How to Restore Gut Health After Taking Antibiotics

Introduction

You just finished your course of antibiotics, and now you can’t stop wondering what they did to your gut.

Maybe you’ve read that antibiotics “wipe out” your microbiome, or even ruin it forever. Every bit of bloating or digestive troubles feels like proof that something is broken. When you go looking for answers, it seems like everyone is just trying to promote a “gut reset”, a new cleanse, or the right probiotic to fix the damage.

I get it. When I started writing about this, I came into it with a lot of the same ideas. Hearing about the damage antibiotics can do to the gut made me stop and wonder how much damage there is, and whether it’s permanent.

You’re not wrong to think any of this. Antibiotics work by either killing bacteria or stopping them from multiplying long enough for your immune system to eradicate them. The problem is that an antibiotic can’t tell the difference between the bacteria making you sick and the trillions of beneficial bacteria that live in your gut, commonly known as your gut microbiome. The antibiotic meant to fight your infection reaches your gut and your microbiome could end up disturbed in the process.

Thankfully, what I found in the research is reassuring. Disturbance isn’t permanent. Left alone, your gut largely rebuilds itself. In one study of healthy adults, the microbiome had returned to baseline in about a month, without anyone buying a thing or trying a cleanse.

I also found out that your gut doesn’t necessarily come back as a copy of what it was. It’s unique to you and can rebuild into a different composition of bacteria while still doing the same job it used to. Most of what those “reset” products promise is something your body already does on its own.

So what happens to your gut microbiome on a course of antibiotics? And what should you do, if anything, to help restore it to health?

What Antibiotics Actually Do to Your Gut

Antibiotics disturb the microbiome in several measurable ways.

Because antibiotics can’t tell which bacteria they’re killing, they can wipe out the beneficial bacteria that are native to your colon. This causes changes in many characteristics of the gut microbiome, specifically microbiome richness, diversity, and composition.

Richness is simply the number of different bacterial species that live in your gut. Diversity accounts for how many species are present and factors in what ratios they exist. A microbiome where no single species dominates is more diverse. Composition is the actual makeup of specific species.

Antibiotics can affect all three. When an antibiotic kills off a certain bacteria species (or several), richness and diversity diminish and composition becomes biased towards hardier bacteria that survive the antibiotic and expand into the open space.

Symptoms Associated With Damage to the Gut from Antibiotics

Because the gut loses many of its beneficial bacteria, the functions those bacteria perform are diminished, at least in the short period following treatment.

Gut bacteria ferment indigestible fibers into molecules called Short Chain Fatty Acids (SCFAs). These SCFAs, specifically one called butyrate, provide energy for the cells lining the colon, help maintain the security of the gut barrier, and can regulate inflammation.

If you lose the bacteria which produce SCFAs at a normal level during your course of antibiotics, the colon loses some of its fuel supply and fermentation slows down. This can leave undigested carbs drawing water into the colon (one of the ways that antibiotics cause diarrhea).

Gut bacteria also help maintain the gut barrier itself. They feed the colon cells with butyrate, as mentioned before, but also stimulate the production of mucus in the gut which serves as a protective layer. This helps prevent unwanted substances from passing through the gut wall and into the bloodstream. Without bacteria regulating the barrier, more substances can get through which can trigger inflammatory responses.

Gut bacteria also help train the immune system to distinguish between harmful and harmless substances. Without the bacteria, the immune system might not respond to threats that it needs to, or it might generate unnecessary inflammation.

How Long Recovery Takes

So, if you’ve taken antibiotics recently, how long should you expect the recovery process to be?

Well, depending on which aspect of recovery we focus on the answer may vary. We talked earlier about microbiome richness, diversity, and composition. In one study of healthy volunteers on a β-lactam, most of these qualities of the microbiome had returned close to baseline around day 30. This movement towards baseline can start as early as one week after treatment.

A full return to the exact prior state, though, is not commonly observed. The microbiome will reshape into a slightly different composition. In one study, several common species were still undetectable after six months post-treatment even though the community as a whole had largely recovered.

