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How to Recover From Antibiotics

Antibiotics are lifesavers, but they can also wreak havoc on your gut microbes.

Key points

  • Oral antibiotics kill gut bacteria as well as pathogens.
  • It can take months to rebuild your gut microbiome.
  • Probiotics don’t actually help, but prebiotics can speed up recovery times.

“Because we humans are big and clever enough to produce and utilize antibiotics and disinfectants, it is easy to convince ourselves that we have banished bacteria to the fringes of existence. Don't you believe it. Bacteria may not build cities or have interesting social lives, but they will be here when the Sun explodes. This is their planet, and we are on it only because they allow us to be.” –Bill Bryson

You may have heard that you should take probiotics or eat yogurt after a round of antibiotics in order to restart a healthy gut. That advice is well-intentioned and reasonable, but misguided. A study by Eran Segal and Eran Elinav of the Weizmann Institute of Science showed that treating a depleted gut microbiome with probiotics can actually further disrupt it. Probiotics are not normal gut residents, but they may gain a foothold after antibiotic treatments and delay the return of indigenous gut microbes. In other words, probiotics can make recovery worse.

A new study shows a better way to recover, and it’s refreshingly simple.

Antibiotics: The good and the bad

Antibiotics are life-saving meds that have changed medicine since the day they were discovered. But they are not without side effects. Among them are depression and anxiety, occasionally lasting for months.

Antibiotics kill bacteria, but they are indiscriminate when it comes to targeting. Not only do they kill pathogens, but they kill beneficial gut bacteria as well. The gut microbiome is a carefully balanced ecosystem that depends on specific “keystone” species to keep things running well. Keystone species represent important links in an ecosystem that many other species depend on. For instance, beavers are a keystone species in forested areas because they build lakes, canals and wetlands that many other creatures depend on.

When keystone bacteria are killed, the entire gut ecosystem is disrupted. A few plucky bacteria can persist in a dormant form. These include bacteria like Clostridium difficile (C. diff) and Salmonella. These are the last bacteria standing, and they can take over the gut, eating away at the mucus lining and then the tissue itself, creating a leaky gut. Diarrhea is a common result.

Dysbiosis can lead to inflammation and metabolic disorders. Via the gut-brain axis, it can also contribute to mood and cognition deficits. Antibiotic-induced gut dysbiosis can make a patient miserable, anxious, and depressed.

Fiber rebuilds a healthy gut.
Source: Midjourney

Recovery from antibiotic treatment

Fortunately, this disturbed state doesn’t last forever. Gut bacteria will slowly recover from remnants of the original ecosystem. As antibiotics sweep through the gut, they miss bacteria hiding out in the nooks and crannies. These leftovers will start to bloom as the gut returns to a favorable environment, which could take months. Slowly, the gut will repopulate, although not necessarily perfectly. With a proper diet, these beneficial bacteria will begin to ferment again, producing gut-healing fatty acids like butyrate.

A new study from Swathi Penumutchu and Peter Belenky of Brown University found that prebiotics significantly enhance this process. By feeding the fermenting bacteria, the process is sped up. They suggest that prebiotics offer a potential therapy after antibiotic treatment.

A healthy microbiome is diverse, so it makes sense to use a blend of prebiotics to feed the many players that are needed to recover. Most people get their microbiome back after a few weeks of consuming prebiotic fiber. However, a smattering of bacterial species may be permanently eradicated.

There is a way to get your gut microbes back quickly, but it’s fairly dramatic and somewhat disturbing: a fecal transplant. Doctors take a sample of your poop before the antibiotics, and then return it to you after. Recovery is swift, usually taking less than two days. This has a high ick factor, but on the upside, it’s your own poop.

How to minimize the downside

A week before you dose with antibiotics, you might want to slow down sugar consumption. That suppresses bacterial metabolism, which seems to protect gut microbes from the antibiotics.

Adding prebiotic fiber preserves the diversity of the microbiome during antibiotic treatment. Fiber is recommended before, during, and after antibiotic treatment. You can get fiber from veggies like lentils, artichokes, asparagus, onions, and leeks. Berries are also full of fiber, partly because you eat their seeds. This will build a hearty microbiome that will quickly shake off the depredations of antibiotics.

As a bonus, these changes minimize inflammation, thus protecting you from all manner of illness including heart disease, type 2 diabetes, obesity, and dementia. It can make you so resilient that you may not ever need antibiotics in the first place.


Penumutchu, S., Korry, B.J., Hewlett, K. et al. Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential. Nat Commun 14, 5161 (2023).

Suez J, Zmora N, Zilberman-Schapira G, Mor U, Dori-Bachash M, Bashiardes S, Zur M, Regev-Lehavi D, Ben-Zeev Brik R, Federici S, Horn M, Cohen Y, Moor AE, Zeevi D, Korem T, Kotler E, Harmelin A, Itzkovitz S, Maharshak N, Shibolet O, Pevsner-Fischer M, Shapiro H, Sharon I, Halpern Z, Segal E, Elinav E. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018 Sep 6;174(6):1406-1423.e16. doi: 10.1016/j.cell.2018.08.047. PMID: 30193113.

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