Antibiotics: the effect on the gut

Antibiotics are a type of antimicrobial substance active against bacteria. Their action is to kill or inhibit the growth of bacteria. Fortunately, antibiotics are still exciting as they are powerful and lifesaving for some people with serious infections. Unfortunately, nowadays antibiotics are sometimes unnecessarily used or given for no reason. 

Antibiotics come in many forms: 

  • tablets
  • capsules
  • liquids
  • creams
  • ointments 

In our gut, we have a diverse and rich gut microbiota, which is essential for our health. A result of poor diversity of the gut ecosystem is a characteristic of chronic diseases including obesity, diabetes, asthma and gut inflammatory disorders. Gut microbiota influences health in many ways: synthesis of vitamins, digestion of food, defence against pathogens, development and maintenance of the immune system. 

How do antibiotics work in your body?

Once administered, the antibiotic kills the pathogenic bacteria by destroying the bacterial cell and prevents cell reproduction. However, at the same time, it kills and inhibits some commensal microbes (the good bacteria that reinforces the immune system, mostly present in your gut). Antibiotics also change the microbial diversity, which can weaken the immune system and disturb the function of certain hormone pathways in the gut. 
Antibiotics work immediately in the gut but it can take longer for you to feel better (about two to three days). 

What do antibiotics do to your body? 

In 1954, Bohnhoff et al. found that after giving antibiotics to mice, they were easily infected by Salmonella Enterica Serovar as their gut microbiota was weakened. They introduced the concept of gut microbiota. 

The antibiotics directly kill the pathogen in the gut microbiota but indirectly destroy the commensal microbes in your gut, which alter the community structure in your gut. Eventually, antibiotic induces dysbiosis (microbial imbalance), which can disrupt the development and the structure of the immune system and increase the risk of developing a disease such as Crohn's disease, other inflammatory bowel diseases (IBD) or an infection disease. 

Antibiotics impact host immunity by altering the bacteria metabolites and the signals transmitted from gut microbiota to the host. Study revealed that antibiotics can have a profound effect on lipids, bile acids and amino acid alteration of gut microbiota. In short, antibiotics show to reduce the production of short-chain fatty acids (key role in microbiota-gut-brain crosstalk) in the gut, which decrease the Tregs cells (prevent autoimmune disease, modulate the immune system) and increase the gut inflammation. 

Many studies explain that the use of antibiotics in the long term alternate the bacteria in our gut and create a dysbiosis in our gut, which disturbs the function of our immune system and the function of the gut. Jernberg et al. 2010 explain that a single course of antibiotics can disturb the microbiome for up to two to four years.

A study done at the University of Copenhagen showed that some of the gut bacteria are washed out by the antibiotics, followed by a gradual recovery of most bacteria species over a period of six months. However, after six months, the participants of this study were still missing nine of their beneficial bacteria and a few potentially non-desirable bacteria had colonised in the gut. 


How can I help my gut after taking antibiotics? 

The first vital point for your gut is to restore a healthful balance in the gut microbiome. To help your gut restore a healthy balance, you can take probiotics overt a short period of time (live microorganisms known as ‘healthy bacteria’). Probiotics increase your commensal microbes, protect your gut against invasive pathogen, which reinforce your immune system. 

When should you take probiotics? 

A study done by Engelbrekston et al. shows that taking probiotics at the same time as antibiotics minimised the disturbance and alteration in the gut microbiota. It also shows that probiotics help to rapidly re-establish the baseline of the microbiota. Taking probiotics at the same time as antibiotics help to reduce the risk of side effects such as diarrhoea and bloating. To minimise the risk of killing the good microbes when taking antibiotics, the study suggests taking the probiotics two-three hours after the antibiotics. 

Prebiotics are good food that feed the good bacteria in the gut. Eating prebiotics before and after taking antibiotics help to feed the good bacteria and also bring back a good balance. 

Fermented food

After finishing the course of antibiotics, try to have some fermented food to increase the good microbes in the gut. 

Fermented foods are:

  • miso 
  • tempeh 
  • kimchi 


Try to avoid eating food high in fibre during the course of antibiotics, as they might affect stomach absorption. After finishing your antibiotics, try to eat fibre as it stimulates the growth of good microbes in the gut and promotes proper digestion and increases elimination. 

Foods high in fibre: 

  • artichokes 
  • bananas 
  • berries
  • beans 
  • broccoli
  • lentils
  • nuts 
  • peas
  • whole grains 

Food to avoid while taking antibiotics

  • Grapefruit juice: it can stop the body from breaking down and correctly absorbing the medication (Bailey et al. 2013) 
  • Orange juice: a study demonstrated that calcium-fortified juice such as orange juice, interferes with the absorption of antibiotics. Try to avoid orange juice while taking antibiotics (Wallace et al. 2013). 

Sometimes we have no choice but to take antibiotics, but if you notice some side effects such as diarrhoea, nausea, vomiting and cramps and if these symptoms persist after stopping your treatment you should contact your GP. 

Nutritionist Resource is not responsible for the articles published by members. The views expressed are those of the member who wrote the article.

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London EC2M & SW18
Written by Melanie Padovani, DIP NT. CNM mBANT, CNHC
London EC2M & SW18

Melanie developed a big interest in Gut issues. She became an expert in this area but her main objective is to find out the root causes of your issues and identify what imbalance or dysfunction is at the heart of a specific health condition and manage it in a sustainable way.

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