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How to Restore Your Gut Health While and After Taking Antibiotics

Updated: Jan 2

Antibiotics can be incredibly useful and important in cases of serious infections. Unfortunately, though, antibiotics are overprescribed and overused in North America, Europe, and most of the world, relying on modern medicine. This can be detrimental to your gut health.

Today, I want to discuss how to restore your gut microbiome health after taking antibiotics.

The Problem with Antibiotics

The goal of antibiotics is to kill bacteria, stop them from multiplying, and stop bacterial infections. The problem is that antibiotics cannot tell the difference between harmful and beneficial bacteria. They don’t discriminate: they kill them all.

When you take antibiotics, they will clean out not only the pathogenic bacteria that are causing your infection but also attack the good bacteria in your system. Good gut bacteria have a vital role in your body, for the gut, and for overall health. Taking antibiotics and killing off good bacteria can lead to serious gut microbiome imbalance.

Gut microbiome imbalance can increase the risk of Candida overgrowth, small intestinal bacterial overgrowth (SIBO), and pathogenic overgrowth. In the long run, this can lead to chronic inflammation, antibiotic resistance, digestive symptoms, other chronic symptoms, and the risk of autoimmunity (1, 2).

Antibiotics and Autoimmunity

Antibiotics can lead to gut microbiome imbalance, also referred to as gut dysbiosis. If gut dysbiosis turns serious, it can lead to chronic inflammation, poor immunity, and leaky gut syndrome. All these factors can increase your risk of developing an autoimmune condition (2, 3).

As a gastrointestinal specialist and SIBO naturopath, I see patients all the time who develop symptoms of ulcerative colitis, Crohn’s disease, or another autoimmune condition after several rounds of antibiotics. Patients with ulcerative colitis or Crohn’s disease may experience flare-ups after antibiotic use.

How to Restore Your Gut Microbiome While and After Taking Antibiotics

Avoiding antibiotics is, of course, the best way to protect your microbiome. However, in cases of serious infections, taking antibiotics is critical and unavoidable. Don’t skip antibiotics if you really need them.

So what can you do if you have to take antibiotics? Let’s look at how to protect and restore your gut microbiome while and after taking antibiotics:

Follow a Healthy Diet

Diet is always the first step. Remove any inflammatory foods, including refined sugar, refined oil, gluten, conventional dairy, overly processed foods, and food sensitivities. Eat plenty of greens, vegetables, herbs, spices, fruits, nuts, seeds, grass-fed meat, and pasture-raised poultry. Eat plenty of probiotic-rich fermented foods, including kimchi, sauerkraut, fermented vegetables, fermented herbs, coconut yogurt, coconut kefir, and kombucha (4).

Take High-Quality Probiotics

Take high-quality probiotics while and after taking antibiotics. Probiotics are good bacteria that help to restore your gut microbiome balance. If you have SIBO, I recommend taking soil-based probiotics. Other probiotics can disrupt your gut flora (5).

Try Collagen

Collagen can help to restore your gut microbiome and improve your gut health. Collagen is particularly important for the villi of your small intestine. The villi look like small little fingers. They help to take nutrients and transport them into your bloodstream to be absorbed. Collagen helps villi to stay healthy and support nutrient absorption. Collagen also supports your gut lining and reduces the risk of leaky gut syndrome (6, 7).

Try Some Microbe-Fighting Herbs

If you are dealing with serious microbiome imbalance and pathogenic overgrowth, you may try some herbs that can take care of bad bacteria and improve your gut flora. I recommend black walnut hull, sweet wormwood, berberine sulfate, and caprylic acid. Turmeric and ginger may help to reduce chronic inflammation in your gut as well (8, 9, 10, 11, 12, 13).

My Recommendation

If you have to take antibiotics or have taken a course of antibiotics recently, follow my tips to restore your gut microbiome balance naturally. If you are looking for natural treatment options for leaky gut syndrome or digestive issues from a Naturopath, I urge you to make an appointment today. As a gastrointestinal specialist and SIBO Naturopath, I specialize in Crohn's natural treatment, Ulcerative Colitis natural treatment, SIBO natural treatment, and many other digestive disorders.

Here are my three favorite supplements to combine together for gut health restoration:

how to restore gut health


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8. Amarowicz R, Dykes GA, Pegg RB. Antibacterial activity of tannin constituents from Phaseolus vulgaris, Fagoypyrum esculentum, Corylus avellana and Juglans nigra. Fitoterapia. 2008 Apr;79(3):217-9. doi: 10.1016/j.fitote.2007.11.019. Epub 2008 Feb 9. PMID: 18325686

9. Wicks S, Taylor CM, Luo M, Blanchard E 4th, Ribnicky DM, Cefalu WT, Mynatt RL, Welsh DA. Artemisia supplementation differentially affects the mucosal and luminal ileal microbiota of diet-induced obese mice. Nutrition. 2014 Jul-Aug;30(7-8 Suppl):S26-30. doi: 10.1016/j.nut.2014.02.007. Epub 2014 Feb 26. PMID: 24985102

10. Zhang L, Wu X, Yang R, Chen F, Liao Y, Zhu Z, Wu Z, Sun X, Wang L. Effects of Berberine on the Gastrointestinal Microbiota. Front Cell Infect Microbiol. 2021 Feb 19;10:588517. doi: 10.3389/fcimb.2020.588517. PMID: 33680978

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12. Scazzocchio B, Minghetti L, D'Archivio M. Interaction between Gut Microbiota and Curcumin: A New Key of Understanding for the Health Effects of Curcumin. Nutrients. 2020 Aug 19;12(9):2499. doi: 10.3390/nu12092499. PMID: 32824993

13. Wang J, Chen Y, Hu X, Feng F, Cai L, Chen F. Assessing the Effects of Ginger Extract on Polyphenol Profiles and the Subsequent Impact on the Fecal Microbiota by Simulating Digestion and Fermentation In Vitro. Nutrients. 2020 Oct 19;12(10):3194. doi: 10.3390/nu12103194. PMID: 33086593


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