5 Steps to Save Your Gut After Antibiotics

While using antibiotics is never ideal, there can be times when they are absolutely essential. Like getting a UTI on day 2 of a 7 day boat cruise around the Galapagos! But don’t worry, if this is you, all hope is not lost. It’s likely to take time and little bit of effort, but there are proven things you can do both during and after antibiotic treatment to reduce the damage, avoid IBS flare-ups and follow-on conditions that come with having your gut destroyed by antibiotics.

Gut After Antibiotics Heal Probiotic Supplements

Gut After Antibiotics Heal Probiotic Supplements

You probably want to know:

>  How antibiotics destroy your gut

>  Why repeated use of antibiotics might stop working and cause other health issues

>  How to minimise the damage of antibiotics and help re-grow good gut bacteria in five simple steps

How antibiotics destroy your gut

If, like me, you’ve ever brought home a travel bug or had recurrent UTIs, tonsillitis or ear infections, you’ve also likely been subjected to the use of antibiotics. Don’t get me wrong, at the time I thought they were my saviour from all things horrid and painful. After all, they did get rid of the symptoms I had been complaining about, in the short term. Little did I know the impact that little antibiotic pill (or course of 7) was having on my poor gut and the downward health spiral that was to follow...

You see, antibiotics not only target bad bacteria in the gut, they also have damaging effects on the number and diversity of good bacteria (1). This is a serious problem because a healthy balance of gut bacteria is so important to the proper functioning of our immune system (2, 3) whose job it is to fight off infection and keep us healthy. There is a huge body of research demonstrating that a lack of diversity in gut-friendly bacteria is linked with conditions like allergies, leaky gut, IBD, asthma, obesity, depression, autoimmunity and countless others (4, 5, 6, 7, 8, 9).

The bad/worse news is that even a single course of antibiotics can permanently alter the gut flora and increase your risk of getting dangerous bacteria, such as Clostridium difficile (10), which cause diarrhea and IBS symptoms.

So what happens if I use antibiotics regularly?

While antibiotics can often be an effective treatment for some infections, the same can’t always be said after more than a few rounds.That is because antibiotic resistance is on the rise, including resistant strains of E coli, the bacteria that cause more than 70% of UTIs (11), the most common bacterial infection (12).

As a result, practitioners are increasingly using two, three or even FOUR antibiotics to kill resistant bacterial infections. These third and fourth-line antibiotics are often ‘broad spectrum’, resulting in even wider destruction of good gut bacteria along the way - like using a grenade to kill a single weed in your veggie patch. You might have killed the infection but you have also increased your risk of a whole bunch of other, potentially more dangerous, ‘weeds’ (i.e. conditions like IBD and autoimmunity) now that your immune system is nowhere to be found.

5 steps to minimise the damage of antibiotics and encourage regrowth of good bacteria

Step 1. Cut out the sugar

And focus on eating real, whole foods, especially when you have an active infection. Sugar feeds infection, so you need to get the sweet stuff out, in all forms, as much as possible. Whole, real foods like vegetables, nuts and seeds, meat, fish, eggs, herbs, spices and good quality oils should make up your diet while you are prone to further infections. This way of eating will help diversify the good gut bacteria and deliver the nutrients and minerals your body and immune system needs.

Step 2. Add in Probiotics.

A good probiotic can further assist the introduction of good bacteria back into your digestive system, reduce side effects and prevent gut infection (13, 14). The most positive outcomes are associated with Lactobacilli and Bifidobacteria strains, commonly found in probiotics. Saccharomyces boulardii can also be effective for some people, as it is a yeast and therefore cannot be killed by the antibiotics. Soil-based (spore) probiotics are another option that I and many other practitioners have seen great success with. While I have seen great results with a particular spore-based product called MegaSporeBiotic, as with most things, the best probiotic will depend on your particular circumstances (i.e. what antibiotic you’re on and the state of your digestive system). It is also important to take any probiotic supplement away from the time you take your antibiotic dose.

Step 3. Add in some fermented foods.

The main difficulty after a course of antibiotics isn’t recovering the number of bacteria, it’s recovering the diversity. Fermented foods help to re-introduce a broad variety of beneficial bacteria into your digestive system. These include foods like sauerkraut, kefir and kombucha.  I like to start with sauerkraut, so try adding a teaspoon and gradually build up to a tablespoon with your lunch or dinner daily.

Step 4. Add in Prebiotics.