But function recovery is entirely different from microbiome composition and diversity recovery. Despite compositional changes, the microbiome has been observed to return to near-normal specific and measurable functions in as little as ten days.

The microbiome’s function isn’t necessarily tied to its exact composition. Many different species can do the same jobs. Even if microbiome composition isn’t what it used to be, it can still be healthy and perform proper functions just with new and different bacteria.

Can Antibiotics Permanently Damage Your Gut?

The short answer is no, probably not. For most healthy adults, the microbiome recovers well after a routine course of antibiotics. Without any specific intervention, gut microbiomes have been shown to return to near baseline in healthy adults in about 45 days.

This means that the gut microbiome has the capacity to find a way to execute the proper functions on its own. But what exactly drives the recovery towards baseline?

What Drives Recovery

There are several factors that drive recovery of the microbiome after taking antibiotics.

The following are things that help along the natural adaptation of the microbiome to disruption, along with a couple of habits that can aid with recovery.

Keystone Species

A 2020 study identified a set of gut bacteria that it referred to as “keystone species”. Once these bacteria returned to the microbiome following antibiotics treatment, they were able to drive the recovery of everything else.

These keystone species, such as Bacteroides (e.g. B. uniformis), are loaded with enzymes that can break down a wide range of carbs. By harvesting the energy from the carbs, they release byproducts that become food for depleted species letting them repopulate. B. thetaiotaomicron and B. adolescentis were shown to speed up the return to microbiome diversity.

Functional Redundancy

Functional redundancy also drives recovery. It’s the idea that multiple different species can carry out the same job in the gut.

This means when one species gets wiped out by an antibiotic, the function it performed isn’t entirely lost. Other bacteria step in and take over those same duties, which can help restore the gut to the prior level of functioning.

Prebiotics

Prebiotics are a category of foods (mostly specific plant fibers) that feed beneficial bacteria.

Some prebiotic foods include:

• Onions
• Garlic
• Leeks
• Asparagus
• Bananas
• Legumes

Prebiotics can help increase healthy bacteria by feeding them. They feed beneficial species, which can help them proliferate after antibiotics.

There’s a caveat, though: prebiotic diets aren’t one-size-fits-all. Because people’s microbiomes can differ so much, the same food can affect two people to different degrees.

Research is moving toward highly individualized prebiotic recommendations based on a person’s unique microbiome, which would make those foods more effective at stimulating microbiome recovery.

The prebiotics with the best documented health benefits are two types of non-digestible oligosaccharides. The first are fructans (found in chicory root, onions, garlic). The most well known fructan is inulin. The other type is galactans, which are found in legumes.

One review found that a daily 6g dose of an inulin-type fructan (the kind found in chicory root) helped protect against antibiotic-induced changes to gut composition.

Fiber

Fiber also helps restore gut function. Fiber is the indigestible part of plant foods. It reaches your colon where it’s fermented by bacteria, producing SCFAs which have various benefits as mentioned above.

It’s theorized that increasing fiber intake prompts the growth of more beneficial bacteria that are capable of fermenting it, although this specific mechanism isn’t yet clearly evidenced.

Some examples of high fiber foods are:

• Black beans
• Lentils
• Oats
• Chia seeds
• Almonds
• Raspberries
• Blackberries
• Avocados

Fermented Foods

Fermented foods also show promise for restoring gut function. Fermented foods are foods that are transformed by microbial fermentation and carry live cultures.

Common fermented foods include:

• Yogurt
• Kefir
• Sauerkraut
• Kimchi
• Kombucha

A diet high in fermented foods may help increase gut microbiome diversity as well as decrease inflammatory markers.

In a Stanford study, subjects worked up to an average of 6.3 servings per day. Higher gut diversity and lower inflammation plausibly translate to a gut that’s better defended and less irritated. This trial was run in healthy adults, not people recovering from antibiotics.

Rather than a proven accelerator of recovery following damage, fermented foods may help build a more resilient gut environment.

