Gut bacteria
How to restore gut bacteria and gut health after antibiotics
After a course of antibiotics, most gut bacteria return on their own within one to two months, though a few species can take six months or longer. Recovery is helped most by a varied, fibre-rich diet with fermented foods, and by avoiding further antibiotics that are not needed. A probiotic can lower the chance of diarrhoea during the course, but it has not been shown to speed the return of your own bacteria.
In short
- Antibiotics save lives. Take them when they are needed and as prescribed, and help the gut to recover afterwards.
- In a study of healthy adults, gut bacteria were close to their earlier state about six weeks after a short, strong course. Nine common species were still missing at six months.
- In a review of 82 trials, taking a probiotic with the antibiotic prevented one case of diarrhoea for every 13 people treated.
- Watery diarrhoea with fever, pain or blood during or after antibiotics needs a doctor the same day.
What do antibiotics do to gut bacteria?
Antibiotics cannot tell harmful bacteria from helpful ones. Within days of starting a course:
- The number of different species in the gut falls
- Bacteria that ferment fibre are reduced
- Resistant bacteria and yeasts have more room to grow
Most people notice nothing. Some have loose stools, bloating or cramps during the course. This is called antibiotic-associated diarrhoea, and it usually settles within days of finishing.
The effect is larger with broad-spectrum antibiotics, longer courses and repeated courses.
How long does recovery take?
- 6 weeks after a short, strong course, gut bacteria were close to their earlier state in a study of healthy adults
- 9 common species were still missing at six months
- 1 in 13 people treated was spared diarrhoea by taking a probiotic with the antibiotic, in a review of 82 trials
In a study of 12 healthy young men given three strong antibiotics for four days, the gut community had largely returned to its earlier state after about six weeks. Nine species that had been common before treatment could still not be detected after six months.
Recovery is slower after repeated courses and on a diet that is low in fibre.
Antibiotics are not the only medicines that change gut bacteria.
What helps gut bacteria recover?
During the course, eat normally
Include curd or buttermilk if you tolerate them. Some antibiotics should not be taken at the same time as milk or curd, so check the label or ask your pharmacist.
Afterwards, feed the bacteria that remain
They recover on fibre from many different plants: dals, vegetables, fruit, whole grains, millets, nuts and seeds. See how to improve your gut microbiome.
Add fermented foods every day
Curd, buttermilk, kanji and overnight-fermented rice. In a ten-week trial, a diet high in fermented foods increased bacterial diversity.
Go slowly if you bloat
Increase fibre in steps over two to four weeks.
Avoid what slows recovery
Alcohol, a diet of packaged food, and antibiotics for colds and other viral illnesses.
Sleep and move
Both support a regular bowel and a steady gut rhythm.
Should I take a probiotic during or after antibiotics?
| Question | Short answer |
|---|---|
| During the course? | Reasonable, especially if antibiotics have given you diarrhoea before. Specific products reduce this risk. |
| After the course, to rebuild the gut? | Not shown to help. In one small study, a probiotic taken after antibiotics delayed the return of people’s own bacteria. |
| How do I take it? | Two to three hours apart from each antibiotic dose, and usually for about a week after the course ends. |
| Who should ask first? | People who are seriously ill, have weak immunity or have a central line, and parents of premature babies. |
A probiotic adds a few strains for a short time. It does not replace the hundreds of species that make up your own community. See what probiotics are and choosing a probiotic in India.
What should I eat after antibiotics?
- Curd rice, buttermilk and other fermented foods
- Dal, sambar and rasam
- Two or more vegetables at each main meal
- Fruit, including banana
- Oats, ragi and other whole grains and millets
- A handful of nuts or seeds
Keep alcohol and sweets low for a few weeks. See an Indian diet for the gut microbiome.
When should I see a doctor?
See a doctor the same day if, during or in the weeks after antibiotics, you have
- Watery diarrhoea three or more times a day for more than two days
- Fever, abdominal pain or blood in the stool
- Very little urine, dizziness or marked weakness
These can be signs of C. difficile infection, which needs a stool test and specific treatment.
Bloating or a changed bowel habit that continues for more than four weeks after a course is also worth a consultation. See gut microbiome restoration.
Questions patients ask me
How long does it take for gut bacteria to recover after antibiotics?
Most return within one to two months in healthy adults. A few species can take six months or longer, and repeated courses slow recovery.
Should I take probiotics during or after antibiotics?
During the course is where the evidence lies: it lowers the chance of antibiotic-associated diarrhoea. Taking one afterwards to rebuild the gut has not been shown to help.
Is curd enough, or do I need a capsule?
For most healthy adults on a short course, curd or buttermilk and a varied diet are enough. A probiotic product is worth considering if antibiotics have upset your stomach before, or if the course is long.
Can I restore gut bacteria naturally, without supplements?
Yes. Your own bacteria regrow when they are fed. Plant variety, fermented foods and time do most of the work.
Do children need probiotics after antibiotics?
The same principle applies: food first. Ask your child’s doctor before giving a probiotic, particularly to a baby or to a child with a serious illness.
Sources
This page is written for patients and is based on the guidelines and studies below. It is for education and does not replace a consultation.
- Study of gut bacteria recovery in healthy adults after antibiotics. Palleja A et al. Nat Microbiol. 2018. PubMed 30349083
- Study of probiotics and gut microbiome recovery after antibiotics. Suez J et al. Cell. 2018. PubMed 30193113
- Systematic review of probiotics for antibiotic-associated diarrhoea. Hempel S et al. JAMA. 2012. PubMed 22570464
- American Gastroenterological Association guideline on probiotics in digestive disorders. Su GL et al. Gastroenterology. 2020. PubMed 32531291
- American College of Gastroenterology guideline on Clostridioides difficile infection. Kelly CR et al. Am J Gastroenterol. 2021. PubMed 34003176
- American Gut citizen-science study of diet and the microbiome. McDonald D et al. mSystems. 2018. PubMed 29795809
- Trial of high-fibre and fermented-food diets and immune status. Wastyk HC et al. Cell. 2021. PubMed 34256014
- International consensus statement on the term probiotic. Hill C et al. Nat Rev Gastroenterol Hepatol. 2014. PubMed 24912386