39 Antimicrobial Herbs and Supplements: List & Expert Guidance

Antimicrobial herbs are a class of medicinal plants with natural antimicrobial actions in humans.  These make wonderful herbal allies for cases of infection and microbial overgrowth, whether acute or chronic.

An added benefit or advantage of working with antimicrobial herbs instead of their pharmaceutical counterparts is that they tend to be more targeted and less broad-spectrum.

In other words, herbs with antimicrobial properties may allow us to effectively eradicate infections without harming our probiotic (healthy) gut microbes. 

(I like to think of this as nature’s way of allowing us to dodge the collateral damage that so often follows taking a pharmaceutical-grade antibiotic.)

In fact, in many cases, antimicrobial herbs have actually been shown to be just as effective (if not more effective) than pharmaceutical antibiotics!

As a clinical herbalist and gut health dietitian, I often recommend and prescribe herbal antimicrobial supplements to help my clients address and resolve stubborn cases of dysbiosis, candida overgrowth, H. pylori, and/or small intestinal bacterial overgrowth (SIBO).

Read on to learn about the dozens of herbs that have antimicrobial properties, which herbal antimicrobial supplements have been the biggest game-changers for my clients, and how we can potentially work together if you’re seeking a custom protocol!

Disclaimer:  This article was written for general educational purposes and should not be taken as medical/nutritional advice. Consult 1-1 with your treatment team to receive recommendations tailored to your unique health goals and bio-individual needs.

Antimicrobial herbs list

The following herbs and herbal extracts have been shown to have antimicrobial properties, in vitro and/or in vivo according to research.

1. Agarita
2. Bayberry
3. Bee balm
4. Black cumin
5. Black walnut (Juglans nigra)
6. Cat claw bark
7. Calendula officinalis
8. Cinnamon
9. Cloves
10. Cumin
11. Cranberry
12. Echinacea
13. Epazote
14. Frankincense
15. Garlic extract 
16. Ginger
17. Goldenseal
18. Grapefruit seed extract
19. Green tea
20. Holy basil 
21. Japanese honeysuckle
22. Juniper berries
23. Licorice root
24. Neem
25. Nutmeg
26. Old man’s beard (LOL)
27. Olive leaf
28. Onion
29. Oregano
30. Pao d’arco
31. Papaya seeds
32. Rosemary
33. Sweet wormwood
34. Tansy
35. Tarragon
36. Tea tree oil
37. Thyme
38. Turmeric
39. Uva ursi

Note that some of these should be applied topically, while others can be safely taken internally.

Narrowing down your options: key considerations

While that may feel overwhelming, and you’re likely thinking “where do I start? How do I choose?!”…Remember this field is never something to navigate without clinical supervision from a qualified naturopathic doctor, functional dietitian/nutritionist, or clinical herbalist.

With that in mind, there are some key factors you and your qualified practitioner(s) should consider.

For example, to help narrow down your options, you may want to first take into consideration the type of infection, your (or your clients’) unique constitutional energetics, the ideal protocol duration, and best delivery method of your herbal antimicrobial protocol.

Some questions you and your team may to ask:

• Are you eradicating a specific strain of bacterial overgrowth? 
• Is it topical or internal, systemic or localized, acute or functional?  
• Will you need to manage or prevent any die-off symptoms? 
• Do you hate swallowing pills? (In this case you may prefer herbal tinctures)
• Are you a supertaster who can’t stomach the sensory experience of herbal tinctures? (In this case, herbal capsules or glycerites would be better!)

Based on personal and clinical experience, I also believe we’re generally better off going with a blend of herbs rather than a single extract, in most cases. 

Many roads can lead to Rome here, as long as you’re following an evidence-based protocol tailored to your bio-individual needs.  There’s no ONE right method.

Below are categories of the best antimicrobial herbs for common types of infections. (Disclaimer: Everyone’s microbiome [aka community of microbes living in and on our body] is as unique as our fingerprint, so please keep in mind one size never fits all.)

Best antimicrobial herbs and supplements for H. Pylori

Helicobacter pylori or “H. pylori” is a type of bacterial infection which can colonize (or set up camp) in our upper gastrointestinal (GI) tract, specifically in our stomach.  

It’s a nasty type of gram-negative, pro-inflammatory bacteria which is largely responsible for many cases of heartburn, ulcers, and even stomach cancer.

(About 50% of the population has H. pylori in our gut, but note that not all cases are harmful or symptomatic.)

However, symptomatic H. pylori infections left unchecked can potentially wreak havoc on our system and should be addressed with antibiotics or an herbal antimicrobial protocol.

The downside of H. pylori pharmaceutical antibiotics (while very effective) is they often kill off our healthy probiotic gut bacteria in the process.

