Clove: Herbal Medicine for the Gut

I use a ton of clove in my herbal medicine dispensary. So much so that it was one of the first few herbs that I bought in bulk to make my tinctures from scratch with. As I treat mainly gut health in my practice what makes clove so appealing? Today we will be diving into the research and the traditional knowledge around clove including what it is used for and how I tend to prescribe it. 

Clove. An Introduction

Syzygium aromaticum known as clove originated in the Maluku islands in Indonesia but is used in the Ayurvedic and Chinese Medicine herbal traditions. It is used in many different ways and is considered to be a pain killer, antioxidant, antiseptic, anti-depressant, antispasmodic, anti-inflammatory, antiviral, antifungal, and antibacterial (1).

Image taken from: Edible Medicinal and Non Medicinal Plants

That’s quite the list of uses!

The last four, being anti-inflammatory, antiviral, antifungal, and antibacterial, are of particular interest to me as a gut focused herbalist. I spend much of my time trying to balance the microbiome, either in the small intestine as SIBO, or in the large intestine as bacterial infections, overgrowths or even parasite infections. 

For a deep dive into SIBO head over and read The Complete Guide to Small Intestinal Overgrowth. You can even download the guide as an ebook and read it at your own pace. 

What Is In Clove?

As most of you would have guessed, clove’s main claim to fame is it’s aromatic essential oil. In fact 20-30% of the clove bud is essential oil. Eugenol makes up the majority coming in at 70-85% of the essential oil (2).

The oil from clove contains a number of other compounds including A-caryophyllene, humulene, isoeugenol, eugenyl acetate, flavonoids, and cinnamic acids (3). It also contains tannins and triterpenoids (4).

So far eugenol is getting all of the attention and is considered the main ‘active constituent’ in clove – I do dislike the idea of active constituents and prefer to think about the whole herbs and the synergy between all of the constituents but we’ll go with it for now.

Let’s dig into the properties of eugenol and why it is such a powerhouse when it comes to gut health.

Image taken from: Syzygium aromaticum L. (Myrtaceae): Traditional Uses, Bioactive Chemical Constituents, Pharmacological and Toxicological Activities showing some of the impacts that the active constituents have on the body. 

Clove’s Main Ingredient – Eugenol 

Many consider eugenol the active constituent in clove so we will discuss it here. Just keep in mind that if you focus too closely on one constituent you may miss the real magic of herbs as medicine. 

Besides clove the polyphenol eugenol is found in a number of other herbs including different basils and cinnamon (5).

Image taken from: Clove: Overview of Potential Health Benefits

There are a number of antimicrobial actions that we can attribute to eugenol – see the image below if you are more of a visual person. Within offending microbes eugenol has been shown to

  1. Disrupting the cell wall
  2. Change the fatty acid membrane
  3. Producing reactive oxygen species
  4. Inhibit their enzymes
  5. Affect the transport of ions and ATP (cellular energy)

Each of these points decreases the infectious microbe’s ability to thrive and survive. Enough eugenol winds up killing the microbe (5).

Image taken from: Antimicrobial activity of eugenol and essential oils containing eugenol: A mechanistic viewpoint

When To Reach For Clove?

Clove is helpful with most forms of dysbiosis, be it SIBO screened for with a SIBO breath test, large bowel infections and overgrowths of bacteria, fungi and even parasites often found using stool testing like The Complete Microbiome Mapping test (the Australian version of the GI MAP).

Let’s break down the science for each. 

clove herbal medicine byron bay naturopath naturopathic medicine gut health herbalist australia

Bacterial infections and overgrowths

Clove has been found to be active against a whole range of gram positive and gram negative infections and overgrowths including (6).

  • Staphylococcus aureus
  • Bacillus cereus
  • Enterococcus faecalis
  • Listeria monocytogenes
  • Escherichia coli
  • Yersinia enterocolitica
  • Salmonella enterica
  • Pseudomonas aeruginosa

Clove bud extracts are even helpful when microbes such as Staphylococcus aureus develop resistance (known as MRSA) to many of the commonly used antibiotics (7).

Eugenol (the main component of clove oil) along with cinnamaldehyde (the main component of cinnamon) have been shown to inhibit the growth of 31 strains of Helicobacter pylori and was more potent than an antibiotic commonly used to treat this infection. Helicobacter pylori did not develop any resistance (8).

The list of bacteria that clove has been shown to be effective against goes on and on. 

Campylobacter jejuni is of particular interest to me. Many patients that present in the Byron Herbalist clinic have a history of food poisoning. Campylobacter jejuni is one of a few bacterial infections that can cause serious food poisoning which can then set the stage for ongoing digestive health issues and even small intestinal bacterial overgrowth (9). More on post-infectious SIBO here.

