What every parent should know about antibiotics and their child’s gut health
One of the questions on my paediatric intake form asks whether the child has ever taken antibiotics. I don't think I've ever seen the answer be "no."
I was always keen for my kids to avoid antibiotics where possible, but the reality is that sometimes they're absolutely necessary. Like most kids, mine needed antibiotics a couple of times along the way.
What antibiotics actually do to the gut microbiome
While antibiotics are sometimes prescribed when they aren't needed (they don’t help with viral infections), they can also be genuinely lifesaving in cases of serious bacterial infection. The problem is that antibiotics aren't selective. While they're busy killing the harmful bacteria, they're also wiping out a significant amount of the beneficial bacteria that live in your child's gut. And that disruption can have long-term effects on far more than just their digestion.
We now know that the gut microbiome established in childhood has a significant influence on long-term immune function, mental health and overall wellbeing - which is why protecting and rebuilding it after antibiotic use matters more than most people realise.
Why some children seem to struggle more than others after taking antibiotics
There are several reasons why one child may be hit harder by antibiotics than others. Perhaps the most important factor is the state of the child’s microbiome before they start the medication. If a child already has a diverse, healthy gut microbiome, they will generally recover more quickly than a child whose microbiome was already less than optimal, perhaps due to previous antibiotic exposure, a diet low in fibre and plant diversity, or other factors like stress or chronic illness.
Repeated courses of antibiotics have a cumulative effect and this is even more of an issue if the microbiome doesn’t have enough time or nutritional support to recover between courses. This is how some children end up caught in a cycle that can be very hard to break - getting sick, taking antibiotics, then getting sick again.
The type of antibiotic also matters. Broad spectrum antibiotics, like Augmentin and Keflex, wipe out a much broader range of gut bacteria than narrow spectrum ones, which are more targeted to specific bacteria.
While young children are generally more resilient and faster to recover than adults, their gut microbiome is still developing, which makes it more vulnerable to disruption. The child’s diet during and after antibiotic treatment also makes a difference. A child eating a diet rich in fibre, prebiotic foods and fermented foods will recover more quickly than a child eating a lot of processed food and sugar, which feeds opportunistic bacteria that can take advantage of the disruption.
What to do while your child is taking antibiotics
Give a good quality probiotic daily, timed at least two hours away from the antibiotic dose so the antibiotic doesn't simply wipe it out before it has a chance to work. Look for a probiotic that includes Lactobacillus rhamnosus GG, Lactobacillus acidophilus, Saccharomyces boulardii and Bifidobacterium species - these are among the most well researched strains for supporting gut health and preventing antibiotic-associated diarrhoea during treatment.
Focus on easy to digest, nourishing meals. Simple, familiar and nourishing is the goal.
Minimise sugar and processed food. Sugar feeds opportunistic bacteria that can take advantage of the disruption to the microbiome, making recovery harder.
Keep up fluids. Antibiotics can sometimes cause loose stools or diarrhoea, so good hydration is important throughout the course.
Include prebiotic-rich foods where possible - bananas, oats, cooked and cooled potato or rice, and apples are all easy options that most children will eat without complaint.
Finish the full course. Stopping antibiotics early because your child seems better is one of the most common mistakes parents make. The full course is prescribed for a reason and stopping early can contribute to antibiotic resistance.
How to support gut recovery following antibiotic treatment
Continue the probiotic for at least four weeks after the course finishes. This is one of the most important and most overlooked steps - most parents stop when the antibiotics stop.
Prioritise prebiotic-rich foods to feed the beneficial bacteria that are repopulating the gut. This is the time to be more intentional about including bananas, oats, legumes, garlic, onion, apples and cooked and cooled potato or rice regularly.
Introduce fermented foods if your child will tolerate them - yoghurt with live cultures, kefir, or small amounts of miso are the most child-friendly options.
Increase variety in fruit and vegetables. Diversity of plant foods increases diversity in the microbiome, and this is particularly important during the recovery period.
Minimise processed food and sugar for at least a few weeks after finishing the antibiotics.
Be patient. The gut microbiome can take several months to fully recover after a course of antibiotics, particularly a broad spectrum one.
When to seek more support
If your child keeps getting sick after antibiotics or has ongoing digestive symptoms, behaviour changes or low mood, it might be time to look more closely at their gut health. A nutritionist is able to conduct a thorough assessment of your child’s clinical symptoms, identify signs of potential nutrient deficiencies and refer for more comprehensive gut testing if needed, including microbiome analysis, which can give a much clearer picture of what's actually going on and help guide a targeted recovery plan.
References
Guo, Q., Goldenberg, J., Humphrey, C., Dib, E., & Johnston, B. (2019). Probiotics for the prevention of pediatric antibiotic-associated diarrhea.. The Cochrane database of systematic reviews, 4, CD004827 . https://doi.org/10.1002/14651858.cd004827.pub5.
Johnston, B., Supina, A., Ospina, M., & Vohra, S. (2008). Cochrane review: Probiotics for the prevention of pediatric antibiotic‐associated diarrhea. Evidence-based Child Health: A Cochrane Review Journal, 3, 280-315. https://doi.org/10.1002/ebch.238.