Our gut is home to trillions of bacteria and other tiny microbes. This community, called the gut microbiome, helps our body in many ways.
It breaks down food, supports the immune system, sends signals to the brain, and does many other jobs that scientists are still discovering. But when this balance of microbes is disturbed—either by losing good bacteria or having the wrong mix—it can affect our entire body.
We already know that antibiotics can harm the gut microbiome, but a new study from Stanford shows that many common medications—not just antibiotics—can also change this delicate balance. These changes can affect our metabolism, immune system, and overall health.
Published in the journal Cell, the study found that a major reason behind these changes is competition for nutrients. When a medication reduces certain bacteria, it also changes which nutrients are available in the gut. Some bacteria take advantage of these changes and grow, while others disappear.
The senior author of the study, Professor KC Huang from Stanford, explained that these changes follow clear patterns. This means we may be able to predict—and even prevent—some of the negative effects drugs have on our gut.
To explore this, the team collected stool samples from nine healthy donors. They grew the microbial communities from those samples in the lab and exposed them to 707 common drugs.
The lead researcher, Dr. Handuo Shi, looked at how each drug affected the bacteria. The team studied changes in bacterial growth, community makeup, and metabolites (tiny chemicals that microbes use or produce).
Out of all the drugs tested, 141 changed the microbiome. Some drugs caused permanent changes, even with short-term use, and even wiped out certain bacteria completely. The main reason: some bacteria are more sensitive to drugs, and those that survive can use the leftover nutrients better than others.
Shi explained that medications don’t just kill microbes—they change the food supply. The ones that adapt to the new “buffet” survive. This insight helps researchers understand why some bacteria thrive while others vanish.
Even though the gut microbiome is complex, the Stanford researchers created computer models to predict how different drugs would affect it. These models considered two main things: how sensitive each type of bacteria is to the drug, and how they compete with each other for nutrients.
This new approach could help doctors understand how a person’s gut will respond to a specific drug. In the future, we may be able to pick medications, diets, or probiotics not only based on how well they treat an illness, but also on how they protect our gut health.
Shi said this is a shift in thinking: instead of focusing on how drugs affect just one type of bacteria, we now look at the entire ecosystem inside the gut. This helps us design better treatments that keep the microbiome healthy.
Looking ahead, the researchers want to use this knowledge to create gut-friendly diets and drug combinations. They are also testing how traditional herbal medicines—used for thousands of years—affect the microbiome. Professor Huang believes herbal remedies may have powerful effects, but we need more research to understand how they work.
The team also wants to track microbiome changes in real-time using new technology that can take samples directly from the small intestine. They are expanding their studies to include how other lifestyle factors like diet, water, and exercise influence our gut bacteria.
As Professor Huang said, understanding how bacteria compete for food can help us predict what happens in the gut. This could reduce the unwanted side effects of medications and lead to healthier treatments in the future.
If you care about gut health, please read studies about how probiotics can protect gut health ,and Mycoprotein in diet may reduce risk of bowel cancer and improve gut health.
For more health information, please see recent studies about how food additives could affect gut health, and the best foods for gut health.
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