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But killing the bad guys responsible for your infection means you’re also killing the good flora that’s important to your health. If you’ve recently gone on a course of antibiotics and are wondering how long it will take to get your microbiome back to normal – or at least you can – read on.
There are approximately 100 trillion bacteria in our gut, so it is impossible to know the exact makeup of someone’s microbiome before or after a course of antibiotics. But modern gut tests can give you a good idea.
How To Fix Your Gut Bacteria
Research has shown that antibiotics have the potential to harm our gut bacteria. This means that the rounds you do for your sinus infection can reduce your gut flora by a tenth of your previous level. Not one in ten, one in ten: that’s 90 percent red (source: NCBI).
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Certain courses of antibiotics appear to be the most destructive (source: NCBI), and higher doses of antibiotics given for longer periods of time have the greatest effect. This can be scary news for many people who—often in their teens—have been taking antibiotics for months to treat acne.
Oluf Pedersen, lead scientist on the 2018 project, which examined the effects of just one antibiotic on the microbiome, noted that most people experience multiple rounds of antibiotic exposure. “The concern is related to the ongoing potential loss of beneficial bacteria after multiple exposures to antibiotics over our lifetime,” he told reporters at the scientific news website ARS TECHNICA (source: DX DOI).
If you go to the doctor with an infection, of course you will receive a broad-spectrum antibiotic. That’s because unless your doctor takes a sample and sends it to a lab for culture, he doesn’t know what kind of bacteria is causing your infection. Putting on a broad-spectrum antibiotic makes the infection easier to treat, but the gut bacteria will be more difficult.
When researchers gave mice 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.
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Mice given broad-spectrum antibiotics failed to regain normal diversity, while other mice given combinations containing amoxicillin usually – but not completely – returned to pre-treatment levels (source: IAI.ASM).
Our early years are critical to creating a healthy microbiome for life. One study found a link between antibiotics taken in the first year of life and later neurocognitive problems such as ADHD, depression and anxiety (source: Wiley), and others found that the more antibiotics people took when they were young, the higher the risk. Juvenile Rheumatoid Arthritis and Inflammatory Bowel Disease Risk (Source: NCBI).
Others have linked antibiotic exposure in utero and early childhood (and altered gut microbial composition) to the development of asthma later in life (source: BMJ) and obesity in children as well as adults (source: Science Direct).
In a healthy and diverse gut microbiome, resident microbes help protect against invading pathogens that can cause infection or disease. They work together, using different methods to prevent pathogens, such as:
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When the population of intestinal microorganisms decreases with the use of antibiotics, this protective function can be interrupted. At this point, pathogenic bacteria can enter and disrupt the balance.
Research has revealed an interesting strategy that some bacteria use to regenerate after taking antibiotics. It uses a resistance gene – which scientists have called a ‘resistome’ – to ensure it is never deleted.
After trying to eradicate certain bacterial species with antibiotics, researchers looked at the microbiomes of 12 healthy people over six months and noted the accompanying damage.
Early changes include the “emergence” of certain potentially harmful bacteria, along with the decline of friendly bifidobacteria and butyrate-producing species. However, the researchers noted that the subjects’ gut microbiota recovered — “almost” to their original levels — within 1.5 months.
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However, it is important to note that nine common species that were present in all subjects before treatment remained undetectable in most subjects after 180 days (Source: DX DOI).
There is no certain way to help restore gut bacteria after taking antibiotics. The fact is that although the science of the microbiome is advancing rapidly, much is still unknown.
There’s one thing we do know: a healthy microbiome is diversity, and antibiotics certainly don’t help it. You can take care of your gut health and learn ways to increase microbiome diversity in the Gut Health Program.
Now, let’s take a look at what research can teach us about how to increase that diversity, whether after taking antibiotics or not.
How To Restore Gut Flora And Reset Your Gut After Antibiotics
Several studies have shown that taking probiotics can reduce the risk of colonization by opportunistic pathogens (Source: NCBI) and diarrhea associated with antibiotics (Source: JAMA). But there is a chance that different strains of probiotics will have different effects on different people.
Some probiotics have been shown to withstand stomach acid and penetrate the intestines to form a protective barrier against potentially harmful bacteria. Culturelle is one example.
The best time to take probiotics is if you take antibiotics at least three hours apart. This gives probiotics the best chance of survival (Source: NCBI).
Saccharomyces Boulardii is a beneficial yeast that can prevent Candida (opportunistic yeast) from spreading after taking antibiotics. Candida is usually present in small numbers in most people, but can take over and cause problems when given the chance. Saccharomyces Boulardii has also been found to protect and repair intestinal obstruction (Source: NCBI). Most importantly, because it’s yeast – not bacteria – antibiotics won’t work.
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Surprisingly, a small recent study showed that probiotics can prevent the return of the original gut microbiota. The original gut microbiome of the group of people who took probiotics for 28 days after taking antibiotics took longer than the group who didn’t take probiotics (Source: Cell).
This particular study also looked at the benefits of so-called “autonomous faecal microbiota transfusion” (aFMT), where scientists recovered bacteria provided by participants before antibiotics by freezing the old pelvis (yeah, phew) and reinserting it into the colon when the course was over.
Sound crazy According to the lead researcher, this resulted in “rapid and almost complete recovery within days of administration.” This is evidence of the benefits of aFMT after antibiotics prompted a UK clinic to offer stool freezing services to people who want to undergo strict antibiotic therapy.
Another strategy for restoring gut flora after antibiotics is to make sure you’re feeding them the right foods: foods that gut microbes love. This means eating foods rich in prebiotics.
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Prebiotics are food for bacteria in the large intestine because they are not absorbed “higher up” in the small intestine. Prebiotic foods are usually rich in plant fiber and polyphenols. So many fruits, vegetables, nuts, legumes and whole grains.
You can also try prebiotic supplements, such as inulin: a plant sugar that has been found to reduce the harmful effects of the antibiotic ampicillin variety in bacterial cultures (source: NCBI).
In a recent study, a team of Italian researchers compared the gut microbes of rural youth in Burkina Faso, Africa, to children in Florence, Italy. Villagers who typically eat millet and sorghum (whole wheat) have more microbial diversity than Italians who eat a typical Western diet. He found that the bacteria in the guts of Italian children adapted to simple proteins, fats and sugars, while the microbiome of Burkina Faso preferred fiber (source: NCBI).
One of the researchers in the Burkina Faso study wanted to know more about the role of fiber in our microbiome, so he conducted another study, feeding one group of mice high fiber and another group a sugary Western diet. Because fiber-fed mice develop a more diverse microbiome, the diversity comes down to Western-like mice. Surprisingly, they also reported that the fiber-starved rats were also worse and harder to handle! (Source: NCBI).
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Research shows that stress triggers a fight-or-flight response that releases hormones in different parts of the body, which also affects the microbiome, reducing diversity (source: NCBI). To make matters worse, the altered population of gut microbes then affects the regulation of neurotransmitters, increasing stress (source: NCBI).
Exercise changes the composition of your microbiome. One study found that exercise can improve the diversity of your microbiome, improving the balance of certain bacterial families, which can lead to weight loss (source: Hindawi).
Moreover, the researchers concluded that exercise stimulates the growth of bacteria that can improve the integrity of the intestinal barrier and protect against gastrointestinal disorders and colon cancer.
Most bacterial families seem to return to normal levels about two months after treatment (Source: NCBI). However, this answer is based on studies that looked at the effects of a single short-term antibiotic. It should be remembered that the “most” family of bacteria does not mean everything, and the missing family can play a key role in the ecosystem of the small intestine (Source: OUP), (Source: ASM).
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