Scientist studying microbes

If you haven’t heard much about your microbiome, it can sound a little like science fiction. Here’s the deal—each of us is home to between 10 trillion and 100 trillion “symbiotic microbial cells.” All together, they weigh in at about three pounds, as much as your brain. Stanford microbiologist Justin Sonnenburg says we can consider the human body “an elaborate vessel optimized for the growth and spread of our microbial inhabitants.” Most of these cells live in our digestive systems, and they include bacteria, fungi, viruses, microscopic animals, and other single- or multi-celled organisms. Your microbiome consists of the genes within these cells. Shockingly, these genes outnumber your own 100 times over.

Your microbiome is in a state of flux throughout your life, and even tiny lifestyle changes can have a major effect. Babies get their first dose of microbial cells from their mothers and continue picking up microbes from their environments and families. From there, events such as dietary changes, illnesses, medication, and stress cause shifts in the internal ecosystem. However, after the age of three, the microbiome stabilizes somewhat and will return to a baseline state after these responses run their course.

More significant changes, such as puberty, pregnancy, or menopause, are accompanied by more significant microbial shifts. Even with all this variability, though, some microbes only flourish in certain locations in the body. That means microbial samples from two different people’s forearms will show more similarity than samples from two different spots on one individual’s body. Science still has a lot of questions about the microbiome, but one thing is clear—your microbiome helps keep you healthy, and changes to the system can cause illness. Let’s take a look at what you can do to keep your microbiome in balance.


What you eat has a speedy impact on the state of your microbiome. Researchers found that groups fed starkly different diets showed a microbial response within just 24 hours as their bodies began to produce more microbes tailored to their diets. That means adjustments to what you eat are a quick way to get your microbiome on track. Here’s what the experts suggest.

  • Avoid going overboard on meat—too much can have negative effects on your microbiome.
  • Feed your flora with foods high in fiber, such as whole grains and raw vegetables, to keep beneficial microbe levels high. When these organisms don’t get enough fiber, they can actually start eating the lining of your gut. In addition to being creepy, that puts you at risk for inflammation and disease.
  • Steer clear of the elements that make up the typical Western diet: sugars, refined flour, artificial sweeteners, and unhealthy fats. These ingredients feed the microbes you want to keep in check.
  • Chow down on fermented foods, such as probiotic yogurt, kimchi, and sauerkraut. These natural probiotics help replenish your supply of friendly microbes.
  • Eat processed foods in moderation. While some scientists worry about the additives in them and others take issue with their “sterility,” these foods tend to be low in healthy fibers anyway.


Antibiotic use has a drastic effect on the number of microbial cells in your stomach, cutting the population of normal ones and causing less beneficial organisms to increase. While of course we’re not saying you should turn up your nose if your doctor prescribes antibiotics for an illness, it’s important to only use them exactly as directed. Your microbiome will eventually reset to its normal baseline. However, one study indicates it’s less likely to bounce back completely after a second course of antibiotics. Here’s how to make sure you’re using antibiotics correctly.

  • Take antibiotics when your doctor prescribes them for bacterial infections. You won’t get any benefits from taking antibiotics to fight a virus, but you may end up with some icky side effects.
  • Don’t use antibiotics that were prescribed to someone else. You should only take antibiotics when your doctor has directed you to do so.
  • Use the complete course of antibiotics you’re prescribed, even if you start feeling better before it’s completed.
  • On a related note, don’t save antibiotics to take for later illnesses. Your doctor’s prescribed them for exactly what you’re experiencing at this time.
  • Schedule your antibiotic doses as directed, and keep to the schedule. Missing doses or taking them late can reduce their effectiveness.


The science community was suspicious that early studies connecting exercise to a healthy microbiome were coincidental—they hadn’t considered diet as a factor. However, new research shows that exercise alone can change your microbial community. More exercise means more diversity in your microbiome, and diversity is a good thing.

A recent study on mice also linked exercise to heightened levels of the bacteria butyrate, which protects against colon cancer. Another study, this one on people, found just 3 to 5 hours of exercise per week boosted levels of microbes that benefit the immune system.

Although we’ve still got a lot to learn about our microbiomes, the adjustments we’ve discussed are beneficial for your health for other reasons, too. Why not try a few and see how you feel? You’re hosting up to 100 trillion organisms—be a good host, and keep them happy and well-fed.



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