Antibiotics can be absolutely essential when we need them—but they don’t just target the "bad" bacteria. They also impact the good bacteria that keep our gut microbiome healthy (Elvers et al., 2020). This disruption can lead to side effects like bloating, diarrhoea, fatigue, and even long-term imbalances like SIBO (Small Intestinal Bacterial Overgrowth) and IBS (Irritable Bowel Syndrome).

The good news? There are simple, science-backed steps you can take to support your gut through the process.

Here’s how to look after your microbiome before, during, and after a course of antibiotics.

1. Yes, You Should Take Probiotics (Just Not at the Same Time).

Let’s clear this up: taking probiotics during a course of antibiotics is a good idea—just make sure you space them out.

Taking a probiotic 2–3 hours after your antibiotic can help reduce side effects like diarrhoea and protect your microbiota during treatment. It’s one of the simplest ways to reduce disruption and start rebuilding your gut while you're still on medication.

2. Choose the Right Strains (and Enough of Them).

Not all probiotics are created equal. If you’re taking them alongside antibiotics, look for:

Lactobacillus rhamnosus GG (Szajewska & Kołodziej, 2015; Szajewska et al., 2006)
Bifidobacterium animalis subsp. lactis BB-12 (Merenstein et al., 2021)
Saccharomyces boulardii (CNCM I-745) (Spatz et al., 2023)

These strains are backed by clinical trials for their ability to support the gut during antibiotic use and reduce the risk of side effects.

TIP: Check the label for at least 1 billion CFU (colony-forming units). This is the minimum dose shown to have clinical benefits.

3. Feed the Good Guys

After antibiotics, your gut needs the right fuel to grow beneficial microbes back.

That fuel? Fibre and polyphenols.

Think oats, legumes, garlic, onions, berries, flaxseeds, dark chocolate, leafy greens, and extra virgin olive oil. These plant compounds help your gut bugs produce short-chain fatty acids (SCFAs), which are critical for gut lining repair, immune balance, and lowering inflammation (Penumutchu et al., 2023).

More plant diversity = more microbial diversity = better recovery.

4. What Not to Do While Your Gut’s Healing

Healing your gut means creating an environment where beneficial microbes can thrive. Here’s what to avoid:

Processed foods: High sugar and refined oils feed the wrong microbes and drive inflammation (Bevilacqua et al., 2024).
Alcohol: Especially in excess, it damages the gut lining and reduces microbial diversity (Engen et al., 2015).
Skipping meals or restrictive diets: Your gut bacteria need regular fuel—don’t starve them.
Too much caffeine: This can irritate your gut, especially if consumed on an empty stomach and increase diarrhoea (Saygili et al., 2024).
Chronic stress: Stress is one of the biggest gut disruptors. Support your nervous system with rest, breathwork, and slowing down - read more about the gut-brain connection here.

5. Can Antibiotics Trigger Ongoing Gut Issues Like IBS?

In short: yes.

Antibiotics can wipe out protective bacteria, and in some cases, this disruption can:

Reduce beneficial gut microbes and microbiota diversity
Increase the risk of developing IBS
Contribute to long-term bloating, food sensitivities, and irregular bowel movements

Frequent antibiotic use in childhood is even associated with a higher lifetime risk of IBS (Mamieva et al., 2022).

Still Feeling Off? Here’s How I Can Help.

If your gut still feels off after antibiotics, you don’t have to just live with it.

As a naturopath, I take a root-cause approach—looking at how your gut, diet, nervous system, and lifestyle are working together. We can run testing if needed, support your microbiome with targeted nutrition and herbs, and build a personalised recovery plan to get you feeling good again.

Emba Emails.

references.

