Antimicrobial herbs are the top natural treatment for gut issues, like SIBO, dysbiosis, parasites and yeast overgrowth.

Here’s all you need to know and how to use them.

Antimicrobial Herbs 101

garlic and different types of Antimicrobial herbs

Herbal therapies have been used for centuries as the preferred “drugs” of choice for addressing illness—from stomach aches, viruses, colds and flu’s.

Long before researchers mentioned the words “gut microbiome,” people knew there was powerful healing in nature’s medicine for reversing disease.

Types of Antimicrobial Herbs

Some of these powerful herbal agents include:

  • Peppermint
  • Berberine
  • Garlic (Alicin)
  • Olive Leaf
  • Oregano Oil
  • Grapefruit Seed Extract
  • Pau d’arco
  • Black Walnut
  • Resveratrol
  • Licorice
  • Echinacea
  • Goldenseal
  • Oregon grape
  • Barberry

  • Wormwood
  • Thyme
  • Stinging Nettle
  • Uva Ursi
  • Yerba Mansa
  • Caprylic Acid
  • Cat’s Claw
  • Manuka honey
  • Tea tree oil
  • Curcumin
  • Clove
  • Cinnamon
  • Astragalus Root
  • Colloidal silver


“Antimicrobial” protocols—herbal therapies—are often part of a “healing” gut protocol if dysbiosis (too much or too little gut bacteria), SIBO, fungal or yeast overgrowth, parasites or gut infections are identified as a “root cause” behind poor health.  Treatment of these  “gut issues” typically a two-stage treatment approach:

  1. Eradicate or reduce pathological organisms
  2. Restore a healthy gut microbiome

In most cases of dysbiosis, except for significant fungal overgrowth, a short period of antimicrobials (30-60 days) commences, followed by a more significant focus on restoring the healthy gut microbiome.

Generally speaking, a blend of botanical herbs in supplement form is recommended for most cases of dysbiosis for a “broad spectrum” approach to healing. However, depending on the certain pathogenic organisms identified on a stool or SIBO breath test, some people find treating specific organisms with research-backed specific agents may be effective (such as grapefruit seed extract for the overgrowth pseudomonas aeruginosa).

Lastly, given the fact that antimicrobial herbs can be powerful, is also recommended you combine antimicrobial treatment with adjunct supports to aid in both complete eradication/reduction of pathogenic organisms, as well as the preservation of any healthy bacteria you do have. Support agents for an antimicrobial protocol include:

Antimicrobial Treatment: Support Agents

  • Quality probiotic & symbiotic (a probiotic + prebiotic).

To maintain a healthy gut microbiome as some bacteria die off. (Ideally taken away from antimicrobial herbs; particularly a soil-based bacteria). Medium-chain fatty acids extracted from coconut oil that are antiparasitic in addition to being antifungal, antiviral, and antibacterial. Great for boosting immunity and warding off yeast.

  • Biofilm Disruptor.

Pathogenic bacteria can form biofilm around their outer layer—sort of like “steel armor” for preventing destruction. Biofilm may be one of the primary drivers of resistance and treatment failure in multiple disease, antimicrobial and/or antibiotic treatments. Biofilm disruptors help break up biofilm to allow your other antimicrobial agents to work. (ex. NAC, Cranberry, Biocidin, Colloidal silver, Xylitol, Manuka honey, Interfase Plus)

  • Least Restrictive “Real Food” Diet. 

Many people go on an “anti-candida,” ketogenic or “no carb” diet while “healing their gut.” However, these can be counterproductive to resetting your gut microbiome, given the fact that some starchy plants and pre-biotics are needed to feed healthy gut bacteria and bring pathogenic bacteria “out to play.” Prebiotics found in starchy plants and veggies help your antimicrobials work even better (so there is bacteria for them to target). Aim for 1 to 2 servings per day of starchy plants and/or prebiotic fibers while on an antimicrobial herbs protocol.

“But isn’t medicine more powerful?”

Herbal therapies are at least as effective as rifaximin—the typical conventional antibiotic treatment for resolution of gut dysbiosis (i.e. SIBO, candida, parasites and IBS)—if not more. In one study, 104 patients diagnosed with SIBO with the lactulose breath test were treated either with Rifaximin (1,200 mg) or a cocktail of herbal antimicrobials (see below) for 4 weeks before repeating the lactulose breath test. 

