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Natural Alternatives to Antibiotics

Updated: Jan 2

If you have been diagnosed with Sibo (small intestine bacterial overgrowth), Helicobacter Pylori, or any other bacterial infection in the digestive tract and you prefer not to take antibiotics, I have good news for you: Herbal and natural antibacterial substances are amazing alternatives for antibiotics and work just as successfully as antibiotic therapy (NOT my words, totally based on research!) There are certain natural substances that have a very significant impact on our gut bacteria's wellbeing, here are few of them: Berberin Berberin is a yellow ingredient extracted from various plants such as Goldenseal, Coptis Chinensis, Oregon grape, and Barberry grapes. Berberin has been in use for thousands of years in traditional medicine. Plants that contain Barberin have been used in ancient Chinese and Ayurvedic medicine to treat various gastrointestinal infections. In the past few years, Berberin has been thoroughly researched thanks to its potential health benefits outside the digestive system such as balancing blood sugar and cholesterol levels and helping treat Alzheimer’s and cancer. Thanks to its anti-inflammatory properties, Berberine has been found effective in treating various infections, with an emphasis on the gastrointestinal tract. It is found to be able to contribute to the health of the digestive system by encouraging the proliferation of friendly bacteria and fighting a wide range of harmful bacteria, such as Sibo and Helicobacter pylori, a bacterium that can cause stomach ulcers. Allicin Allicin is an active ingredient derived from Garlic. Besides being an important herb in our kitchen, Garlic has been widely used in ancient traditional medicine for thousands of years thanks to its healing properties. Allicin, its active ingredient, has been widely studied for its antibacterial, antifungal, antiviral, and immune-stimulating properties. As a matter of fact, Allicin appears to be very effective in treating Sibo, by helping break down colonies of bacteria and prevent their resistance to antibiotic treatment. It is also excellent as part of the treatment of systemic Candida and intestinal parasites.


Polyphenols are natural compounds found in plants and various foods such as fruits, vegetables, and spices. There are over 8000 types of polyphenols and they are rich in antioxidants and substances that help the body deal with diseases and inflammation. 5-10% of the polyphenols are absorbed in our small intestine and the rest make their way to the colon, where they are broken down by the bacteria into important metabolites. One of the most notable benefits of polyphenols is their beneficial effect on intestinal bacteria and their ability to repair damaged intestines as a result of inflammation or infection. Studies have found that the link between polyphenols and our gut bacteria is reciprocal: polyphenols alter the composition of bacteria, and the bacteria is responsible for the metabolism and breakdown of polyphenols into their bioactive metabolites.

Essential oils

Essential oils are found in plants in very small amounts (less than 1%), but they are strong enough to have a medicinal effect. They are absorbed into the bloodstream and have an effect on the whole body. In their pure form, essential oils are used for flavoring (such as lemon, garlic, etc.) and for healing purposes (eucalyptus, peppermint, etc.). They have a strong antiseptic and antibacterial activity and are also excellent for relieving abdominal pain and cramps. The antimicrobial components found in the oils manage to destroy harmful bacteria by breaking down their cell membrane. The leading antibacterial oils are oregano oil, clove oil, peppermint oil, and thyme oil. These oils may help treat a wide range of bacteria, infections, and fungi in the digestive tract.

Remember, even if you choose to treat your infection naturally, I recommended not to do it by yourself, but to work exclusively with a Naturopath or a qualified Clinical herbalist who will tailor the most accurate treatment for your needs.

Here are some great products from IHERB:

A natural alternative to antibiotics
Medical herbs


1. Yin J, Xing H, Ye J. Efficacy of berberine in patients with type 2 diabetes mellitus. Metabolism [Internet]. 2008 May [cited 2022 Jun 27];57(5):712–7.

2. Lan J, Zhao Y, Dong F, Yan Z, Zheng W, Fan J, et al. Meta-analysis of the effect and safety of berberine in the treatment of type 2 diabetes mellitus, hyperlipemia, and hypertension. Journal of Ethnopharmacology [Internet]. 2015 Feb [cited 2022 Jun 27];161:69–81.

3. Chen C, Yu Z, Li Y, Fichna J, Storr M. Effects of Berberine in the Gastrointestinal Tract — A Review of Actions and Therapeutic Implications. The American Journal of Chinese Medicine [Internet]. 2014 Jan [cited 2022 Jun 27];42(05):1053–70.

4. Ben Arfa A, Combes S, Preziosi-Belloy L, Gontard N, Chalier P. Antimicrobial activity of carvacrol related to its chemical structure. Lett Appl Microbiol. 2006 Aug;43(2):149-54

5. Si W, Gong J, Tsao R, Zhou T, Yu H, Poppe C, Johnson R, Du Z. Antimicrobial activity of essential oils and structurally related synthetic food additives towards selected pathogenic and beneficial gut bacteria. J Appl Microbiol. 2006 Feb;100(2):296-305

6. Reiter J, Levina N, van der Linden M, Gruhlke M, Martin C, Slusarenko AJ. Diallylthiosulfinate (Allicin), a Volatile Antimicrobial from Garlic (Allium sativum), Kills Human Lung Pathogenic Bacteria, Including MDR Strains, as a Vapor. Molecules. 2017 Oct 12;22(10):1711.

7. Ankri S, Mirelman D. Antimicrobial properties of allicin from garlic. Microbes Infect. 1999 Feb;1(2):125-9.

8. Chedid V, Dhalla S, Clarke JO, Roland BC, Dunbar KB, Koh J, Justino E, Tomakin E, Mullin GE. Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Glob Adv Health Med. 2014 May;3(3):16-24


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