Clove essential oil has been shown to be an effective antimicrobial against Campylobacter. One research team in Hungary demonstrated this. They found that clove essential oil acted on Campylobacter in a number of ways  

  • Upsetting Campylobacter’s expression of virulence factors – fancy science speak for the bacteria’s ability to invade and cause issues.
  • Alter Campylobacter’s gene expression. Clove essential oil treatment showed an increase in stress genes.
  • Caused Campylobacter to straighten and shrink 
  • Campylobacter lost the ability to move 

Finally, the study showed that there was more at work than just eugenol, often considered the ‘active constituent’. The researchers found that linalool, terpinen-4-ol, and calamenene were also antimicrobial and effective against Campylobacter jejuni (10).

Antifungal Properties of Clove

The main antifungal property of clove comes, again, from eugenol. The thinking here is that this particular compound can induce lysis in the fungal overgrowth. 

Lysis – the breaking down of the membrane of a cell – Wikipedia

Clove oil and eugenol has evidenced antifungal activities against Candida, Aspergillus and dermatophytes including Microsporum canis, Microsporum gypseum, Trichophyton rubrum, Trichophyton mentagrophytes and Epidermophyton floccosum

The in-vitro study showed the antifungal properties of eugenol and clove oil were, at least in part, due to their ability to penetrate the fungal cell wall. ‘The fungicidal effect resulted from an extensive lesion of the cell membrane’ (11).

clove herbal medicine byron bay naturopath naturopathic medicine gut health herbalist australia

Cloves are Anti-inflammatory

This last little piece is of interest for a number of reasons.

In traditional medicines clove has been used for upper respiratory congestion and for musculoskeletal pain as well. Often we find that science backs up the views of herbal medicine traditions. 

The anti-inflammatory effects of the eugenol containing clove oil is due to its ability to inhibit cyclooxygenase-2 (COX-2) (12).

More to Clove Than Expected

We didn’t spend a whole lot of time exploring clove during my clinical herbalist training. The more I look into the herb the more impressed I am. Not only is it a potent antimicrobial showing effect against numerous bacterial infections and overgrowths as well as being antifungal, it also has more to give. 

Clove appears to be hepatoprotective. This means that it can protect the liver from damage much like the renowned milk thistle. One animal study showed that clove protected the livers of rabbits from paracetamol induced damage (13).

Yet another study showed hepatoprotective activity. Administering eugenol-rich fraction of clove to cirrhosis models showed a decrease in ALP and GGT (markers of liver damage) and other biochemical changes in liver cirrhosis (14).

While this isn’t the first herb I turn to when I am looking to support and protect the liver it is a handy additional bonus.

Finally, cloves appear to have properties that may support its use in cancer. There are a few studies exploring the impact of clove on cancer progression. One animal study showed that clove reduced the proliferating cancer cells and increased programmed cell death (apoptosis). Clove also down regulated a number of growth-promoting proteins (15).

I prefer not to look at herbal medicines as anti-cancer agents. Rather looking at the mechanism of action (reducing proliferating cells, increasing apoptosis, etc) helps us to learn how the herb is impacting the body and correcting imbalances. 

Final Thoughts on Clove 

Clove as a herbal medicine wasn’t top on my list when I started practicing as a clinical herbalist here in Byron Bay, Australia. Over time I have found myself using more of it and getting great results. 

It is antibacterial, antifungal and even anti-inflammatory. Clove contains a large amount of a well studied polyphenol, eugenol, as well as a range of other constituents that play their own role in the treatment of a range of digestive health imbalances. 

If, like me, you had not given clove the attention it deserves I urge you to take some time and explore this powerful plant medicine. 

References and Resources

  1. Syzygium aromaticum L. (Myrtaceae): Traditional Uses, Bioactive Chemical Constituents, Pharmacological and Toxicological Activities
  2. Phytochemical evaluation and pharmacological activity of syzygium aromaticum: A comprehensive review
  3. Clove: Overview of Potential Health Benefits
  4. Eugenol-rich Fraction of Syzygium aromaticum (Clove) Reverses Biochemical and Histopathological Changes in Liver Cirrhosis and Inhibits Hepatic Cell Proliferation
  5. Antimicrobial activity of eugenol and essential oils containing eugenol: A mechanistic viewpoint
  6. Antibacterial Potential of Elletaria cardamomum, Syzygium aromaticum and Piper nigrum, their synergistic effects and phytochemical determination.
  7. In vitro antibacterial activity of cloves (Syzygium aromaticum) against MRSA
  8. Antimicrobial activities of Eugenol and Cinnamaldehyde against the human gastric pathogen Helicobacter pylori
  9. Campylobacter jejuni: molecular biology and pathogenesis
  10. Antimicrobial and Virulence-Modulating Effects of Clove Essential Oil on the Foodborne Pathogen Campylobacter jejuni
  11. Antifungal activity of the clove essential oil from Syzygium aromaticum on Candida, Aspergillus and dermatophyte species.
  12. Anti-inflammatory and antinociceptive activities A of eugenol essential oil in experimental animal models
  13. Syzygium Aromaticum: A potential hepatoprotective agent
  14. Eugenol-rich Fraction of Syzygium aromaticum (Clove) Reverses Biochemical and Histopathological Changes in Liver Cirrhosis and Inhibits Hepatic Cell Proliferation
  15. Clove ( Syzygium aromaticum L.), a potential chemopreventive agent for lung cancer
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  1. Hello! I found your article of high interest as I just recently learned through DNA testing and complete stool testing that I have an overgrowth of Kliebsiella oxytoca, Enterococcus faecalis and Pseudomonas aeruginosa. I am very interested in utiziling clove and wonder how I might purchase the type you’re referring to for medicinal purposes. Thank you for any resources you might offer.

