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Anti-Microbial Herbs for Dysbiosis

By Claire Bacon, ACN, CNC

Have you ever suspected you may have a gut infection, like parasites, yeast, or mold?  These infections are sometimes hard to figure out and can become persistent.  The failure to properly identify one of these gut issues can be detrimental, as seemingly unrelated problems such as hormonal imbalance or fatigue may arise. Because your immune system is stressed – constantly fighting the infection – your cortisol levels rise in response to stress, and sex hormone levels will drop because your body is using all its raw materials to produce excess cortisol. Did you know that herbs can help?

When left untreated, parasites can damage organs, tissues, muscle and cause the immune system to develop auto immune disorders due to the chronic inflammation and toxins from the parasites. Combine parasites with other things like bacteria and fungus and it creates the perfect storm to create serious conditions. Weight gain, infertility, acne, and menstrual irregularities can occur, in addition to more obvious digestive symptoms like gas and bloating.

But luckily, there are so many things you do to take back control over your gut! Nature gives us a million herbs with anti-microbial properties. I’m sure we don’t even know all the herbs we could use! We have a brief list for you below, with some of our favorite products to easily get these benefits working for you.

Anti-Microbial Herbs for Parasites

Common parasites that can infect the human gut include:  various worms, Giardia, amoebas like hystolitica, Cryptosporidium, Blastocystis, and Dientamoeba fragilis.  They generally enter the body from contaminated food or water.  Your stomach acid should kill them as they enter, but if your stomach acid isn’t working well, they have a better chance of surviving and infecting you. 

Causes of weak upper digestion include: 


The dried and ground green hull of the Black Walnut contains tannin, which is organic iodine, as well as juglandin, extractive matter from the juice of the green shucks of the walnut. Black walnut has been used for centuries to expel various types of worms, including parasites that cause skin irritations such as ringworm. It oxygenates the blood, which also helps kill parasites. Black Walnut is very effective against tapeworms, pinworms, Candida albicans (yeast infections) and malaria. It is also effective in reducing blood sugar levels, and helping the body rid itself of toxins.

Did you know? Black Walnut is included in our Wormwood Complex product, and in Biotics Ultra VirX and HistoPlex. We also carry Orthomolecular Paracid Forte.


This is one of the most powerful tools in the parasite-killing herb kingdom. It is most effective against roundworms, hookworms, whipworms and pinworms. Wormwood contains the potent chemicals thujone and iso-thujone, which are the primary components that kill parasites. Also known as Artemisia, Wormwood also contains santonin, an effective remedy for parasitic diseases.

Wormwood is the second most bitter herb known to man and has been proven as an effective remedy for malaria. It also contains sesquiterpene lactones, which work similarly to peroxide by weakening the parasites membranes therefore killing them. This herb also promotes bile production, which helps most digestive functions and prevents constipation.

Our favorite products are Wormwood Complex from Mediherb and Dysbiocide from Biotics. We also carry Paracid Forte from Orthomolecular.


Cloves contain eugenol, caryophyllene, and tannins, which are powerful antimicrobial agents. These components travel through the bloodstream, killing microscopic parasites and parasitic larvae and eggs. Eugenol has a pleasant, spicy, clove-like odor, and is the main biologically active compound in clove cigarettes.

Cloves are tremendously effective in killing malaria, tuberculosis, cholera, scabies and other parasites, viruses, bacteria and fungi, including Candida. Cloves also destroy Pseudomonas aeruginosa (a pathogen from plants), all species of Shigella, Staphylococcus, and Streptococcus.

Guess what? We mentioned Wormwood Complex above; it also contains cloves! In addition, we may recommend Orthomolecular Intestin-ol, or Biotics Bio-HPF.


Thyme contains flavonoids that are most commonly known for their antioxidant activity, and thymol and carvacrol, which are effective in killing bacteria, fungal infections, and yeast infections. It is especially effective in killing hook-worms, roundworms, threadworms and skin parasites. Thyme also destroys Cryptococcus neoformans, Aspergillus, Saprolegnia, Salmonella typhimurium, Staphylococcus aureas, and Escherichia coli.

Used as an antibiotic, thymol is 25 times more effective than phenol (a manufactured substance found in a number of consumer products known to cause liver damage), yet less toxic to parasites. Many years ago, Thyme was the primary ingredient in the original LISTERINE® mouthwash because of its germ-killing power.

Thyme is a key ingredient in Mediherb products Broncafect and ResCo.


Hyssop contains essential hormone oil that is very effective in destroying a variety of parasites and is very effective against the herpes simplex virus. In our office, we carry the product Hyssinol from Premier Research labs.


Garlic is known to slow and kill more than 60 types of fungi and 20 types of bacteria, as well as some of the most potent viruses known to humans. It has a long history of killing parasites and controlling secondary fungal infections, detoxifying while gently stimulating elimination, and has antioxidant properties to protect against oxidation caused by parasite toxins.