As I mentioned earlier, antimicrobial herbs are less likely to cause the same level of collateral damage compared to their pharmaceutical counterparts when it comes to treating H. pylori infections and they can be just as effective when done properly. 

Below are the most effective research-backed herbs and supplements shown to play a role in inhibiting the growth and/or preventing adhesion (sticking) of H. pylori bacteria in our stomach: 

• Turmeric (1)
• Cumin (1)
• Chili (1)
• Black caraway (1)
• Ginger (1)
• Borage (1)
• Bismuth (1)
• Cranberry (2, 3)
• Green tea (or matcha) (4)
• Oregano (1, 5)
• Mastic gum (6)
• Black currant seed oil (7, 8)
• Pyloricil
• Berberine (9)

If you’d like support with an effective and evidence-based, customized H. pylori herbal protocol, and you live in the United States, I invite you to apply to work with me 1-1 [here] as a private practice client!

Best antimicrobial herbs and supplements for SIBO

Small intestinal bacterial overgrowth (SIBO) is a common underlying IBS imposter, in that the symptoms of SIBO are almost identical to the symptoms of irritable bowel syndrome (IBS).

The key difference from an etiology (cause) standpoint is that SIBO symptoms are caused by the underlying overgrowth of unhealthy microbes which have colonized in the small intestine.  

Since microbes generally don’t belong in our small intestine (they’re supposed to live in our colon), SIBO victims will usually experience pretty severe gas/bloating, alongside constipation and/or diarrhea and abdominal pain, caused by the fermentation of undigested food particles.

With SIBO being relatively novel in the world of gastroenterology, I’ve found in my private practice that the most common SIBO treatment challenges are (1) properly identifying and diagnosing SIBO (which often flies under the radar), and (2) keeping it from coming back after it’s been eradicated.

Since we can’t starve out SIBO microbes, they need to be killed with either Rifaximin (a pharmaceutical antibiotic) or with the right therapeutic blend of antimicrobial herbs.

As you’ll see below, there are specific herbs which have been shown to help eradicate specific types of SIBO which vary based on the type of microbial overgrowth.

Recommended reading:  Anatomy of a Holistic & Natural SIBO Treatment Plan

Methane SIBO

This is a type of SIBO which manifests (and often gets mis-diagnosed) as IBS-C, or constipation-dominant IBS.

It’s caused by an overgrowth of methane-producing microbes (aka “methanogens”) in the small intestine.

Constipation aside, a few tell-tale clues that you (or your clients) could be dealing with methane SIBO versus IBS-C would be:

• Weight gain
• Extreme fatigue
• Bloating no matter what you eat, which gets worse as the day goes on
• FODMAP intolerances (feeling better on a low FODMAP diet)
• Feeling worse after taking probiotics

Antimicrobial herbs for methane SIBO

• Oregano
• Allicin (garlic extract)
• Bismuth
• Black cumin
• Neem

Best methane SIBO supplements

• Atrantil
• Berberine
• Biocidin
• Biofilm Phase 2 Advanced
• Dentalcidin (oral mouth wash)
• Dysbiocide
• FC-Cidal
• Olivirex
• Candibactin AR & BR
• GI Microb-X

Recommended reading:  Anatomy of a Holistic & Natural SIBO Treatment Plan

Hydrogen SIBO

From a symptoms standpoint, hydrogen SIBO is very similar to methane SIBO except with diarrhea instead of constipation, and without the weight gain.

This type of SIBO is caused by hydrogen-producing microbes in the small intestine. The treatment protocol for hydrogen SIBO is very similar to that of methane SIBO.

Herbs for hydrogen SIBO

• Oregano
• Allicin (garlic extract)
• Bismuth
• Black cumin
• Neem

Best hydrogen SIBO supplements

• Berberine
• Biocidin
• Dentalcidin (oral mouth wash)
• Dysbiocide
• FC-Cidal
• Candibactin AR & BR
• GI Microb-X

Recommended reading:  Anatomy of a Holistic & Natural SIBO Treatment Plan

Hydrogen sulfide SIBO

Hydrogen sulfide SIBO is unique in that it often shows up as a flatline on a SIBO breath test. This has to do with the microbes consuming the hydrogen gases during the timeframe of the test.  

Hydrogen sulfide SIBO is caused by an overgrowth of hydrogen sulfide gas producing microbes such as Sulfibrio.

This type of SIBO is often responsible for a sulfur intolerance, which means foods as well as any herbal supplements containing garlic will most likely make you or your clients feel worse.

This protocol is different from the above SIBO protocols for that reason, and it also contains Uva ursi which can’t be taken for more than 30 consecutive days.