Probiotics After Antibiotics: Should You, Which, and When

It’s commonly thought that since taking antibiotics can damage the microbiome and wipe out beneficial bacteria, then probiotics should be able to restore those bacteria right?

But does the evidence support taking probiotics with antibiotics? And if so, should everyone do it? And which types of probiotics, and at what time?

These are all important questions with important answers which could impact your recovery.

Should you take probiotics after antibiotics

What does the evidence say about taking probiotics to help restore your gut’s microbiome following a course of antibiotics?

As with most things, it depends on what we measure.

The strongest evidence behind probiotics being helpful after antibiotics is with symptom control. Many people may experience a phenomenon known as Antibiotic-associated Diarrhea (AAD) after treatment with antibiotics. There are multiple studies that tested the incidence of AAD in patients who took antibiotics and compared incidence rates between those who took probiotics and those who did not.

More often than not, the group taking the probiotic experienced less incidence of AAD as a whole. But is the lower incidence of symptoms enough to confidently say that probiotics are behind the restoration of the gut? We can’t exactly be sure.

Preventing a symptom isn’t exactly a guarantee that the gut microbiome has healed. But, a gut that isn’t succumbing to AAD is arguably in better functioning order, which may connect to the broader benefits of healthy bacteria covered above.

Important to note, the probiotic payoff is never a guarantee. Not all probiotics are equal. Some probiotic strains have been shown to benefit the gut by preventing symptoms associated with antibiotics. Others seem to have no effect at all.

As we discussed earlier, microbiomes vary greatly between different people. In the same way that the same antibiotic might affect two separate microbiomes differently, the same probiotic can have different effects across people.

This leads us to an exciting movement within the research of probiotics.

If we could one day map a person’s microbiome the way we read a fingerprint, we might match each person to the specific probiotic their gut would actually benefit from. This would reflect a personalized approach instead of a one-size-fits-all guess.

Note: if you are seriously immunocompromised or critically ill it can be dangerous to take a probiotic. If you are unsure of your condition or if a probiotic is right for you, contact a trusted clinician.

Which strains work

So for now, which strains have been known to actually help prevent symptoms after taking antibiotics?

Probiotics span a handful of commonly used genera. The main three are Lactobacillus, Bifidobacterium, and the yeast Saccharomyces. Each of these contain many species, and each species contains many different strains.

Two probiotics of the same species but different strains can have different effects. This is why individualized, strain specific recommendations matter so much. The strains with the best evidence behind them for preventing AAD are Saccharomyces boulardii (this is actually a yeast, explaining its own resistance to antibiotics) and Lactobacillus rhamnosus GG.

Can probiotics delay recovery?

The assumption is that antibiotics kill your bacteria, so swallowing replacement bacteria will help rebuild the microbiome.

That assumption got put up to the test in a 2018 study. Researchers gave subjects antibiotics and then either let their microbiome recover on its own, gave an 11-strain probiotic, or implanted the subject’s own pre-antibiotic stool.

The group that received the 11-strain probiotic actually demonstrated the slowest recovery back to normal microbiome quality out of any of the groups.

The group that performed best was actually the group that received their own pre-antibiotic microbiome via their stool.

This is another testament to the fact that every person’s microbiome is different, and different people may benefit from different compositions as well as the fact that probiotics are not a one-size-fits-all treatment.

Other studies conducted at a similar time found that when testing different strains and higher doses, probiotics actually helped the microbiome to recover.

One high quality study isn’t enough to declare that all probiotics are bad, forever. It should prompt you to think, however, if the probiotic you take is something you genuinely need and something that synergizes with your own personal microbiome.

Antibiotic-associated Diarrhea (AAD) & How to Prevent it

A common symptom that is associated with taking antibiotics that many people may experience is diarrhea, commonly referred to as Antibiotic-associated Diarrhea (AAD).

What is AAD?

After antibiotics diminish gut bacteria, two things can lead to diarrhea. The normal bacteria that colonize the gut act as crowd protection. Their presence blocks out the over-colonization of harmful bacteria like C. difficile, which is notoriously known for causing diarrhea when present in great amounts. When your beneficial bacteria are absent, C. difficile can grow to occupy the space that was left behind, leading to diarrhea.

