard's Nutrition Source notes that it is originally determined by a person's DNA, and that the first real exposure to microbes comes at birth, during delivery through the birth canal, and then through breast milk.
In a review in the Biochemical Journal, Elizabeth Thursby and Nathalie Juge describe how babies born vaginally carry plenty of lactobacilli in their first few days, while babies born by cesarean section are slower to acquire one major group of gut bacteria, Bacteroides. Breastfed babies typically have a lot of Bifidobacterium; formula-fed babies have less. By around two and a half, a child's gut microbiota resembles an adult's in its makeup, its diversity and what it is able to do.
In people over 65 the community shifts again, and the same review describes a group of centenarians whose gut microbiota was markedly less diverse. In between, Harvard notes, the relative abundance of different species can fluctuate daily, weekly and monthly with diet, medication and exercise.
Diet, and fiber in particular
Alongside genes, environment and medication, diet plays a large role in deciding which microbes live in the colon. Thursby and Juge note that extreme diets, whether almost entirely animal-based or plant-based, produce wide-ranging changes in the gut microbiota of people who eat them.
The body can't digest dietary fiber on its own; it can only be broken down and fermented by enzymes from microbes living in the colon. That fermentation releases short-chain fatty acids, which lower the pH of the colon. The more acidic environment favors some microbes over others and limits the growth of some harmful bacteria, including C. difficile, a bacterium behind some persistent gut infections. Researchers are also studying wider effects of short-chain fatty acids, such as stimulating immune cell activity and helping keep blood glucose and cholesterol at normal levels.
Thursby and Juge point out that the typical Western diet is substantially lower in the carbohydrates gut microbes can use, and Cleveland Clinic says a diet high in sugar and saturated fat tends to favor the less helpful types of microbes. Processed foods tend to lack fiber and micronutrients, and they often come with additives and preservatives that Cleveland Clinic describes as potentially harmful to the microbiome.
Antibiotics and other medicines
Antibiotics are designed to kill bacteria, and they don't spare the helpful ones. Thursby and Juge describe antibiotic treatment as dramatically disrupting the gut's microbial balance in both the short and the long term, reducing the variety of bacteria present. How fully and how quickly the microbiome recovers varies from person to person. Cleveland Clinic adds that the disruption sometimes lets the wrong kind of bacteria come back stronger, and Harvard lists prolonged antibiotic use among the causes of dysbiosis, the term for an unbalanced gut microbiome.
As Cleveland Clinic puts it, there are times when you need them and times when you really don't, and the useful question for a prescriber is which of those you're facing. Some clinicians suggest prebiotics or probiotics after a course of antibiotics to help the microbiome recover; whether that makes sense for you is a conversation to have with the person who prescribed them.
Acid blockers can also affect the microbiome by changing the pH inside the gut, according to Cleveland Clinic. That is not a reason to stop a prescribed medicine on your own, but it's worth knowing if you take one long term.
Environment, chemicals and stress
Thursby and Juge list geography, smoking and living arrangements among the environmental factors linked to differences in the microbiota. Cleveland Clinic names alcohol, tobacco smoke and pollutants as chemicals that can harm it. The microbiome can usually recover from a temporary exposure, it notes, but chronic exposure can change its composition.
Much of the research on specific chemicals has been done in animals. Studies supported by the National Institute of Environmental Health Sciences (NIEHS) found that the artificial sweetener sucralose, arsenic and ultrafine air-pollution particles all altered the gut microbiome in mice. In another mouse study, chronic stress disturbed the gut microbiome, triggered an immune response and promoted colitis, a type of inflammation in the colon. Mouse findings like these don't show that the same thing happens in humans at everyday exposures, and NIEHS itself says "big questions remain."
What's reasonable to do
Cleveland Clinic recommends a variety of whole foods, especially whole grains, vegetables and fruit, and points out that a varied community of microbes needs a variety of plant fibers to thrive. Fruits, vegetables, beans and whole grains such as wheat, oats and barley are all good sources of prebiotic fiber, the kind that feeds beneficial bacteria. According to Harvard, the richest sources, eaten raw, are:
- garlic and onions
- leeks and asparagus
- Jerusalem artichokes
- dandelion greens
- bananas
- seaweed
Go slowly if you're adding a lot. A sudden jump in prebiotic foods can increase gas and bloating. Harvard's advice for people with sensitive guts, including those with irritable bowel syndrome, is to start with small amounts and see how they're tolerated. Tolerance may improve with time.
Fermented foods such as yogurt with live active cultures, pickled vegetables, tempeh, miso, kimchi, sauerkraut and kombucha may contain live microbes that further alter the microbiome. Not all of them do, though. Foods that are heated or pasteurized after fermentation lose their live bacteria.
On probiotic supplements, Harvard poses the question without answering it: would a relatively healthy person benefit from taking probiotics, or is a fiber-rich diet enough? If you're considering one, Cleveland Clinic suggests letting a healthcare provider help you choose, since the right probiotic depends on your situation.
Why microbiome test kits aren't much use yet
Plenty of companies will analyze a stool sample and send back a report on your gut bacteria, often with recommendations attached. Cleveland Clinic notes that clinical healthcare providers generally don't use or recommend these tests. The reason is that we still don't know enough about the different types of gut microbes, or how they affect health, for the reports to be useful as personal health advice.
An international consensus statement published in Lancet Gastroenterology & Hepatology in late 2024 reached a similar view. Its panel of 69 experts from 18 countries found insufficient evidence to widely recommend routine microbiome testing in clinical practice. The panel noted that direct-to-consumer tests are sold without any agreed regulation and can raise false hopes. It also found there isn't enough information to set strict healthy reference ranges for how abundant particular species should be, and no common definition of dysbiosis that could be used in clinical practice. The experts discouraged testing companies from including treatment advice in their reports, and said testing should be ordered by a physician or another licensed healthcare professional.
Because the balance of species can shift from week to week, a single sample captures one moment in a system that keeps moving. The panel does see potential for testing in managing some disorders, but says more studies are needed to show its value.
If you buy a kit out of curiosity, read the report that way, and don't change your diet or start supplements on the strength of it. If gut symptoms are the reason you're looking, a clinician is a better first stop. Our guide to how your digestive system works explains when symptoms are worth getting checked.
This article is for general education only and isn't medical advice, so please talk to a doctor or other qualified clinician before making changes to your diet, supplements or medicines.
Sources
- The Microbiome, The Nutrition Source, Harvard T.H. Chan School of Public Health
- Introduction to the human gut microbiota, Thursby E, Juge N. Biochemical Journal, 2017
- Gut Microbiome, Cleveland Clinic
- Microbiome, National Institute of Environmental Health Sciences
- International consensus statement on microbiome testing in clinical practice, Lancet Gastroenterology & Hepatology, 2024