Herbs

• Oregano
• Black cumin
• Uva ursi
• Garlic-free herbal mouthwash

Supplements

• ADP Oregano (emulsified)
• Biofilm Phase II Advanced
• Atrantil (shown to help sequester hydrogen, which feeds the hydrogen sulfide-producing bacteria)

Recommended reading:  Anatomy of a Holistic & Natural SIBO Treatment Plan

Dysbiosis

Dysbiosis is a broad-spectrum term which essentially describes a state in which your gut is deficient in certain key healthy probiotic microbes, and/or high in “dysbiotic” (disease-promoting) unhealthy gut microbes.

Common examples of opportunistic and/or dysbiotic gut microbes associated with gut issues like IBS and/or inflammatory bowel disorder (IBD) include, but most definitely aren’t limited to:

• Klebsiella spp.
• Citrobacter freundii
• Morganella spp. 
• Pseudomonas spp. 
• Staphylococcus aureus 
• Streptococcus spp.
• Desulfovibrio spp. 
• Methanobacteriaceae 

Note that dysbiosis is a common underlying root cause of IBS as well as many other conditions related to our gut and immune system (think: inflammatory bowel disease and autoimmunity).

(If you’d like to know what kinds of microbes are living in your colon, for better or worse, you can find this out by running a comprehensive stool analysis test such as a GI MAP or Gut Zoomer.)

There are infinite ways to reduce dysbiosis, and I don’t recommend going straight to antimicrobial herbs if you haven’t first established a solid foundation in terms of optimizing your nutritional status, nervous system regulation and circadian rhythms.

I also have found in private practice (and from my functional dietitian mastermind) that many cases of dysbiosis can be “crowded out” with the right customized blend of you-friendly butyrate-producing prebiotics and probiotic foods/supplements.

Consider this BEFORE going straight to antimicrobial herbs, which aren’t always necessary or effective if the foundation hasn’t been properly set.

Recommended reading:

• Why & How to Increase Butyrate in Your Gut (Directly or Indirectly)
• Fiber and Probiotics: A Dynamic Duo
• Probiotic Foods List PDF (Free Download)
• Should You & Can You Take Prebiotics and Probiotics Together?
• Prebiotics vs. Probiotics

Best antimicrobial herbs and supplements for dysbiosis

In my functional nutrition practice, my clients have had success with various blends of the following types of herbs and herbal antimicrobial supplements (in no particular order):

• Oregon grape root
• Echinacea
• Goldenseal
• Agarita
• Oregano
• Thyme
• Rosemary
• Cinnamon
• Olivirex
• Biocidin
• Candicid Forte
• Undecylex™

Frequently asked questions (FAQ’s)

Is berberine for SIBO effective?

Yes and no! It depends on the context. In my experience and training, my understanding is that the whole is greater than the sum of its parts.  

In other words, berberine may be effective as part of a SIBO herbal protocol but it will not have the same level of effectiveness as a stand-alone intervention.

This is one of the many reasons I don’t recommend attempting to self-prescribe an antimicrobial herbal regimen without clinical oversight… you may not know what you don’t know!

Recap & final thoughts

There are dozens of different herbs with antimicrobial properties as shown on the lists above, which are not exhaustive.  

A major benefit of opting for antimicrobial herbs over their pharmaceutical counterparts is they are more targeted (versus broad spectrum), which can help to preserve our healthy probiotic microbes.

Most antimicrobial herbs tend to be aromatic or bitter from an herbal energetic standpoint, since the volatile oils are the constituents with antimicrobial properties.  

Some herbs have an affinity for certain types of microbes, such as H. pylori or a certain type of SIBO. However, I’ve noticed there’s also a lot of overlap between antimicrobial and antifungal herbs.

Generally it’s best to stick with herbs that have been well-researched for eradicating specific types of infections.  

Other important considerations of a protocol are a person’s constitution (which should be compatible with the herbs from an herbal energetics standpoint), dosing, delivery method, duration and the specific blend or combination of herbs.

Foundational elements such as nutritional status, hydration, sleep and stress should be in place before beginning an antimicrobial protocol, and it’s also important to incorporate supportive herbs/supplements such as detox binders, lymphatic drainage herbs, liver support herbs, antimicrobial herbal mouthwash, digestive support herbs (think: herbal bitters), butyrate producers, and/or gut repair supplements to name a few.

Next steps

For IBS sufferers & other with gut issues…

As a functional dietitians, we’ve received extensive training and have a great deal of experience working with antimicrobial herbal protocols for gut health. If you’re interested in working together 1-1 and you live in the United States, we’re currently accepting new clients and past clients.  😀

Apply for 1-1 nutrition services HERE if it feels like a great mutual fit.

RDNs & nutritionists…

Are you interested in going deeper and learning more about herbs? Let’s stay in touch! Download my free PDF list of my top 10 online herb stores for RDNs and other health profs.

Wishing you all the best on your journey!

XX – Jenna