Antibiotics and gut flora: how to rebuild it after antibiotics

The bladder infection is gone, the bronchitis is over, the pack of antibiotics is finished. Yet your stomach is still rumbling, your stool is looser than usual, and you wonder: what has actually happened to my gut flora – and how can I rebuild it after antibiotics?

Antibiotics are among the most important medicines we have. But they do not only act on the bacteria that make us ill. Here you will learn what happens in the gut, how long recovery can take, which foods play a role and how the state of your microbiome can be measured.

Antibiotics and gut flora: what happens in the gut

Trillions of bacteria from hundreds of species live in your gut. Together they form the gut microbiome, often called gut flora. These bacteria break down fibre, produce short-chain fatty acids that nourish the gut lining and keep unwanted germs in check.

An antibiotic does not distinguish between “good” and “bad” bacteria. Depending on the substance, duration and dose, diversity in the gut falls during treatment; some groups become rarer, others increase. Reviews therefore describe antibiotics as one of the strongest external influences on the composition of the microbiome (PubMed 33330122).

One possible consequence is antibiotic-associated diarrhoea. In rare cases the germ Clostridioides difficile uses the gap and causes serious inflammation of the bowel (PubMed 33330122).

Gut flora after antibiotics: how long does recovery take?

The good news: the microbiome is resilient. In a study of healthy men who received a combination of three antibiotics for four days, composition had largely returned towards baseline after about one and a half months. However, some previously common species were still undetectable after six months (PubMed 30349083).

An earlier study with repeated ciprofloxacin courses showed that recovery differs from person to person and is not always complete (PubMed 20847294). So there is no single number that applies to everyone. How long it takes depends on the substance, the length of treatment, previous courses of antibiotics and your diet.

Gut flora disturbed by antibiotics: possible signs

Typical complaints during or shortly after antibiotic treatment are loose stools or diarrhoea, bloating and an unsettled stomach (PubMed 33330122). Bloating can also have other causes, see Bloating despite a healthy diet. They usually settle within a few days after the course ends.

Not every change in digestion is caused by the gut flora, and the microbiome can change without you noticing anything. Symptoms are a hint, not a diagnosis.

Please see a doctor if you have watery diarrhoea lasting several days, blood or mucus in your stool, fever or severe abdominal pain – especially during or after taking antibiotics.

Rebuilding gut flora after antibiotics: which foods play a role

What you eat is food for your gut bacteria. Fibre from vegetables, pulses, whole grains, nuts and fruit reaches the large intestine undigested, where bacteria turn it into short-chain fatty acids. A low-fibre diet, by contrast, can reduce diversity in the gut (PubMed 29902436).

Fermented foods such as plain yoghurt, kefir, sauerkraut or kimchi are also being studied. In a 17-week study, microbial diversity increased in participants who ate several servings of fermented foods daily. In the group on a particularly high-fibre diet, diversity remained stable during that period, while the metabolic capabilities of the bacteria changed (PubMed 34256014). The two are not opposites: fibre and fermented foods complement each other in a varied diet.

None of these foods is a cure-all. They are part of an everyday life that gives the microbiome good conditions.

Antibiotics and rebuilding gut flora at the same time: what does research say?

Many people ask whether to take probiotics while still on antibiotics. The evidence is mixed. A Cochrane review found indications in children that certain probiotics can lower the risk of antibiotic-associated diarrhoea (PubMed 31039287). A small study in adults, on the other hand, observed that the mucosal gut flora returned to baseline more slowly after antibiotics when a probiotic was taken than without (PubMed 30193113).

This does not lead to a general recommendation for or against any product. Whether a probiotic makes sense in your situation, and which one, is best discussed with your doctor or pharmacist.

Measure instead of guessing: how gut flora can be tested

You cannot tell from the outside whether your microbiome has changed after antibiotics. A stool analysis can make it visible. The gut profile microbiome & gut barrier measures selected key bacteria such as bifidobacteria, lactobacilli and Akkermansia, plus markers of the gut barrier and digestion. If you want to know how diverse your gut flora is overall, the molecular genetic Microbiome Maxi Plus analysis with gut barrier and absorption covers this: among other things it determines diversity, butyrate producers and a dysbiosis index.