Bevilacqua, A., Speranza, B., Racioppo, A., Santillo, A., Albenzio, M., Derossi, A., Caporizzi, R., Francavilla, M., Racca, D., Flagella, Z., De Santis, M. A., Elia, A., Conversa, G., Luchetti, L., Sinigaglia, M., & Corbo, M. R. (2024). Ultra-Processed Food and Gut Microbiota: Do Additives Affect Eubiosis? A Narrative Review. Nutrients, 17(1), 2. https://doi.org/10.3390/nu17010002
Elvers, K. T., Wilson, V. J., Hammond, A., Duncan, L., Huntley, A. L., Hay, A. D., & van der Werf, E. T. (2020). Antibiotic-induced changes in the human gut microbiota for the most commonly prescribed antibiotics in primary care in the UK: a systematic review. BMJ open, 10(9), e035677. https://doi.org/10.1136/bmjopen-2019-035677
Engen, P. A., Green, S. J., Voigt, R. M., Forsyth, C. B., & Keshavarzian, A. (2015). The Gastrointestinal Microbiome: Alcohol Effects on the Composition of Intestinal Microbiota. Alcohol research : current reviews, 37(2), 223–236.
Mamieva, Z., Poluektova, E., Svistushkin, V., Sobolev, V., Shifrin, O., Guarner, F., & Ivashkin, V. (2022). Antibiotics, gut microbiota, and irritable bowel syndrome: What are the relations?. World journal of gastroenterology, 28(12), 1204–1219. https://doi.org/10.3748/wjg.v28.i12.1204
Merenstein, D., Fraser, C. M., Roberts, R. F., Liu, T., Grant-Beurmann, S., Tan, T. P., Smith, K. H., Cronin, T., Martin, O. A., Sanders, M. E., Lucan, S. C., & Kane, M. A. (2021). Bifidobacterium animalis subsp. lactis BB-12 Protects against Antibiotic-Induced Functional and Compositional Changes in Human Fecal Microbiome. Nutrients, 13(8), 2814. https://doi.org/10.3390/nu13082814
Penumutchu, S., Korry, B. J., Hewlett, K., & Belenky, P. (2023). Fiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential. Nature communications, 14(1), 5161. https://doi.org/10.1038/s41467-023-40553-x
Saygili, S., Hegde, S., & Shi, X. Z. (2024). Effects of Coffee on Gut Microbiota and Bowel Functions in Health and Diseases: A Literature Review. Nutrients, 16(18), 3155. https://doi.org/10.3390/nu16183155
Spatz, M., Wang, Y., Lapiere, A., Da Costa, G., Michaudel, C., Danne, C., Michel, M. L., Langella, P., Sokol, H., & Richard, M. L. (2023). Saccharomyces boulardii CNCM I-745 supplementation during and after antibiotic treatment positively influences the bacterial gut microbiota. Frontiers in medicine, 10, 1087715. https://doi.org/10.3389/fmed.2023.1087715
Szajewska, H., & Kołodziej, M. (2015). Systematic review with meta-analysis: Lactobacillus rhamnosus GG in the prevention of antibiotic-associated diarrhoea in children and adults. Alimentary pharmacology & therapeutics, 42(10), 1149–1157. https://doi.org/10.1111/apt.13404
Szajewska, H., Ruszczyński, M., & Radzikowski, A. (2006). Probiotics in the prevention of antibiotic-associated diarrhea in children: a meta-analysis of randomized controlled trials. The Journal of pediatrics, 149(3), 367–372. https://doi.org/10.1016/j.jpeds.2006.04.053

Taking Antibiotics? Here’s How to Support Your Gut Before, During, and After.

1. Yes, You Should Take Probiotics (Just Not at the Same Time).

2. Choose the Right Strains (and Enough of Them).

3. Feed the Good Guys

4. What Not to Do While Your Gut’s Healing

5. Can Antibiotics Trigger Ongoing Gut Issues Like IBS?

Still Feeling Off? Here’s How I Can Help.

Emba Emails.

references.

emba wellness.

Follow Us.

Taking Antibiotics? Here’s How to Support Your Gut Before, During, and After.

1. Yes, You Should Take Probiotics (Just Not at the Same Time).

2. Choose the Right Strains (and Enough of Them).

3. Feed the Good Guys

4. What Not to Do While Your Gut’s Healing

5. Can Antibiotics Trigger Ongoing Gut Issues Like IBS?

Still Feeling Off? Here’s How I Can Help.

Emba Emails.

references.

Are You Starving Your Gut Bacteria?

emba wellness.

Follow Us.