    1. Hi Ami, thanks for your comment. The clove that I use in my clinical practice is a 1:2 tincture (very strong whole plant extract) that I make myself. I am restricted by our Australian TGA from providing to anyone except the patients I work with. Unfortunately I don’t believe it is available in a retail product (you may find clove oil but this misses some key constituents). Wish I could be more helpful! Best, Todd

      1. Todd,

        We are a Laboratory and we produce clove-based extract HTBE (Highly Titrated Botanical Extracts). I would be pleased to exchange with you by email or LinkedIn or any way of communication. Our website is and of course, we are fully dedicated to the world of Clove !

  2. Thank You! I read the entire article and am now about to post it on an authors Facebook page that promotes Veganism. In doing so, I will be providing a Header Link giving you credit for your work. Thank You once again!

      1. Hi Todd, I’ve been recommended to take clove oil (1:1) 3 times a day after meals (total of 5ml of clove oil a day). Just wondering if it seems like a big dose with my history of UC (IBD) and Gilbert’s syndrome (affecting my liver). I’d appreciate your thought. Thank you

        1. Hi Ania, yes this does seem like a large dose. I prefer to start with the whole herb and work up to the extracts and oils only if needed. Clove has a bunch more to offer than just the essential/volatile oils 🙂

  3. Hello,
    I wish I could work with you but I live in the US.
    How should you take herbal extracts? With or without food? 2 or 4 times a day?
    I will sometimes blend fresh oregano, thyme, clove spice, and lemon zest in blender and strain and drink. Is that a good way to take herbs also? I find this somewhat effective in helping my constipation from what I believe is hydrogen sulfide/ methane SIBO. Also have crohn’s that was in remission for a long time on the Specific carbohydrate diet. My only real problem is constipation and insomnia now. I still follow a very limited SCD. I think it is bilophilia overgrowth, along with strep, staph, psudomonas and bacillus. I would like to kill down with herbs, and use probiotics Biogaia drops don’t seem to be working that well.

  4. Do you have any research showing the effect of clove on beneficial acetate-producing bacteria such as Bifidobacteria? I read that garlic kills Bifido, but I could not find anything regarding clove.

    Would you take clove hours before ingesting any probiotics or probiotic foods like yogurt?

      1. I’m glad I found this website. Thank you so much for this article. I am in USA, recently diagnosed with H. Pylori. I used whole clove buds in July 2021 and it helped me tremendously. I would just chew 3-4 cloves straight up, 3-4 times a day. But I was not diagnosed at that time though. Now that I have a diagnosis, I want to resume using this, but do not want to chew them anymore for obvious reason – it destroyed my taste buds. I’m glad to know that encapsulating the powder is an option. What size capsule would you recommend and dosage suggestion please ? Thank you in advance. I would like to treat using herbs I already have in my kitchen than using the synthetic antibiotics.

      2. Hi, any success with treating enteroccus faecalis? And are there herbs that can be used to increase the effectiveness of antibiotics especially for this bug. I have oregano oil but wondered if I should wait until AB treatment is finished. They started me on augmentin forte for 3 full I’m on amoxil 500 3x a day. I’m on day 6..urine came back still positive. Do you do appointments interstate? I’m in Perth WA

  5. Hi Todd. Thanks for this info. Whole cloves have always been part of my travel kit – used to make a tea with. Currently I’m investigating whether clove would be a good choice to treat my SIBO. If I were to make a tea with cloves for this, may I ask, how would I go about administering it? How many cloves, steeped for how long, how many times a day, and for how many days. I appreciate you, your work and time. Thank you.

  6. What was the moderate daily dosage of clove (in ml) that was used in the methane case study on your youtube channel?

  7. Hi, will cloves have a negative effect on the microbome? Will it affect genus/species like lactobacillus, bifido, akkermansia, Faecalibacterium Prausnitzii, Roseburia, prevotella, etc. Thank you.

  8. As a herbalist in Canada, cloves has been a relatively new comer to my herbal armamentum. It is extremely potent with broad spectrum effects in all the different categories that Todd outlines. I use it principally for inflammation along with other herbs. Some people find that the higher doses can cause herx die off symptoms which produce brain fog and a sensation of mild pressure in the head or behind the eyes. When using this medicine remember to drink lots of water, supplement with herbs to support lymphatic drainage and keep the bowels moving.

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