Because bacteria are diminished, fermentation slows down. This can leave undigested carbs drawing water into the colon also causing diarrhea.

How to Prevent it

If you’ve taken antibiotics and suffer from AAD, there are a handful of things that can aid prevention:

• Probiotics have some good evidence behind them for prevention of AAD when tested in clinical trials. Specifically, S. boulardii or L. rhamnosus GG when started within 2 days of the first antibiotic dose were shown to reduce risk of AAD incidence.

• Plenty of fiber in the diet along with fermented foods can also be sensible choices to help with recovery. These foods feed healthy bacteria and may contribute to their growth.

The more healthy bacteria that grow, the higher likelihood that your gut returns to proper functioning.

What to Do After Taking Antibiotics

1. Give it Time

The easiest and most important factor determining your recovery is to simply give your gut time to return to function.

Measurable gut microbiome functions can return to baseline level in about ten days without having to do anything at all. You should understand that the disturbance is real and should be respected, but that your gut is able to find its way back.

During the first days and weeks, the most useful thing you can do is protect your gut from further disruption while it recovers.

In general, these habits can help preserve a healthy gut environment:

• Reduce or eliminate known disruptors
  
  • Ultra-processed foods or certain additives like emulsifiers can disturb the gut microbiome in humans.
  • Excess alcohol and added sugars are worth cutting too.

• Exercise
  
  • Regular movement has some evidence that suggests it's beneficial for the gut. It's been linked to greater gut microbiome diversity. Exercise is also known to keep the bowels moving.

• Sleep
  • It's possible that maintaining a high quality of sleep can help protect gut function. The mechanism might not be clearly understood. However, getting a good night's sleep is strong health advice in general and certainly won't hurt.

2. Eat More Fiber

Fiber is great because bacteria ferment it to produce short-chain fatty acids, a molecule that plays a crucial role in maintaining gut health.

How much

General advice is to eat around 25g per day for women and around 38g for men but most people eat only half of that.

One diet study we looked at today worked subjects up to consuming near 45g per day. There’s no specific standard target for fiber intake for recovery, so we recommend that during this time period you make an effort to hit the standard 25g or 38g per day goal.

Instead of adding the deficit of fiber you need to reach your fiber goal right away, it’s important to integrate more fiber in your diet slowly. You need to give your bacteria time to adjust. Fermenting too much fiber at once can actually lead to uncomfortable gas and bloating.

How to gradually add fiber:

• If you started at week 0 with a fiber intake of 10g/day, then your first month would look like...
• Week 1: 13-15g/day
• Week 2: 16-18g/day
• Week 3: 19-21g/day
• Week 4: 22-24g/day
• and so on...

Divide your fiber across three meals.

• For week one, that's about 4-5g per meal.
• For week two, 5-6g per meal.
• For week three, 6-7g per meal.
• For week four, 7-8g per meal.

Pair the extra fiber with plenty of water. Fiber works partly by holding water to maintain good stool quality.

How often

You should aim to hit the fiber goal for the week every day. Fiber cannot be stored by your body since it isn’t directly digested, so its continual presence to produce SCFAs via its fermentation is necessary.

Ways to include fiber in your diet

Some foods high in fiber include:

• chia seeds (~8g/2 tbsp)
• black beans (~15g/cup cooked)
• lentils (~15g/cup cooked)
• raspberries (~8g/cup)
• blackberries (~7.6g/cup)
• avocados (~4.6g/half).

Hack: Since chia seeds are the most dense source of fiber on this list, eating them is an easy way to meet your fiber goals. Only two tablespoons will get you to about one-third of your daily fiber needs. It’s easy to sprinkle them throughout your day, especially in a smoothie. Find a list of ideas on including chia seeds in your diet here.

3. Add Prebiotic-rich Foods

While we’re talking about fiber, prebiotic-rich foods deserve their own mention.

These foods are specific types of fiber which feed your healthy bacteria. The types with the best-documented effects are fructans (like inulin) and galactans.

