How Long Does It Take For Gut Flora To Restore After Antibiotics?

Antibiotics kill bacteria. That’s their job, after all. It’s how they’ve saved millions of lives over the last hundred years.

But killing the bad guys responsible for your infection means you also kill good flora crucial for your health. If you’ve recently taken a course of antibiotics, and you’re wondering how long it will take to get your microbiome back to normal—or even if it’s possible at all—read on.


How badly do antibiotics damage our gut flora?
Why is diversity so important?
The composition of gut bacteria almost recovers after antibiotics for most people
How can I help my gut bacteria to recover after antibiotics?
How long does it take to restore good bacteria after antibiotics?
Can some people’s gut bacteria can recover from antibiotics in around six months?
Key takeaways


How badly do antibiotics damage our gut flora?

There are around 100 trillion bacteria in our guts, so it’s impossible to know the precise composition of anyone’s microbiome before they start a course of antibiotics, or after they finish. But modern gut testing can give us a good idea.

Research has revealed that antibiotics have the potential to decimate our gut bacteria. That means that the round you took for your sinus infection could have cut your gut flora down to one tenth of its previous level. Not by one tenth, to one tenth: that’s a 90 percent reduction (Source: NCBI).

The damage done appears to depend on a few factors.


1. The length and number of courses

Multiple courses of antibiotics appear to be the most damaging (Source: NCBI), and higher doses of antibiotics taken over a longer period of time have the biggest impact. This might be shocking news to the many people who—often as teenagers—took antibiotics for months on end in an attempt to treat their acne.

Oluf Pedersen, chief scientist on a 2018 project that looked at the impact of just one course of antibiotics on the microbiome, pointed out that most people will get multiple rounds of exposure to antibiotics. “The concern relates to the potentially permanent loss of beneficial bacteria after multiple exposures to antibiotics during our lifetime,” he said to journalists for the science news website ars TECHNICA (Source: DX DOI).


2. The type of antibiotic

If you go to your doctor with an infection, you’re very likely to come away with a broad-spectrum antibiotic. That’s because unless your doctor takes a sample and sends it to a lab to be cultured, they don’t know what type of bacteria is causing your infection. Prescribing a broad-spectrum antibiotic makes it more likely to work on your infection, but your gut bacteria will take a harder blow.

When researchers gave mice either a broad-spectrum cephalosporin antibiotic, or a combination of three antibiotics (amoxicillin, bismuth and metronidazole), both antibiotic treatments caused significant changes in the gut microbial community.

The mice given the broad-spectrum antibiotic didn’t recover their normal diversity, but the other mice given the amoxicillin-containing combination mostly—but not completely—returned to pre-treatment levels (Source: IAI.ASM).


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3. At what stage of your life you take them

Our first years seem to be crucial for setting up a healthy microbiome for life. One study found an association between antibiotics given in the first year of life and later neurocognitive difficulties, such as ADHD, depression and anxiety (Source: Wiley), and others have found that the more courses of antibiotics a person receives during childhood, the higher their risk of juvenile rheumatoid arthritis and inflammatory bowel disease (Source: NCBI).

Others have linked antibiotic exposure in the womb and early childhood (and the subsequent altered gut microbial composition) to the development of asthma later in life (Source: BMJ) and obesity in children as well adults (Source: Science Direct).

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Why is diversity so important?

In a healthy, diverse gut microbiome, the resident microbes help protect against invasion by pathogens that could cause infection or disease. They work together, using different methods to inhibit pathogens, such as:

  • producing antimicrobial compounds that fight bad bacteria off
  • crowding pathogens out and preventing them from getting ‘real estate’ space in the gut
  • maintaining the mucus layer that lines the intestines so pathogens can’t reach intestinal cells and set up home
  • training the immune system to respond to pathogens

When the resident gut microorganisms are reduced during antibiotic use, these protective functions may stop. That’s when pathogenic bacteria can move in and upset the balance.

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The composition of gut bacteria almost recovers after antibiotics for most people

Research has revealed an interesting strategy that some bacteria deploy to re-establish themselves after antibiotics. They use resistance genes—called the ‘resistome’ by scientists—to make sure they’re never wiped out.

After attempting to eradicate certain bacterial species with antibiotics, researchers looked at the microbiomes of 12 healthy men over a six-month period and documented the collateral damage.

Initial changes included ‘blooms’ of certain types of potentially harmful bacteria, along with the depletion of friendly Bifidobacterium and butyrate-producing species. However, the researchers state that the gut microbiota of the subjects recovered—‘almost’ to original levels—within 1.5 months.

It’s important to note, though, that nine common species, which were present in all subjects before the treatment, remained undetectable in most of the subjects after 180 days (Source: DX DOI).

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How can I help my gut bacteria to recover after antibiotics?

There’s no definitive way to help your gut bacteria recover after antibiotics. The reality is that even though the science on the microbiome is advancing fast, there’s still so much we don’t know.

There’s something we know for sure: a healthy microbiome is all about diversity, and antibiotics definitely don’t encourage that. You can take charge of your gut health and learn ways to improve the diversity of your microbiome on our Gut Health Program.

For now, let’s take a look at what research can tell us about how to increase that diversity, whether that’s after antibiotics or not.


1. Take probiotics

The clinical evidence for the benefits of taking probiotics during and after antibiotic use is confusing.

Some studies found that taking probiotics can decrease the risk of invasion by opportunistic pathogens (Source: NCBI), and antibiotic-associated diarrhoea (Source: JAMA). But it’s likely that different strains of probiotics have very different effects in different people.

Some probiotics have been proven to survive your stomach acid and reach your gut to form a protective barrier against potentially harmful bacteria. Culturelle is one example.

