How Antibiotics Wreck Your Gut

Most people know I am not a fan of antibiotics. However, I understand that there is a time and a place for them. I also understand that there are tons of herbal remedies that can be just as effective as antibiotics and do a lot less harm. My personal favourite is wild oregano: you can find it in my shop on my website by clicking the Fullscript (Canadian) or Spectrum Supplements (International) link.


The main reasons I go to herbal formulas before antibiotics is because they have less negative effects on gut flora than broad spectrum antibiotics, they are natural biofilm disruptors which is what bacteria can hide in, they do not deplete key vitamins/minerals and they do not cause intestinal permeability. Many people do not understand the importance of having a healthy balance of gut flora. There are severe long term consequences like permanent changes to the microflora associated with antibiotics that most people are not informed about. This disturbance in normal intestinal flora is responsible for the overgrowth of dangerous pathogens so antibiotics are kind of counterintuitive. They will kill any pathogenic bacteria (along with the good bacteria) in that moment but they set your microbiome up for failure in the future as you will be more susceptible to pathogenic overgrowths when you have dysbiosis. When you have an an abundance of bad bacteria, they will release enterotoxins which increase the permeability of the intestines. Once that intestinal lining becomes permeable, you are not only missing your physical defence mechanism against pathogens but you are not going to be able to digest your food effectively which will result in large food particles seeping through that your body does not identify. This is called leaky gut. Your body will then produce immunosuppressive proteins causing immune dysfunction, damaging epithelial cells and an energy metabolism imbalance. Many researches state that antibiotic use are the leading cause of autoimmune disorders for this exact reason. Balanced bacteria plays the most significant role in a healthy immune response. Not to mention, a round of antibiotics will deplete calcium, magnesium, potassium, vitamin K and B vitamin stores pretty quickly. Minerals especially our 4 main macro minerals (calcium, magnesium, potassium and sodium) play a key role in every body process because minerals are what run enzymes.

Antibiotic use has been associated with:


-All autoimmune conditions





-Ulcerative Colitis


-Yeast Infections or any fungal infection like Candida


-Leaky Gut & Dysbiosis

-Blood Clotting

-Kidney Stones

-Malabsorption/nutrient deficiencies

and so much more...

It's important to know that antibiotics don't always work against all bacterial infections (and definitely don't work against non bacterial infections like viruses). Due to the frequent use of antibiotics, there is resistant strains of bacteria in which antibiotics will not work for. Resistant bacteria tends to develop when antibiotics are used too often or incorrectly. You can test your specific antibiotic resistant bacteria with a GI Map stool test.

Now sometimes antibiotics are unavoidable so here is what to do if you absolutely must take them:

  • Nourish your body with plenty of nutrient dense, easy to digest foods

  • Get lots of rest and avoid partying, staying up late, alcohol etc.

  • Replenish your microbiome both during and after with a stable probiotic. I would take saccharomyces boulardii at dinner while on antibiotics because it is an inactive yeast so the antibiotics won't actually kill it. You can find this in my website shop on Fullscript (Canadian) or Spectrum Supplements (International). After antibiotics, I would switch to a high dose spore based probiotic like MegaSpore by Microbiome Labs to properly colonize the bacteria. These are the only two strains of probiotics that I notice actually survive past stomach acid and are able to integrate into your gut.

  • Focus on lots of gut healing foods like gelatin gummies and bone broth during and after a course of antibiotics to improve the integrity of the intestinal lining

  • Support your liver and detoxification pathways by eating enough glucose, saturated fats and animal protein

  • Replenish minerals with lots of adrenal cocktails and mineral smoothies

As always, this is not medical advice. Speak to your practitioner.


Katie xx

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