Familiar with the Four F’s? You should be.
Antibiotics are a modern medical marvel. Thanks to them, so many issues that were once severe if untreated (like strep throat and urinary tract infections) can be resolved within a matter of days. They’ve saved countless lives over the years — but also created a brand-new medical challenge.
Studies have repeatedly shown that antibiotic use can cause serious harm to your gut microbiome. The implications of a damaged gut microbiome range from mild and uncomfortable (like a bad case of diarrhea) to life-threatening (like developing a gene resistance to antibiotics).
To get to the core of how antibiotics affect your gut microbiome, we spoke with Christopher Damman, M.D., a board-certified gastroenterologist at the Digestive Health Center at UW Medical Center and a UW associate professor of gastroenterology and medicine.
What is a gut microbiome, anyways?
First, we should probably explain what gut microbiomes are, exactly, and why they play such an important role in your overall health.
When someone says “gut microbiome,” they’re referencing a system of trillions (and trillions) of bacteria, viruses, fungi, and other microscopic living things, all of which exist mainly in your large intestine and serve your body in an astonishing number of ways. “The microbiome help protect the body from foreign invaders as sentinels that maintain the integrity of the barrier,” says Dr. Damman. “They also serve as little factories that aid in the absorption of nutrients from our diet that we’re not able to process without them.”
Your microbiome helps your body digest fiber, controls your immune system, moderates brain health, and more. A healthy microbiome has been shown to reduce the risk of obesity, cancer, heart disease, and other life-threatening ailments.
When your gut microbiome is thrown off, however, that can lead to a wide range of health issues, from weight gain or loss to irritating skin conditions to the body’s inability to process the necessary amount of nutrients from food.
That’s where antibiotics come in — and they don’t always help you for the better.
How antibiotics affect your gut microbiome
When you visit the doctor for a sore throat, ear infection, or even a major surgery, you often leave the clinic or hospital with a prescription for some type of antibiotic. And when you take that antibiotic, you’re likely focused on feeling better or preventing infection. What you’re likely not focused on (or maybe even aware of at all) is how your antibiotic might be hurting your body at the same time that it’s theoretically helping it.
What you need to know is that in the process of flushing out the “bad” bacteria from your body, antibiotics often end up killing a lot of the necessary bacteria in your gut microbiome along the way.
Once the round of antibiotics is finished (usually around 5-7 days), “the diversity [of your microbiome] returns,” Dr. Damman says. “However, with prolonged and repeated use of antibiotics, the gut is less and less able to return to its previous healthy state.”
A growing number of studies are showing that even short courses of antibiotics can permanently alter the general makeup of your gut microbiome. Perhaps more alarmingly, the part of your microbiome that does survive the antibiotics can often develop a resistance gene against those same antibiotics in the future.
This means that the next time you need to use that same antibiotic, your body might not respond to it as well as it did the first time.
How to protect your microbiome
Oftentimes, antibiotics are fundamentally necessary for healing — but sometimes, they’re prescribed as an option to speed up your body’s natural recovery process.
Dr. Damman urges you to only take antibiotics when you really need them.
“Using antibiotics indiscriminately for viral colds, for example, will not speed up recovery and will take its toll on one’s microbiome, so it’s important to follow your health care provider’s recommendation and advice when it comes to antibiotics,” Dr. Damman explains.
Of course, the decision to take or skip antibiotics is one only you and your medical provider can make. And when your trusted doctor says a round of antibiotics is necessary, you should absolutely take them. But if your doctor says you have a cold and will likely recover in a few days, with or without antibiotics, you might want to consider forgoing a dose.
The next step you can take to restore and protect your microbiome is to make sure you’re consuming probiotic supplements and foods rich in probiotics (more on those below) regularly — but especially make a point to pair your antibiotics with probiotics, when you can. And beyond probiotics, there’s another nutritional strategy you can take to rebuild your gut microbiome: When you’re grocery-shopping, remember the “Four F’s.”
“We’re essentially starving our microbiome with many modern ultra-processed foods,” Dr. Damman explains. “The nutrients are easily remembered as the four phonetic F’s of food: fiber, phenols, bioactive fats, and ferments.”
For fiber, look for whole grains like oatmeal, beans, nuts, and seeds. As for phenols, they’re what gives color to the fruits and vegetables, so keep that in mind as you wander the produce aisle. (That’s what doctors mean by recommending you “eat a rainbow,” Damman notes.)
You can find good fats in avocado, olives and their oils, and fatty fish, to name a few. And lastly, ferments are those probiotic-rich foods we touched on above, including yogurt, kefir, sauerkraut, kimchi, and pickles. All together, they make up a delicious way to keep your gut microbiome in tip-top shape.
