This text is for education only and does not replace medical advice. Only your doctor decides when antibiotic treatment starts, how it goes and when it ends.
Antibiotics are one of the most important achievements of medicine. They made it possible to treat infections that were often severe in the past. But they act widely: they target microorganisms, and microorganisms are not only at the place of infection. Below, we describe what research shows about changes in the microbiota after antibiotic treatment.
Why an antibiotic does not act only on bacteria that cause disease
Antibiotics act on specific processes in a bacterial cell: building the cell wall, making proteins or copying genetic material. Many species share these processes, not only the species that caused the infection.
This is why there are narrow-spectrum and broad-spectrum antibiotics. The choice depends on the type of infection, where it is and the results of microbiological tests, if there were any.
The digestive tract has a large population of bacteria, so a medicine that reaches the bloodstream or passes through the gut also acts on them. This is a result of how this group of medicines works.
Read more: Gut microbiota – how it develops and what shapes it throughout life
The doctor chooses the antibiotic, the dose and the length of treatment, based on the type of infection and the patient’s situation. The doctor weighs the benefits and the risks.
What studies observe in the microbiota after antibiotic treatment
Speed of change
Studies with people have described changes in the composition of the microbiota in the first days of taking an antibiotic. These changes affect the variety of the community and the proportions of different groups of bacteria.
The size of these changes depends on the medicine, the dose and the length of treatment. It also differs between people who follow the same treatment plan (Palleja et al., 2018).
Some studies also describe a temporary increase in the share of bacteria that are less sensitive to the medicine. This is an observation about the composition of the sample, not a diagnosis of a disease.
Return to the starting state
After treatment ends, studies have described a gradual return of the composition towards the state before treatment. It can take weeks or months and differs between people.
In a study of 12 healthy men who took three antibiotics for four days, the microbiota largely recovered within about six weeks. But after six months of observation, some species that were there at the start were still missing (Palleja et al., 2018).
Several factors probably affect the speed of return at the same time: the type of antibiotic, the length of treatment, age, diet and the state of the microbiota before treatment. The available studies have not separated their roles well.
Why study results sometimes differ
| Factor | Why it affects the study result |
|---|---|
| Type of antibiotic | Medicines differ in their spectrum and in how much of them reaches the gut |
| Length and dose of treatment | Short and long treatment plans give different observations |
| Time of measurement | The composition changes over time, so the result depends on when the sample is collected |
| Length of observation | A short observation may miss a return that happens later |
| Method of analysis | 16S rRNA sequencing and metagenomics give results with different resolution |
| Study group | Age, diet, other diseases and the starting state of the participants’ microbiota |
| Type of study | Observational studies describe things that happen together, intervention studies allow stronger conclusions |
There is also a limit that applies to the whole field: there are no reference values to compare the result of one person with. So descriptions of changes are comparisons within a group, not differences from a norm.
Read more: What has a negative effect on the gut microbiota – diet, stress, medicines, sleep
Antibiotic resistance – why you must not stop treatment
Antibiotic resistance is the ability of bacteria to survive even when a medicine is present. It is seen as one of the serious challenges of modern medicine. To limit it, antibiotics must be used rationally.
A doctor leads the treatment and decides how long it lasts. Take the antibiotic exactly as advised, in the given doses and at the given intervals, until you finish the recommended plan.
It is not safe to stop treatment yourself when the symptoms go away. If your fever or pain goes away, this does not mean that the infection is under control. The doctor decides when to end treatment.
Remember these rules for the rational use of antibiotics:
- Do not change the doses or the intervals between them yourself.
- Do not stop treatment without talking to your doctor, even if you feel better.
- Do not use antibiotics left over from earlier treatment or given to you by other people.
- Do not take antibiotics for viral infections, because they do not work against viruses.
- Tell your doctor about all the medicines, supplements and herbal products that you take. Read more: Food supplements and medicines – why it is worth talking to a doctor or pharmacist
What to ask your doctor or pharmacist
The list below is a list of questions, not advice. The answers depend on the medicine and the situation, so the person who leads the treatment gives them.
- How long should the treatment last, and at what times should I take the medicine?
- Should I take the medicine with a meal or on an empty stomach, and are there any foods that I should avoid during this time?
- What side effects are typical for this medicine, and which of them mean that I should contact a doctor?
- What should I do if I miss a dose?
- Can the medicines, supplements or herbal products that I take interact with this antibiotic?
