What You Should Know About Antibiotics and the Gut Microbiome

Arivale Team,
Arivale Team

Antibiotics revolutionized how we treat infections that, only a century ago, could have been fatal. However, it’s not without a cost.

Our bodies harbor more bacteria cells than human cells and they live in unique ecosystems throughout our bodies. The gut microbiome is our body’s largest, most diverse, and arguably, most important community of bacteria. It educates our immune system, regulates our metabolism, and can impact everything from digestion to possibly even mood.

Contrary to making us sick, most of these bacteria actively keep us well. In fact, bacteria in our body constantly produce their own antibiotics to fight off harmful invaders. Bacteria have been fighting other bacteria for millions of years, and they’re really quite good at it.

The Gut Microbiome and Antibiotics

When there’s an overgrowth or invasion of one bacterial species, you might need antibiotics to fight off the infection. Antibiotics do this well, but they can also cause a lot of damage to our body’s stores of healthy bacteria.

“Antibiotics are a huge blow to the gut microbiome,” explained Dr. Ohad Manor, Arivale’s Bioinformatics Machine Learning Scientist and resident gut microbiome expert, “They’re largely untargeted and kill the good bacteria along with the bad.”

Additionally, Dr. Manor argues, most antibiotics cannot specifically target the location of the infection. Take strep throat for example. While strep bacteria exists throughout our body, an overgrowth in the throat causes lots of problems and is commonly treated with a course of antibiotics. One would hope that a doctor could prescribe a type of antibiotic that only attacks the strep bacteria in the throat, but unfortunately, it also decimates millions of species throughout your body.

This can create somewhat of a domino effect. When some species are wiped out, it allows for other species to spread, which can, in turn, cause new infections.

C. Diff or Clostridium difficile is a pathogenic bacterial infection that causes inflammation of the colon, diarrhea, fever, and in severe cases, even death. It is often caused by the disruption of healthy bacteria in the gut by antibiotics and is common in hospitals,” said Dr. Manor.

Another example is yeast infections, which commonly strike women taking antibiotics. Candida is a fungus, and thus, isn’t affected by antibiotics. Bacteria and fungi usually prevent each other from overgrowing, so if the bacteria are killed off, the fungi will flourish.

Rebuilding Your Gut Microbiome

Many studies have examined how long it can take the gut microbiome to recover after a course of antibiotics. While every gut is different, most studies show it can take anywhere from two to three months to an entire year for the gut to attain its pre-antibiotic state. While our guts do bounce back, some studies show that certain species of bacteria never recover and in fact, go extinct in your gut.1-2

Most wellness resources would advise taking probiotics during or after an antibiotic treatment to counter the effects of antibiotics, though there isn’t yet good scientific evidence that this is helpful.

The not-quite-as-exciting advice is to keep eating the same things you ate before. Your gut composition is largely determined by the foods you eat, so keeping up with your regular habits will help you build it back to its previous state.

Alternatively, you can look at the antibiotic annihilation as an opportunity to rebuild and improve your gut diversity. After antibiotics, you do have an opportunity to colonize your gut with healthy bacteria … and your best shot at that comes from eating a healthy diet, high in plants and low in processed foods.

Arivale’s Take

There’s a lot of good things about antibiotics. They easily treat many infections that might otherwise be fatal or at least involve a long and painful road to recovery. However, the negative impact they can have on our body’s important microbiomes should be a reminder to only use them when truly needed. Unnecessary use of antibiotics (like for viral infections) not only decimates your body’s vast stores of good bacteria, it also paves way for antibiotic-resistant pathogens that will negatively impact us all. So, tread carefully.