Antibiotics and the effect on your child's gut microbiome

Antibiotics are an important medical treatment that has saved billions of lives worldwide but the overuse of antibiotics has devastating impacts on the gut microbiome, particularly that of a child's. 

Antibiotics and effects on gut health

Antibiotics are an important medical treatment that has saved billions of lives worldwide but the overuse of antibiotics has devastating impacts on the gut microbiome, particularly that of a child's.

In our recent webinar 'An Introduction to Kids Gut Health' I discussed the impacts on a child's gut microbiota development.

Having received the results of the Kids Gut Health Check-up Quiz and chatting to parents post-webinar, it's clear there is a high use of antibiotics amongst young children.

Australia’s antibiotic treatment rates are high by international standards and at the same time, antibiotic resistance has reached alarming levels. We're are also exposed to antibiotics through their use in animals and agriculture.

Antibiotics are deemed to have one of the most detrimental effects on an immature gut microbiome affecting your child's overall health in the short and long term.

How antibiotic treatment affects a child's gut microbiome

Antibiotic use, especially in the first year's of life, has a lasting impact on your child's health. Left unaddressed, this could result in lifelong health problems.

Reduces gut bacterial diversity

Broad-spectrum antibiotic use has been associated with reduced gut bacteria diversity. In fact, one course can affect the abundance of about 30% of the microbial communities. When more and more new research suggests diversity is key for a healthy gut and overall health outcomes, this is of concern.

Low bacterial diversity in infants and children has been linked with conditions such as asthma, atopic eczema, allergies, inflammatory disease, autoimmunity and irritable bowel syndrome (IBS).

Reduces protective ("good bacteria") species

Early childhood antibiotic exposure also alters the bacterial composition with a reduced number of protective species such as Bifidobacterium.

Bifidobacterium spp. are among the first microbial colonisers of the infant's gut, making up about 60% of the gut microbiome. Bifidobacteria play an important role in their health including the digestion of sugars found in breastmilk and modulating the immune system.

It's interesting to note, infants who haven't had a course of antibiotics, but whose mum's received antibiotics prior to delivery had the same alterations in their gut bacteria composition as those infants who did receive the medication.

Increases the risk of atopic diseases

Early-life antibiotic use is likely to increase the risk of allergies and atopic diseases such as eczema, asthma and rhinoconjunctivitis. There is evidence to suggest antibiotic-induced dysbiosis, disrupted gut microbiome composition and bifidobacteria deficiency may be associated with the rise in these conditions.

Increases the risk of weight gain

Antibiotic use before the age of 2 years, especially broad-spectrum antibiotics, is believed to increase the risk of the child becoming obese by the age of 5. An increased risk of significant weight gain was also seen in children whose mums took antibiotics in the second or third trimester.

Breastfeeding was found to be protective against obesity with researchers theorising this could be because breast milk contains a diverse range of gut microbes and promotes gut health.

Alters the effectiveness of the immune system

The effect antibiotic use on a child's gut is likely to influence several immune system outcomes including its ability to fight infections causing long-term health issues.

Research suggests antibiotics taken in the early years of life specifically impacts the T cells. T cells have the ability to activate the immune process or keep it down-regulated and non-responsive. This means the microbial communities living in a healthy gut has a greater number of peacekeeping T cells to regulate the immune responses and control some of the more aggressive cells.


Free Kids Gut Health Check-up Quiz

Take the Kids Gut Health Check-up quiz online now to see how you can best support your child's health by healing and nourishing the gut.


Improving your child's gut microbiome after antibiotics

There is evidence to suggest taking probiotics during and after a course of antibiotics can help improve the gut microbiome balance, reduce the risk of opportunistic pathogens and decrease the likelihood of antibiotic-associated diarrhoea.

Probiotics may also be beneficial for mum if antibiotics are taken during pregnancy and for baby once he/she is born.

However, it's important you choose strain-specific, quality probiotic and there is some evidence to suggest probiotic supplementation may prevent native gut microbiota returning after the antibiotic use.

One of the best strategies to improve your child's gut microbiome after antibiotic treatment and in general is through food. A diet of probiotic-rich foods, prebiotic fibres and variety is key to help enhance the diversity in your child's gut and encourage the "good" bacteria to repopulate.


Bailey, L. C., Forrest, C. B., Zhang, P., Richards, T. M., Livshits, A., & DeRusso, P. A. (2014). Association of Antibiotics in Infancy With Early Childhood Obesity. JAMA Pediatrics, 168(11), 1063.

Francino, M. P. (2015). Antibiotics and the Human Gut Microbiome: Dysbioses and Accumulation of Resistances. Frontiers in Microbiology, 6, 1543.

Hill, C. J., Lynch, D. B., Murphy, K., Ulaszewska, M., Jeffery, I. B., O’Shea, C. A., … Stanton, C. (2017). Evolution of gut microbiota composition from birth to 24 weeks in the INFANTMET Cohort. Microbiome, 5(1), 4.

Practitioners, T. R. A. C. of G. (n.d.). RACGP - Prescribed antibiotic use in Australian children aged 0–12 years. Retrieved from–12-years/


The gut microbiome testing provides in-depth insights into the microorganisms living in your child’s gut and the effect on their health.

This powerful tool provides you with a detailed report about the gut bacterial species and other micro-organisms, the diversity and their function. This can inform treatment approaches or simply be used to help optimise your child’s overall health and wellbeing. Find out more about gut testing here