Allicin and Ajoene are the components in garlic that kill parasites, including one-cell varieties, as well as pinworms and hookworms. Allicin is not present in garlic in its natural state. When garlic is chopped or otherwise damaged, the enzyme alliinase acts on the chemical alliin converting it into allicin. Ajoene is the principal chemical responsible for garlic’s anticoagulant properties and contributes to its strong odor.

Did you know, garlic has antimicrobial properties, including antibacterial, antiviral, antifungal, antiprotozoal, and antiparasitic benefits. This herb effectively kills:

  • Bacillus subtilis (which also produces Nattokinase, by the way)
  • Escherichia coli,
  • Proteus mirabilis (often antibiotic resistant)
  • Salmonella typhi and enteritidis,
  • Methicillin-resistant Staph aureus,
  • Staphylococcus faecalis,
  • Vibrio cholerae
  • Citrobacter,
  • Klebsiella,
  • Hafnia, and
  • Aeromonas.

It is also very effective against Mycobacterium tuberculosis. Garlic also eliminates Candida albicans. Feel like you need a therapeutic dose? Try out Garlic Forte from Mediherb. It’s the most potent Garlic supplement we recommend!


This herb is known to be antiparasitic. Fennel seed is used to help remove and expel parasites and their wastes. Fennel is also very effective against Candida albicans. You will love finding new ways to use fennel in your diet! Of course it’s delicious just roasting it with other vegetables. Check here for our favorite recipes.

Fennel is one of our favorite herbs to promote lung health – whether you’re recovering from an infection or dealing with chronic asthma – even exercise-induced asthma. Fennel is a key herb present in Mediherb ResCo and PulmaCo.


As a member of the Capsicum genus, cayenne is known for promoting:

  • healing,
  • improved circulation,
  • cleansing,
  • indigestion,
  • urinary tract health, and
  • colds and flu.

Among other benefits too numerous to mention, cayenne also destroys parasites. 🙂

Cayenne is one of the key herbs in Mediherb Sinus Forte. Could it be possible to have parasite infections in your sinuses?!? Yes!! Cayenne is also included in Biotics Bio-Immunozyme Forte – a wonderful multivitamin for general immune support.


The components of gingerol, the active constituent of fresh ginger, destroys parasites including the roundworm, the blood fluke, the anisakid worm, and the Salmonella bacteria. You can easily add fresh ginger to your diet – either in a smoothie or chopped in a stir fry. And when you eat sushi – you want to eat the pickled ginger! It’s there for a reason – to stimulate your digestive acids and kill “whatever” might be hiding in the raw fish!

If you need an extra bump to your digestive system, consider Mediherb Digest Forte, which contains ginger. Other choices might include Biotics KappArest (broad anti-inflammatory support) or Motility Pro from Orthomolecular.

Always eat the ginger with your sushi!

This herb is wonderful for ridding the body of parasites including plasmodia, which is a malaria-causing parasite. Gentian is also good for treating anemia and counteracting the effects of parasite toxins in the body by stimulating the liver to produce more bile.

Your digestive system could benefit greatly by including Digest Forte in your protocol. It includes Gentian, Ginger, Wormwood, Tangerine, and Feverfew – all well known herbs to promote digestive acids and reduce the potential for “infestation”. Are you vegetarian? You may like to check out this special blend from Orthomolecular called Digestzyme-V – designed for vegetarians and including gentian.



Silymarin is the primary component in Milk Thistle that removes liver toxins. Milk Thistle promotes liver cell regeneration, and its antioxidant action protects against cell damage from toxins. Milk Thistle is most helpful in cleansing the toxins given off by parasites. And Milk Thistle Forte or LivCo are two easy ways to ensure you get a good daily dose. Especially on nights when you go out drinking! Milk Thistle has a protective effect on the liver. It protects from damage caused by alcohol, and by microbes, as well!


Marshmallow Root contains mucilage, a gummy substance obtained from certain plants. When Marshmallow Root gets wet, it becomes soft and sticky, which soothes the mouth, throat, stomach and intestinal tract. When parasites are dislodged from body tissue, they can leave an open sore. Marshmallow Root coats these sores so there is less irritation.

When you need it, it’s so easy to get the benefits from Marshmallow if you can keep Herbal Throat Spray in your purse. The Marshmallow extract is soothing to irritated throat tissues. Great to use at the first sign of a cold, or even for a long day of public speaking!


Pau d’Arco is used for Candida, yeast infections, fungal infections, viral infections, and parasitic infections. It also helps relieve cystitis, prostatitis, ringworm, gonorrhea, and syphilis. Pau D’Arco is one of the most powerful antioxidants known, and stimulates the immune system. Pau d’Arco also helps relieve leaky bladder syndrome. (Could that be because parasites might be disrupting proper bladder function?) Try it and see if you find relief!

In our office, we have a plentiful supply of Nature’s Way Pau d’Arco. This is one of our most affordable products that can go a long way towards getting your gut environment right! Contact Traci at our front desk to order.


Burdock removes accumulated waste and toxins from the skin, kidneys, mucous and serous membranes. A very effective blood purifier, Burdock is wonderful for head, face and neck skin problems including, eczema, psoriasis, boils, carbuncles, eyesores, and dermatitis.