- In my case, does it make sense to use any products during the treatment, and if so, which ones and when?
- What symptoms after the end of treatment should make me contact a doctor?
- Do I need a follow-up visit or a test after the treatment ends?
General lifestyle rules during and after treatment
This is general information about daily habits, not treatment advice. It does not replace the guidance that you get from your doctor.
- Drinking enough. Drinking water regularly is part of general health advice, especially if you have a fever or loose stools.
- Regular meals. Regular mealtimes can be easier to keep than sudden changes in diet.
- Fibre from food. Vegetables, fruit, wholegrain products and pulses as part of your usual diet.
- Sleep and rest. A regular daily rhythm is part of common health advice.
- Be careful with alcohol. Some medicines require you to avoid it, so ask about this when you collect your prescription.
If your doctor gave you personal advice about diet or lifestyle, follow it before any general advice.
When you must contact a doctor
In the situations below, contact a doctor. If the symptoms are severe, get urgent medical help. This is not a complete list.
- Signs of an allergic reaction: rash, itching, swelling of the face or throat, difficulty breathing.
- Severe or watery diarrhoea, especially if it does not stop or starts after the end of treatment.
- Blood or mucus in the stool.
- Strong stomach pain, high fever or signs of dehydration.
- No improvement, or the symptoms of the infection get worse even though you take the medicine.
- Symptoms that your doctor told you to report.
If you have questions about taking the medicine, a pharmacist at the pharmacy can also help.
Summary
Antibiotics act on processes that many bacteria share, so they also affect the gut microbiota. Studies in humans describe fast changes in composition and a gradual return towards the starting state, at a different speed in different people.
The results of individual studies sometimes differ, because the studies use different medicines, observation times, methods of analysis and study groups.
The most important practical rule stays the same: a doctor leads the treatment, you take it exactly as advised and you do not stop it yourself. Ask your doctor or pharmacist questions about the treatment and any additional products.
This text is for education only and does not replace medical advice. For questions about treatment, doses and symptoms, contact a doctor or pharmacist.
FAQ
Should I take a probiotic while I take an antibiotic?
Ask the doctor who leads your treatment or a pharmacist, because the answer depends on the medicine, the reason for treatment and your health. A probiotic means live microorganisms given in an adequate amount, and the properties described in studies refer to specific strains, not to the whole category. We do not give a recommendation on this question here.
How long does it take for the microbiota to return to its state before treatment?
Studies have described a return towards the starting state over weeks or months. The speed differed between people, and some studies had a short observation time. There is no single number that works as a rule.
Is it worth doing a microbiota test after an antibiotic?
Such a result is hard to interpret, because there are no widely accepted reference values for an individual person, and the result describes the state of the sample at the moment of sampling. Talk to your doctor about whether tests after treatment make sense.
Does diet matter during treatment?
Diet is one of the factors described in microbiota research, but the data about the period of antibiotic treatment is limited. Personal diet advice from your doctor comes before general advice.
Sources
- Hill C., Guarner F., Reid G. et al., Expert consensus document. The International Scientific Association for Probiotics and Prebiotics consensus statement on the scope and appropriate use of the term probiotic, Nature Reviews Gastroenterology & Hepatology, 2014, vol. 11, no. 8, pp. 506-514.
- Gibson G.R., Hutkins R., Sanders M.E. et al., Expert consensus document: The International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on the definition and scope of prebiotics, Nature Reviews Gastroenterology & Hepatology, 2017, vol. 14, no. 8, pp. 491-502.
- Berg G., Rybakova D., Fischer D. et al., Microbiome definition re-visited: old concepts and new challenges, Microbiome, 2020, vol. 8, no. 103.
- Commission Regulation (EU) No 432/2012 of 16 May 2012 establishing a list of permitted health claims made on foods, other than those referring to the reduction of disease risk and to children’s development and health.
- World Health Organization, Global action plan on antimicrobial resistance, Geneva 2015 (adopted by World Health Assembly resolution WHA68.7).
- National Antibiotic Protection Programme (Poland), educational materials and recommendations on the rules of antibiotic treatment, https://antybiotyki.edu.pl
- Palleja A., Mikkelsen K.H., Forslund S.K. et al., Recovery of gut microbiota of healthy adults following antibiotic exposure, Nature Microbiology, 2018, vol. 3, no. 11, pp. 1255-1265.