Herbal Antimicrobials VS Antibiotics

barberry herbal medicine gut health parasites

Herbal antimicrobials is a subject I am very interested in.

With a bit of tweaking I managed to eradicate two parasites (Blastocystis hominis and Dientamoeba fragilis) using differrent herbal antimicrobials, immune boosters and anti-inflammatories.

As a student of herbal medicine I strongly believe that plants can offer something that pharmaceuticals like antibiotics cannot. They have a long history of safe use and when administered appropriately they can be very effective. Modern conventional medicine seeking to cure disease has followed the path of simplifying and reducing, focusing on an individual mechanistic solution to chronic disease. There is benefit to reductionist thinking and even though I hate to admit it, I am a bit of a reductionist.

That being said I do think that conventional medicine has many things wrong including heavy reliance on antibiotics.

Before I go too far down the doctor bashing route I think it’s important to mention that modern medicine has acute, trauma related injuries and disease well worked out! It’s the more chronic “western” or “civilised” diseases that they need help with.


The Complexity of Herbal Antimicrobials

An excellent point on the difference between pharmaceuticals and herbal medicine is seen in the use of antibiotics.

In the highly recommended book Herbal Antibiotics, Stephen Harrod Buhner writes about bacterial resistance to modern antibiotics and the comparative complexity of many herbs.

He uses garlic as an example writing that it “has been found to contain at least 33 sulphur compounds, 17 amino acids, and a dozen other compounds.” He continues “pharmaceuticals in contrast are usually made from one chemical constituent only” (1).

Many conventional protocols are now incorporating 2, 3 and sometimes 4 different pharmaceuticals when trying to eradicate antibiotic resistant organisms (2).

So far we have one strike against modern day antibiotics.

Overly prescribed they are helping to contribute to antibiotic resistant organisms that are becoming increasingly hard to treat conventionally. It is true that organisms can develop resistance to herbal antibiotics as well but the complexity of the herbs, especially in combination makes it much harder. Plus there is a long list of effective herbal antimicrobials to cycle through.


Don’t Forget the Gut And Herbal Medicine Connection

Next let’s talk disrupted gut microbiome.

Antibiotic use can cause dysbiosis, an imbalance in the gut flora. Knocking down the resident microbes leaves an unoccupied niche that the more opportunistic bacteria can grow into. Staphylococcus and Candida are prime examples of opportunistic organisms that can exploit a disrupted gut micro biome (3).

Dysbiosis is described as

“ a pathological imbalance in a microbial community that is becoming increasingly appreciated as a central environmental factor that is affected by host genetics, diet and antibiotic use. Furthermore, dysbiosis likely results from or is a cause of numerous disease states including atopy, autoimmune disease, inflammatory bowel disease (IBD), obesity, diabetes, non-alcoholic fatty liver disease (NAFLD), and hyperlipidemia” (4).

The list of potential issues arising from a disrupted gut microbiome is shocking to say the least. Add to the list neurodevelopmental disorders including autism and multiple sclerosis and we have a subject of huge importance (5).


Won’t Probiotics Fix The Problems With Antibiotic Use?

For the longest time we were told to follow antibiotics up with a round of probiotics.

This is still highly recommended but our thinking around probiotics has changed dramatically over the past few years. Up until recently it was thought that probiotics took up residence as part of our permanent gut flora, hence the recommendation after antibiotics.

Recent evidence is showing a different story. It appears that probiotic supplements are more like short staying guests. They come, they stay a short period of time, then they leave. High quality probiotic supplements are still highly recommended due to their beneficial influence on the immune system while they are present.

So far we have one strike against antibiotics for their increasing ineffectiveness and producing resistant bugs.

Add another strike against them for their gut biome disrupting mechanisms. Next let’s talk about possible herbal alternatives to antibiotics.


Herbal Antimicrobials And Their Use

Buhner lists the top 15 antibiotic herbs as Acacia, Aloe, Cryptolepis, Echinacea, Eucalyptus, Garlic, Ginger, Goldenseal, Grapefruit Seed Extract, Honey, Juniper, Licorice, Sage, Usnea and Wormwood. Obviously this is not the full extent of herbal antibiotics but they make a good start! (1)

Before we head straight into the ‘killing’ or the ‘weeding’ phase it is best to work on building yourself up.

Many adept Functional Medicine clinicians have outlined the importance of this step including Dr. Dan Kalish and Dr. Justin Marchegiani. Personally I have seen the effects on people that go straight into the killing phase when trying to rid a parasite and it’s not pretty. Generally there is the issues of severe side effects, even when using herbs, and more likely than not a lack of complete eradication of the parasite.