In theory, prebiotics are much more effective than probiotics at promoting the growth of beneficial bacteria in the gut. I say ‘in theory’ because for me and many of my clients with IBS symptoms, prebiotic foods haven’t done much beyond feeding the bad bacteria in their gut. In some people however, prebiotic rich foods with resistant starch, like starchy tubers, squash and peeled fruits, are a great way to boost the level of good bacteria in your gut (15). But, from personal experience, this is something to discuss with your practitioner and tread slowly with so I won’t go into much detail about how to implement this here.

Step 5. Support your liver.

As the organ responsible for detoxifying medications and lipopolysaccharides (from bacterial die-off), the liver can take a hit during a course of antibiotics (16, 17). A liver support supplement that contains milk thistle and turmeric, such as Gaia Herbs’ Liver Health (1 capsule twice daily between meals), as well as glycine-containing bone-broth are a great place to start when supporting the liver during and after antibiotic use. I really like the the dehydrated chicken and beef broth by Broth of Life (add 1 teaspoon daily to soup or sprinkle over a hot meal).

Next steps…

If you have used antibiotics regularly in the past and now struggle with IBS or other digestive complaints as I did, please head to the Work With Us page to learn more about how I work online with clients in many countries to test for and treat the many root causes of IBS symptoms and other GI conditions. I know you can do it because I did, and now live happily antibiotic and infection free.

Note: Affiliate links for iHerb have been included within this blog post.


  1. Macfarlane, S. (2014). Antibiotic treatments and microbes in the gut. Environ Microbiol, 16(4), 919-24 LINK

  2. Maslowski, K., Mackay, C. (2011). Diet, gut microbiota and immune responses. Nat Immunol, 12(1), 5-9 LINK,

  3. Rook, G. A. W., & Brunet, L. R. (2005). Microbes, immunoregulation, and the gut. Gut, 54(3), 317–320 LINK

  4. Fasano, A., Shea-Donohue, T. (2005). Mechanisms of disease: the role of intestinal barrier function in the pathogenesis of gastrointestinal autoimmune diseases. Nat Clin Pract Gastroenterol Hepatol, 2(9), 416-22 LINK

  5. Kostic, A., Xavier, R., Gevers D. (2014). The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology, 146(6):1489-99 LINK

  6. Russell, S., et al. (2013). Perinatal antibiotic treatment affects murine microbiota, immune responses and allergic asthma. Gut Microbes, 4(2), 158-64 LINK

  7. Ley, R., et al. (2006). Microbial ecology: Human gut microbes associated with obesity. Nature, 444, 1022-1023 LINK

  8. Dash, S., et al. (2015). The gut microbiome and diet in psychiatry: focus on depression. Curr Opin Psychiatry, 28(1), 1-6 LINK

  9. Tlaskalová-Hogenová, H., et al. (2004). Commensal bacteria (normal microflora), mucosal immunity and chronic inflammatory and autoimmune diseases. Immunol Lett, 93(2-3), 97-108 LINK

  10. Ambrose, N., et al. (1985). The influence of single dose intravenous antibiotics on faecal flora and emergence of Clostridium difficile. J. Antimicrob. Chemother, 15 (3), 319-326 LINK

  11. Nickel, J. C. (2007). Urinary Tract Infections and Resistant Bacteria. Reviews in Urology, 9(2), 78–80 LINK

  12. Foxman, B. (2003). Epidemiology of urinary tract infections: incidence, morbidity, and economic costs. Dis Mon, 49(2), 53-70 LINK

  13. Can M, Beşirbellioglu BA, Avci IY, Beker CM, Pahsa A. (2006). Prophylactic Saccharomyces boulardii in the prevention of antibiotic-associated diarrhea: a prospective study. Med Sci Monit, 12(4) 19-22 LINK

  14. Sazawal, S., et al. (2006). Efficacy of probiotics in prevention of acute diarrhoea: a meta-analysis of masked, randomised, placebo-controlled trials. Lancet Infect Dis, 6(6), 374-82 LINK

  15. Topping, D., Fukushima, M., Bird, A. (2003). Resistant starch as a prebiotic and synbiotic: state of the art. Proc Nutr Soc, 62(1), 171-6 LINK

  16. Robles M., et al. (2010). Antibiotic-induced liver toxicity: mechanisms, clinical features and causality assessment. Curr Drug Saf, 5(3), 212-22 LINK

  17. Westphal, J., Vetter, D., Brogard, J. (1994). Hepatic side-effects of antibiotics. J Antimicrob Chemother, 33(3), 387-401 LINK