If you don’t have any idea what that means, don’t worry. I’ll explain.

Fructans and galactans are just long chains of carbs that are normally indigestible by our gut without the help of bacteria. Inulin is just one specific type of fructan chain.

How Much

One review found about 6g per day of an inulin type fructan could help protect against antibiotic disturbance of the microbiome. These 6g would count towards your daily fiber goal.

How Often

As with fiber, your goal should be to include these prebiotic-rich foods daily, as they contribute to your total fiber amount.

Ways to include prebiotic foods in your diet

Some inulin-type fructan containing foods are chicory root, garlic, leeks, onions, and asparagus. Chicory root is by far the richest source of inulin, serving as the basis of many inulin supplements.

4. Include Fermented Foods with Live Cultures

In the Stanford study we looked at today, a diet rich with fermented foods was shown to raise microbiome diversity and lower inflammatory markers, which may help ease any discomfort in your gut.

How Much

Participants in the study worked up to an average of about 6 servings per day, but that’s a little vague. What exactly is a serving?

• 6 oz of yogurt or kefir
• 1/4 cup of sauerkraut or kimchi
• 6 oz of kombucha

That sounds like a lot. Are 6 servings really necessary to see beneficial effects?

There’s no established minimum, so start small. As little as 1-2 tablespoons (or 10-15g) of fermented vegetables per day can get the job done. As with fiber, work your way up.

Start by adding 5g per week, being sure to be aware of how your gut tolerates it. If you can handle more and you enjoy it, add more.

How Often

Similar to fiber, eating fermented foods is less about “loading up” one time to “reset” your gut, and more of a daily habit. Your gut responds to and adapts to regular frequencies over time. Aim to meet your fermented food goal for the week every day.

Ways to include fermented foods in your diet

The foods mentioned above don’t have to be the core of your meals. They can simply be a small addition. Here are some ideas:

• Have a bowl of yogurt with breakfast
• Drink a small glass of kefir with your lunch
• Add a few spoonfuls of fermented vegetables like sauerkraut or kimchi as a side to your dinner.

It really doesn’t have to be complicated! Find more ideas on fermented food recipes here.

5. Consider a Probiotic if Necessary

Don’t just throw in a probiotic to your daily routine just cause I told you so. It’s better to understand first if a probiotic is really necessary for your situation.

When related to antibiotics, a probiotic’s best-evidenced job here is preventing antibiotic-associated diarrhea. If you are experiencing symptoms of that nature, you can consider taking a probiotic to see if it will ease your symptoms.

Which Kind

Two types of probiotic came up in our research today as being effective for reducing incidence of AAD: Saccharomyces boulardii and Lactobacillus rhamnosus GG.

Make sure for whatever you buy, you’re checking labels and strains to make sure that a) what you buy contains what it says it does, and b) what you buy doesn’t contain anything else unnecessary.

How Much

Studies used at least 5 billion CFU per day, or up to around 10 billion. For S. boulardii, the standard clinical dose is 500mg per day in two 250mg doses.

How Often

A probiotic should start soon after antibiotic treatment if you are experiencing symptoms, within 2 days of starting the treatment. Since we’re advocating probiotics as a method of symptom control and prevention, it may be unnecessary to continue their use once symptoms resolve.

6. Monitor Your Symptoms

Don’t take my word for everything. You know your body better than anyone else.

Continue to monitor your symptoms throughout your antibiotic course and in the following days. Write down or journal your experiences. Try some of the ideas listed above and continue to write and think about how you feel.

Ask yourself: Are these new foods making me better? Am I experiencing discomfort more or less often? Do I notice a difference in how I feel since adopting change?

It’s important to stay attentive whenever you adopt a new habit. Is something not working for you? Cut it back, or cut it out. General recommendations can only take you so far.

Remember, your microbiome is unique and it might not respond to something the same way someone else does. Don’t be afraid to experiment and vary.

Your microbiome is powerful to adapt, so don’t be discouraged if you’re not getting the results you hoped for right away. Consistency above all is what feeds your microbiome and positions it for a good recovery.