The best time to take probiotics if you’re taking antibiotics is at least three hours away from each other. That gives the probiotics the best chance of surviving (Source: NCBI).

Saccharomyces Boulardii is a beneficial yeast that can help stop the spread of Candida (an opportunistic yeast) after a round of antibiotics. Candida is usually present in small amounts in most people, but it can take over and cause problems when it has a chance. Saccharomyces Boulardii has also been found to preserve and restore the intestinal barrier (Source: NCBI). Most importantly, because it’s a yeast—not a bacteria—antibiotics don’t affect it at all.

Restore gut flora infographic

Interestingly, a recent small study found that probiotics may actually inhibit the return of the native gut microbiota. The original gut microbiome of a group of people who consumed probiotics for 28 days following antibiotic use took longer to return when compared to a group who didn’t take probiotics (Source: Cell).

This particular study also looked into the benefit of something called ‘autologous fecal microbiota transfusion’ (aFMT), where scientists restored the bacteria the participants had before antibiotics by freezing their old stools (yes, poo) and placing it back into their large intestine when the course was over.

Sounds crazy? According to the lead researcher, it induced a “rapid and near complete recovery within days of administration.” This proof of the benefits of aFMT after antibiotics has prompted one clinic in the UK to offer a stool freezing service for people about to undergo heavy antibiotic treatment.


2. Make the most of prebiotics

Another strategy to restore your gut flora after antibiotics is to make sure you feed it well: with foods that your gut bugs love. This means eating foods that contain high levels of prebiotics.

Prebiotics are food for bacteria in our large intestines because they aren’t digested ‘further up’ in our small intestines. Prebiotic foods are usually high in fibre and plant polyphenols. So eat lots of fruits, vegetables, legumes, nuts and whole grains.

You could also try prebiotic supplements like inulin: a plant sugar that’s been found to reduce the diversity-busting effects of the antibiotic ampicillin in bacterial cultures (Source: NCBI).


3. Eat like a hunter-gatherer

A diverse, fibre-rich diet is your best bet for increasing the diversity that antibiotics can threaten (Source: NCBI).

In a recent study, a group of Italian researchers compared the intestinal microbes of young villagers in Burkina Faso, Africa, with those of children in Florence, Italy. The villagers, who ate mostly millet and sorghum (whole grains), harboured far more microbial diversity than the Italians, who ate a typical Western diet. They found the bugs in the Italian children’s’ guts were adapted to protein, fats, and simple sugars, while the Burkina Faso microbiome favoured fibre (Source: NCBI).

One of the researchers on the Burkina Faso study wanted to know more about the role of fibre in our microbiomes, so they went on to lead another piece of research that fed one group of mice plenty of fibre, and another group a sugary Western diet. While the fibre-fed mice developed a more diverse microbiome, diversity plummeted for the ones on the Western-like diet. Interestingly, they also reported that the fibre-starved mice were also meaner and more difficult to handle! (Source: NCBI).


4. Reduce stress

Studies have found that stress triggers a fight-or-flight response that releases hormones in various parts of your body, which in turn affects your microbiome, reducing diversity (Source: NCBI). To compound the situation, that altered gut microbial population then affects the regulation of neurotransmitters, intensifying stress further (Source: NCBI).


5. Exercise

Exercise changes the make-up of your microbiome. One study found that exercise is able to enrich diversity in your microbiome, improving the balance of specific families of bacteria which could potentially contribute to reducing weight (Source: Hindawi).

What’s more, researchers concluded that exercise stimulates the growth of bacteria which can improve the integrity of your gut barrier, and protect against gastrointestinal disorders and colon cancer.


Other tactics to support healthy gut flora include:

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How long does it take to restore good bacteria after antibiotics?

It seems that most families of bacteria return to normal levels at around two months after treatment (Source: NCBI). However, this answer is based on studies that look at the effects of one, short-term course of antibiotics. We have to remember that ‘most’ families of bacteria doesn’t mean all, and the lost families could play a key role in the delicate ecosystem of our gut (Source: OUP),(Source: ASM).

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Can some people’s gut bacteria recover from antibiotics in around six months?

Some research released in 2018 found that it took around six months for our gut flora to get back to normal after antibiotics (Source: DX DOI). The media picked up on it, and so a lot of people today think that you get your old gut back precisely six months after antibiotics. This study is just one of many though, all with different results.

If you’re feeling overwhelmed by all this information, you can get some strategic help with our no obligation symptom checker.

It’s possible that your gut bacteria might never return to normal. But that doesn’t mean that you can’t take steps to increase your diversity. Everyone can benefit from taking care of their gut, but if you’ve taken antibiotics recently there’s an even bigger reason to do it.

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Key takeaways

  • Sometimes you might have to take antibiotics. If you do, there are ways you can mitigate the damage to your gut flora
  • The main problem with antibiotics is their potential to drastically reduce the diversity of your microbiome
  • It’s possible that your microbiome will return to normal within weeks or months
  • To give your gut bugs their best chance, do everything you can to increase their diversity
  • Simple steps include loading up on fibre, prebiotics and looking after your gut in general

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Alexandra Falconer MA (Dist) DipCNM mBANT is a Registered Nutritional Therapist specialising in IBS and related conditions. A graduate of Brighton’s College of Naturopathic Medicine, she is committed to fighting the root causes of chronic illness and bringing functional medicine to everyone who needs it.

 Before her natural health career, Alex was a journalist and copywriter. She continues to write for magazines and media agencies, and now combines her two great passions—writing and health—by creating content that empowers people to claim their right to a healthy body and mind.

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