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Experts say some antibiotics, including tetracyclines and macrolides, can kill healthy gut bacteria. RECVISUAL/Getty Images
  • Researchers say some antibiotics, including commonly prescribed tetracyclines and macrolides, can kill healthy gut bacteria during use.
  • They said the lack of healthy gut bacteria can lead to gastrointestinal ailments and recurring infections.
  • Experts say people taking antibiotics should eat foods rich in probiotics, such as yogurt and sauerkraut, while using the medications.

The roughly 40 trillion microbes that live in our body, most of which are in our gut, can impact everything from how we digest our food to how we defend ourselves against outside threats such as viruses, parasites, and bacteria.

The microbes create a gentle balance that can be disrupted by a variety of medical treatments, especially antibiotics.

The discovery of antibiotic medications marked a new future for humans, including making things like dental surgery possible and survivable.

They remain powerful tools, although their use doesn't come without side effects. That can include unintentionally killing off the good bacteria in our gut.

New research adds to the growing pile of information on how important our microbiome is and how common antibiotics can kill off certain helpful gut bacteria, highlighting the importance of mitigating potential unwanted side effects while a person goes through a course of antibiotics.

In a recent study published in the journal Nature, an international research team based primarily in Germany looked at how 144 antibiotics commonly used in humans impact our gut health.

Most importantly, they found that two classes of antibiotics — tetracyclines and macrolides — create "collateral damage" by wiping out good bacteria in the gut, leaving it open to gastrointestinal ailments and recurring infections from a type of bacteria known as Clostridioides difficile (C. diff), which can cause severe diarrhea, nausea, fever, stomach pain, and even death.

Tetracyclines are a type of broad-spectrum antibiotics. There are five types of macrolides: erythromycin, clarithromycin, azithromycin, fidaxomicin, and telithromycin. They are used to treat a variety of common infections, from acne to sexually transmitted infections.

The researchers found tetracyclines and macrolides not only stopped good bacteria from growing, but they lead to the death of about half of the strains of microbes found in the gut the researchers tested for.

"Many antibiotics inhibit the growth of various pathogenic bacteria. This broad activity spectrum is useful when treating infections, but it increases the risk that the microbes in our gut are targeted as well," Lisa Maier, DFG, the Emmy Noether group leader at the University of Tübingen in Germany and one of the two lead authors of the study, said in a statement accompanying the research.

Camille Goemans, a postdoctoral fellow at the University of Tübingen and the study's other lead author, said researchers didn't expect to see that kind of impact from tetracyclines and macrolides, as it was believed they didn't kill bacteria.

"Our experiments show that this assumption is not true for about half of the gut microbes we studied," she said.

The researchers didn't recommend that doctors stop prescribing those kinds of antibiotics, but rather explored some undisclosed drug therapies that could mitigate the effects as "antidotes."

The researchers say they tested some of those drugs in mice, and while early results were promising, more research is needed. (It should be noted that the research was funded by in part by a grant from the European Molecular Biology Laboratory, which has filed a patent on using the methods identified in the study to prevent and/or treat dysbiosis — or the disruption of gut microbes — and "for microbiome protection.")

In the meantime, health experts say there are other ways to help your gut bacteria remain plentiful and healthy while you're being treated with antibiotics.

One commonly recommended method is eating yogurt and other foods rich in probiotics.

Becky Bell, MS, RDN, LN, a dietician with Rooted Nutrition Therapies, recommends that her clients supplement their diets with certain strains of bacteria while undergoing antibiotic therapy. That includes Lactobacillus acidophilus, which can be found in many common yogurts.

"There is no way around the fact that antibiotics kill both harmful and beneficial bacteria in the gut," Bell told Healthline. "It's extremely important to focus on nourishing and rebuilding the gut after antibiotic treatment by eating a wide variety of prebiotic- and probiotic-rich foods."

However, every person's gut biome is unique to them and changes throughout their lives, so there's no one-size-fits-all approach to keeping it healthy.

Nonetheless, some experts say getting probiotics from foods during antibiotic treatments is the best route to go.

Dr. Andrea Paul, a medical advisor to the nutritional supplement company Illuminate Labs, says fermented foods such as sauerkraut, yogurt, kimchi, and tempeh contain probiotics and are cheaper than purchasing probiotic supplements.

She recommends that her patients start off slow with a small serving of probiotic-rich foods during an antibiotic course to make sure their stomachs can tolerate it.

"Sometimes it can create a bit of digestive discomfort, so it's up to the patient to determine their level of tolerability, but many patients feel better when consuming fermented foods during an antibiotic course," she said.