How to Tell Your Gut is Recovering

Taking antibiotics and worrying about your gut is normal. The reassuring truth is that the damage isn’t permanent.

Composition and diversity may take a month or two to settle, but that’s not the same as microbiome function which has been shown to recover a lot sooner.

The most tangible sign of returning microbiome is simple: disruption symptoms fade and normal bathroom habits return. Beyond that, most of the recovery that happens is invisible and internal.

You can’t see or feel microbiome diversity. But knowing your gut is built for recovery and adaptation can help calm your nerves while recovery happens. It can restore itself and adapt without having to rely on a magical cure.

You don’t have to be scared into buying something you don’t need or worry about ever getting back to health.

Common Myths About Antibiotics and the Gut

“Antibiotics ruin your gut forever”

This is overstated. One study has shown that specific measurable gut microbiome functions return after standard antibiotic courses in around ten days.

While microbiome composition and diversity may remain altered for a couple of months, the microbiome can adapt to its new situation and return to performing the functions it needs to do. This return towards function even happens without any specific intervention.

“The gut isn’t affected by antibiotics”

Your gut bacteria are bacteria, just like the ones antibiotics are designed to kill.

It is true, however, that the microbiome is not entirely made up of only bacteria. Viruses, fungi, and archaea belong there too. Gut bacteria make up a large majority of the microbiome and perform many of the important functions.

Antibiotics can surely disrupt the important functions of your healthy gut, although only temporarily.

A probiotic “resets” your microbiome

Probiotics can introduce gut bacteria into the microbiome after a course of antibiotics.

However, the extent to which these probiotics meaningfully shift the microbiome isn’t clearly understood. In some cases, probiotics have even delayed normal rates of recovery.

The reason behind this is because “probiotic” is such a broad term that encompasses many genera, species, and strains of bacteria which can all have different effects and degrees of effectiveness. The most reliable job a probiotic can do is to help manage symptoms associated with antibiotics in the short term, but they are not absolutely necessary to “reset” a microbiome. Your microbiome is capable of adapting and replenishing on its own.

Conclusion

If you’ve taken antibiotics and are wondering what to do to restore your gut health, the single most useful thing to know is that you should expect to recover well, and mostly on your own. When left alone, the research shows that the gut microbiome returns close to its previous state in about a month. And much of its normal functioning returns well before then.

Understand that “restoration” looks a little bit different for everyone. The gut is a living environment that constantly reshapes and adapts to its surroundings. The goal is less about rebuilding your microbiome into exactly what it used to be and more about giving it what it needs to be resilient.

If you’re looking for something extra to help your gut along, the best evidence points to eating for long-term recovery, not a quick reset. The gut doesn’t need to be “reset” or “cleansed” after antibiotics. The antibiotics already cleared most of what was in there. What the surviving bacteria need isn’t a detox, it’s food. Specifically, high fiber and prebiotic foods are what they ferment to help rebuild.

If you’re thinking about a probiotic, take it for the right reason and understand what’s actually happening when you take one. There’s no guarantee the probiotic you buy is compatible with your personal microbiome. Everyone’s internal environment is different, so the same probiotic can have different effects in two people. In some cases, it may even disturb or delay recovery rather than help it.

What the evidence does point to is towards symptom control. Probiotics taken alongside antibiotics have been shown to lower the risk of antibiotic-associated diarrhea. If that’s what you’re after, the two best-supported options are Saccharomyces boulardii and Lactobacillus rhamnosus GG, ideally started within the first couple of days of your course.

Whatever you buy, verify. Check that the product actually contains what it claims at a dose that matches the research, and that the specific strains are the ones shown to help your situation. If you’re not getting the results you want, don’t be afraid to step back and question whether the product is really capable of doing what it promised. When in doubt, ask a clinician. You know your body better than anyone, and you know when something feels seriously wrong. But for the vast majority of people, recovering from a course of antibiotics isn’t something you need to fear or fight. It’s something your gut is already built to do.