The 5 R’s of Gut Health

So how can you build yourself up before heading into the antimicrobial phase, hopefully using herbs. The 5 R’s of Functional Medicine come in handy here as a great way to lay out a program.

  1. Remove all offending foods
  2. Replace stomach enzymes and hydrochloric acid
  3. Repair your body – This can be accomplished by reducing stress and taking a load off of your adrenals, taking herbs and nutrients to help repair your mucosal lining in your GI tract, eliminating toxins, sleeping 8-9 hours each night, getting suitable exercise (not too much, not too little)
  4. Remove gut infections – Here is the ‘killing’ phase that people jump straight into. Many herbs work together and specific protocols can be worked out with your Functional Medicine practitioner
  5. Retest! It is very important to retest to be sure you have completely eradicated the parasite. Many times people skip this step because they feel much better only to become progressively more symptomatic over time. Herbal protocols can be repeated many times and should be if the test comes back positive.


Boosting the Immune System

In multiple books Buhner speaks on the importance of the strength of the host’s immune system when considering a herbal antimicrobial intervention. He quotes an insightful Chinese proverb “the man is not sick because he has an illness; he has an illness because he is sick” (1).

This speaks to Chinese Medicine’s traditional approach to keeping people well with regular acupuncture and herbs, even when the patient is not ‘sick’. Dr. Wright also speaks to this effect and writes about certain individuals in rural India that did not succumb to a cholera outbreak (due in part to sufficient stomach acid when tested) (8).


Making The Choice Between Herbs and Antibiotics, Natural Treatment and Pharmaceutical Treatment.

The choice between herbal antimicrobials and conventional medicine’s antibiotic approach is something that everyone has to decide for themselves.

To me it’s reasonably simple.

I would only consider antibiotics as a last resort, and for that I am happy we have them on hand.

Herbal antimicrobials are my first port of call. If after numerous rounds of different herbs I still haven’t managed to clear the infection then I would consider antibiotics.

What side of the fence do you fall on, herbs or antibiotics? Leave a comment below.


References and Resources

  1. Herbal Antibiotics – Stephen Harrod Buhner
  2. The challenge of Helicobacter pylori resistance to antibiotics: the comeback of bismuth-based quadruple therapy
  3. Are They Curing Us Or Killing Us? : The Catastrophic Impact Of The Over-Prescription Of Antibiotics On Our Health
  4. Emerging science of the human microbiome
  5. Human Microbiome: When a Friend Becomes an Enemy
  6. The Kalish Institute – Functional Medicine Training
  7. Justinhealth – Functional Medicine Clinician
  8. Why Stomach Acid Id Good For You
Legal and Affiliate Disclosures: This post may contain affiliate links. That means if you decide to make a purchase through one of these links, I may earn a small commission at no extra cost to you. Learn more here

You may also like


  1. Hey Todd, I stumbled on your website this morning and I can’t stop reading your articles. I have had a long term battle (about 8 years) with Blastocystis hominis – 3 goes with the big guns – including antibiotic infusion (3 antibiotics administered at the site in a colonoscopy). This was successful in eradicating the bug, but was super aggressive – and now it’s back again anyway.

    I have used a herbal treatment from Mullum herbals – along with raw garlic, nigella seeds and plenty of yogurt. I felt great after this treatment – but after a few months it was back again.

    I don’t want to go down the antibiotic path again – I’m sure it’s not the answer.

    What you say rings true with me and I am keen to try out some herbs and diet changes etc.

    Thanks for sharing your learnings…

    1. No problem at all!

      I am experiencing much the same as you and there are many others out there in the same boat. Glad that some of the info is helping.

      The mullum herbals protocol is decent although it may not be long enough for the tough to treat cases. Jason Hawrelak who helped developed the protocol talks about a three month approach with the lactulose prebiotic to help acidify the gut. Apparently the protozoan parasites don’t thrive in a lower pH.

      Keep us posted on your progress so we can all learn what helps.

  2. Hi, I’m looking for help with herbal remedies for Dientamoeba fragilis
    Blastocystis species
    This is for my 18 yo daughter. She has been given 3 courses of Flavyl over 12 months but is still infected with the parasite and as a result is gluten intolerant. Appreciate any guidance you can provide.

  3. Hi Todd,
    First and foremost, I have to leave you with a big thank you for the time and effort you put into your helpful articles. Because of SIBO I got the recommendation to use digestive enzymes. In your article you wrote that these should be replaced.
    Do they have a bad effect on the intestinal flora or what exactly is the reason?
    Should the enzymes be replaced with motality enhancing herbs like ginger?

    Thank you very much!

    Translated with http://www.DeepL.com/Translator (free version)

Leave a Reply

Your email address will not be published. Required fields are marked *

Hello. Add your message here.