This herb is to the lungs what Marshmallow Root is to the digestive tract. It is a natural expectorant, which helps coat and soothe the lungs as impurities are coughed up and expelled. Elecampane also has an antibacterial effect that purifies the lungs.


Licorice is also an expectorant and demulcent just like elecampane and fenugreek. It also is an anti-inflammatory, anti-spasmodic and mild laxative. It purifies the organs and the endocrine system, especially the liver. With so many benefits, we recommend it often for different reasons. For immune support, Viranon might be the best choice for seasonal flu, shingles, or problems with warts. We might think of ResCo when an immune challenge might prominently affect the lungs.



The ingredients of Barberry, columbamine, berberine, and oxyacanthine, have antibacterial and antiviral properties. Research indicates that berberine in Barberry is specifically effective against cholera, giardia, Shigella, Salmonella and E. coli. The berberines aid in the secretion of bile and are good for liver problems.

Barberry is also a mild laxative and helps the digestive processes. Barberry also helps with Staphylococcus, Streptococcus, Salmonella, cholera and chronic candidiasis (yeast). Berberines are highly bactericidal, amoeboidal and trypanocidal.  Barberry acts the same as chloramphenicol, a commonly prescribed antibiotic drug. Barberry helps to purify the respiratory and digestive systems, and also has an antiparasitic effect. We highly recommend Biotics Bio-HPF as a rich source of Barberry and other antimicrobial herbs.


Also known as Buckthorn, Cascara Sagrada stimulates increased wavelike contractions of the large intestines. Cascara has also been known to expel parasites through its wavelike actions in the lower intestines, and is highly recommended during parasite removal. Cascara Sagrada is considered one of the safest laxatives and is useful in detoxifying the colon. Our favorite herbal laxative is Colax – an effective blend containing Cascara Sagrada. Just one or two tablets at bed – with a full glass of water – should do the trick!


Senna is a powerful laxative that is excellent for expelling worms. It works best when combined with other anthelmintic herbs (used in the treatment of roundworm), such as ginger or fennel. These herbs increase regularity and reduce the chance of bowel cramps due to Senna’s strong action. Senna effectively cleans the elimination system, and has a vermifuge action that repels parasites. Senna is the ingredient in many over-the-counter laxatives. We recommend Southern Botanicals’ Intestinal Cleanse I.


Sage has the power to relax the muscles lining the digestive tract. It contains relatively high levels of thujone which is the same ingredient in wormwood that kills parasites. Sage is also used to increase circulation, and is considered an excellent remedy for poor digestion and stomach problems. Not only that, Sage is a cooling herb that can also be helpful with hot flashes! It’s found in Biotics Ultra-VirX and Mediherb Wild Yam Complex.


Psyllium removes toxins from the colon and is useful in cleaning out all of the pockets in the colon wall. It swells up to 50 times its size, and is powerfully effective in removing waste and toxins from the colon. Psyllium husk is the main ingredient in Gastro-Fiber. We sometimes use it as part of our 21 Day Cleanse program. It’s excellent for improving bowel motility and sweeping out unwanted toxins!


Works as a laxative, but unlike other laxatives, yellow dock also promotes bile flow, which purifies the blood. It is rich in digestible iron that helps restore blood nutrients to the body. You can find this herb in DermaCo. It’s a blend of herbs specifically selected to clear impurities from the blood, and clear inflammation and acne from the skin.


The components of Cramp Bark (Vitamin K, viburnin, isovalerianic acid, hydroquinines, coumarins, salicin, salicosides, arbutin, sterol, tannin, and resin) greatly calm gastrointestinal cramping by relaxing the smooth muscles. It also helps with general muscle cramping; reducing any cramping that might occur while the colon is working to expel parasites. We like to order this herb in a bulk powder from Mountain Rose Herbs. You can add it to a tea in a looseleaf tea bag.


Peppermint is well known for relieving indigestion, but it also relaxes the stomach muscles, relieves gas, and is also good for nausea and vomiting. It also has anti-parasitic properties. You may like to use a topical essential oil blend like DigestZen, or a strong peppermint tea with meals.

So Many Choices!

Yes! Nature gives us sooo many choices! That’s where muscle testing comes in. Sometimes we can listen to your history and what you’re dealing with, and feel confident which herbs to use based on our experience. Other times, when it seems there are too many great choices, we may like to use muscle testing to check your energetic compatibility with different formulations.

A Comprehensive Approach with Anti-Microbial Herbs

If you keep your gut in good balance and eat well and take herbs specific that help keep infestation away you should only need to “de-worm” every six months. So this may include starting with a couple cleanses, cleaning up diet and moving forward. You may also like to consider hyperbaric oxygen therapy, ozone, and/or high dose vitamin C.

We utilize several targeted approaches in our practice, and we can modify any protocol to suit your individual needs. Let us know if you would like some guidance on clearing infections and improving your gut health – once and for all!

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