The study showed that 46% of the patients treated with herbal antimicrobials were successfully treated while only 34% were free of SIBO after taking Rifaximin (1).

 Recommended Antimicrobial & Support Agents to Buy

Here are my top recommended supplements for using in your “gut healing protocol.”


Sample Antimicrobial Protocol


  • Symbiotic Probiotic (probiotic + prebiotic)


  • Antimicrobial Herbs (broad spectrum supplement)
  • Monolaurin


  • Biofilm Disrupter


  • Soil Based Probiotic


  • Biofilm Disrupter


  • Antimicrobial Herbs (broad spectrum supplement)
  • Monolaurin

Post Dinner

  • Herbal Tea (optional)

Antimicrobial Protocol Treatment Timeline

  • Dysbiosis-Pathogenic (high amount of pathogenic and/or commensals bacteria): 60 Days
  • Dysbiosis-Healthy Overgrowth (high amount of “beneficial” bacteria on stool test and possibly yeast markers): 30 Days
  • Insufficiency Dysbiosis (lack of healthy bacteria with a few pathogenic bacteria): 30 Days, followed by emphasis on Probiotics & Prebiotics
  • Parasites: 60 Days
  • SIBO: Low/Mild: 30 Days, Moderate: 60 Days, High: 90 Days

 Beware: Herx (“Healing”) Reactions May Happen

A die-off reaction, also called a Herxheimer reaction or “Herx reaction”, can occur whenever you first start a new supplement or antimicrobial protocol—often a sign of a “detox” or die off of certain bacteria.

woman lying on bed with Herxheimer reaction Antimicrobial herbs

Typically, Herx symptoms develop within a couple of hours to several days after treatment and last anywhere from a few days to several weeks or months—depending on the severity of the underlying pathology you are treating. However, depending on the location of the bacteria, symptoms may develop later. The Herxheimer reaction is especially seen during antimicrobial treatments (gut healing protocol) because antimicrobials destroy numerous microorganisms and bacteria.

Although the Herxheimer reaction is typically not harmful, it does frequently cause temporary pain, discomfort, and worsening of symptoms. Symptom severity is often indicative of the level of inflammation triggered by the immune system.

Common symptoms that may develop or worsen due to a Herxheimer response include:

  • Bloating
  • Brain Fog
  • Chills
  • Cold Sweats
  • Constipation
  • Cramps
  • Diarrhea
  • Fatigue
  • Fever

  • Irritability
  • Joint Pain
  • Headaches
  • Lethargy
  • Muscle Pain
  • Nausea
  • Skin Irritation
  • Sore Throat


Because of the sudden worsening of symptoms, it is common for patients to feel that the severity of their condition has increased due to the treatment. However, even though treatment causes a temporary increase in symptom intensity due to greater release of toxins the condition ultimately improves. The body responding in this way usually means that the treatment is actually working effectively.

Nevertheless, even though a Herxheimer reaction indicates that treatment is working effectively, it doesn’t make the patient’s condition any more comfortable in the immediate.

Fortunately, there are several ways of limiting the symptoms of a Herxheimer reaction without inhibiting treatment efficacy. The following suggestions can and should be used when detoxing, using antibiotics, or being treated for infections and other forms of chronic disease to limit Herxheimer intensity, including:

How to Deal with HERX Reactions

  • Drink H20. Drink plenty of fluids to aid in the removal of toxins and help cleanse the GI tract.
  • Get Your Zzzz’s. The body conducts many restorative processes while at rest that it cannot accomplish when it is awake. When experiencing a Herxheimer reaction due to greater toxicity, it is best to allow more time for quality sleep.
  • Sweat. Sweat it out with heated yoga, sauna and daily movement—a natural essential for detoxification.
  • Try Dry Brushing & Rebounding. Two lymphatic “cleansing” tactics to help flush the lymphatic track.


  1. Chedid, V., Dhalla, S., Clarke, J. O., Roland, B. C., Dunbar, K. B., Koh, J., Justino, E., Tomakin, E., … Mullin, G. E. (2014). Herbal therapy is equivalent to rifaximin for the treatment of small intestinal bacterial overgrowth. Global advances in health and medicine, 3(3), 16-24.