Such a test is more meaningful a few weeks after finishing antibiotics than in the middle of treatment, because the microbiome is still changing considerably during that time (PubMed 30349083). A result is a snapshot and does not replace a medical examination.

What to discuss with professionals

Take an antibiotic for as long and in the way it was prescribed. Do not stop a prescribed medication without talking to your doctor first. These questions can help in the conversation afterwards:

• How many courses of antibiotics have I had in recent years?
• Are my digestive complaints lasting longer than expected?
• Are there warning signs that call for further examination?
• Is a stool analysis suitable for my situation, and when is the right time?

The ORY expert team can also help you interpret a microbiome result.

In short

• Antibiotics also affect beneficial gut bacteria and can temporarily reduce the diversity of the gut flora (PubMed 33330122).
• In many people the microbiome returns towards baseline within weeks – not always completely (PubMed 30349083).
• Fibre-rich and fermented foods are among the dietary factors studied for a diverse microbiome (PubMed 29902436) (PubMed 34256014).
• The evidence on probiotics is mixed; discuss the choice with professionals.
• A stool analysis a few weeks after treatment shows how your gut flora is doing.

Frequently asked questions

How can I rebuild my gut flora after antibiotics?

A varied, fibre-rich diet with vegetables, pulses, whole grains and fruit feeds your gut bacteria (PubMed 29902436). Fermented foods can be an addition (PubMed 34256014). Whether a probiotic makes sense as well is something to discuss with your doctor or pharmacist.

Which foods help rebuild gut flora after antibiotics?

The best-studied are fibre-rich foods such as oats, lentils, beans, vegetables and nuts, and fermented foods such as plain yoghurt, kefir or sauerkraut (PubMed 29902436) (PubMed 34256014). No single food “repairs” the gut flora; the overall diet is what counts.

How long does gut flora take to recover after antibiotics?

In studies, the microbiome of many participants had largely recovered after about six weeks, but some species were still missing after six months (PubMed 30349083). The time it takes varies between individuals (PubMed 20847294).

Do antibiotics destroy your gut flora?

“Destroy” is usually not the right word. Antibiotics change the composition and temporarily reduce diversity; the microbiome can largely recover afterwards (PubMed 30349083). Repeated courses can, however, make recovery harder (PubMed 20847294).

What are the symptoms of gut flora disturbed by antibiotics?

Loose stools, diarrhoea and bloating are common (PubMed 33330122). These complaints are non-specific. Persistent watery diarrhoea, blood in the stool, fever or severe abdominal pain should be checked by a doctor.

Can I take antibiotics and rebuild my gut flora at the same time?

A fibre-rich diet is possible during treatment. Whether a probiotic at the same time is useful has not been clearly settled (PubMed 31039287) (PubMed 30193113). Clarify this with your doctor or pharmacist – also because some products need to be taken at a different time from the antibiotic.

When can I start rebuilding and testing my gut flora after antibiotics?

You can start with a fibre-rich diet straight away, even during treatment. Because the microbiome changes considerably in the first weeks after treatment, a test a few weeks after finishing is more meaningful than one taken during the course (PubMed 30349083).

Sources

1. Ramirez J et al. Antibiotics as Major Disruptors of Gut Microbiota. Front Cell Infect Microbiol. 2020. PubMed 33330122
2. Palleja A et al. Recovery of gut microbiota of healthy adults following antibiotic exposure. Nat Microbiol. 2018. PubMed 30349083
3. Dethlefsen L, Relman DA. Incomplete recovery and individualized responses of the human distal gut microbiota to repeated antibiotic perturbation. PNAS. 2011. PubMed 20847294
4. Makki K et al. The Impact of Dietary Fiber on Gut Microbiota in Host Health and Disease. Cell Host Microbe. 2018. PubMed 29902436
5. Wastyk HC et al. Gut-microbiota-targeted diets modulate human immune status. Cell. 2021. PubMed 34256014
6. Guo Q et al. Probiotics for the prevention of pediatric antibiotic-associated diarrhea. Cochrane Database Syst Rev. 2019. PubMed 31039287
7. Suez J et al. Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT. Cell. 2018. PubMed 30193113