The Downside of Taking Antibiotics

How antibiotics disrupt the gut

Our gut is home to trillions of bacteria, both helpful and harmful, that live in a finely tuned ecosystem. These microbes support digestion, immunity, nutrient absorption and even emotional well-being. When antibiotics are introduced, they don’t just target the bad guys, they also wipe out beneficial bacteria that play a key role in maintaining gut balance.

Even short-term use of antibiotics can lead to long-lasting changes in your microbiome. A 2025 study published in Nature[1] found that after just five days of antibiotic treatment, participants showed a sharp decline in microbial diversity. Beneficial strains were lost, while resistant strains quickly multiplied and lingered for up to a year.

[1] https://www.nature.com/articles/s41586-025-08781-x

Rise in antibiotic-resistant bacteria

Bacteria are highly adaptable. When exposed to antibiotics, they can mutate or acquire resistance genes from other microbes through horizontal gene transfer. This allows them to survive treatment and thrive in an antibiotic-altered gut environment. Alarmingly, some resistant strains retain full function, enabling them to flourish and spread long after treatment ends.

Antibiotic resistance isn’t just a hospital problem or limited to people with recurring infections – it’s a growing global concern. Even if you haven’t recently taken antibiotics, your gut may still harbour resistant bacteria, especially if you live in or travel to countries with high antibiotic use.

For example, people in countries like Spain or Italy tend to carry more antibiotic resistance genes than those in countries with stricter prescribing practices such as the Netherlands or Denmark. This shows how your environment influences your gut health.

International travel adds to the challenge, as travellers can pick up resistant strains abroad and bring them home, contributing to the worldwide spread of resistance. This highlights that antibiotic use affects not only individual health but public health globally.

Antibiotic use in childhood has long-term consequences

Perhaps even more troubling is how early exposure to antibiotics can shape gut health for life. A study using animal models found that giving antibiotics in early life caused a significant, lasting reduction in microbial diversity. Keystone strains (the foundational species that support the entire gut ecosystem) were wiped out, and the microbial network never fully recovered. These changes impacted metabolism and immune function well into adulthood. [2]

This may help explain why early antibiotic use, particularly in infancy and childhood when the gut microbiome is still developing, has been associated with a greater risk of chronic health issues later in life. A systematic review in children found that antibiotic exposure leads to long-term reductions in beneficial bacteria like Bifidobacteria and Lactobacillus, alongside increases in potentially harmful strains such as E. coli. These microbial shifts have been implicated in the development of conditions such as type 1 diabetes, Crohn’s disease and other autoimmune disorders, asthma, allergies and obesity. [3]

[2] https://www.nature.com/articles/s41467-022-28525-z

[3] https://pmc.ncbi.nlm.nih.gov/articles/PMC7928022/

How to protect your gut naturally

If you’ve taken antibiotics in the past, don’t panic. The key now is to support your gut moving forward. Here’s how:

Heal your gut lining. Antibiotics don’t just affect your gut flora, they can also inflame or damage the gut lining, leading to issues like leaky gut. Include gut-healing foods such as bone broth, aloe vera juice, slippery elm and L-glutamine. Nutrients like zinc, vitamin A and omega-3 fatty acids also play a key role in repairing the gut barrier and reducing inflammation.

Eat fermented and fibre-rich foods daily. Foods like sauerkraut, kefir and kimchi introduce beneficial bacteria into the gut. Pair these with prebiotic-rich vegetables, including garlic, leeks, onions, asparagus and Jerusalem artichokes, to feed the good bacteria and encourage them to thrive.

Take a high-quality probiotic supplement. After a course of antibiotics, a well-formulated probiotic can help reintroduce diversity to your gut microbiome. Choose a broad-spectrum product with multiple strains and a high CFU (colony-forming units) count. This probiotics podcast episode explores what to look for in a probiotic and how to choose the right one for you.

Support keystone species. Keystone strains are the foundational microbes that maintain balance and structure within your gut ecosystem. One of the best ways to support them is by eating a wide range of colourful plant foods – aim for 30+ different types each week. This diversity provides a variety of fibres and polyphenols that feed different bacteria and promote microbial richness.

Reduce hidden antibiotic exposure. Most conventionally farmed meats and dairy products contain antibiotic residues, which can affect your microbiome over time. Choose organic, pasture-raised, grass-fed and antibiotic-free animal products whenever possible.

Focus on natural immune support. Instead of turning to antibiotics at the first sign of illness, consider gentle, naturopathic remedies that support your immune system without disrupting your microbiome. Herbs such as echinacea, garlic, thyme, elderberry and oregano have powerful antimicrobial and immune-modulating properties. For personalised guidance and a gut-healing protocol tailored to your needs, consider working with a qualified naturopathic practitioner.