Last week, I talked about the importance and health benefits of probiotic foods and supplements, and how to choose them, to enhance the number and diversity of the beneficial micro-organisms in your microbiome.

Today we will look at the flip side, and talk about the best anti-microbial foods, herbs, and spices that you can use to help reduce the number of disease-causing micro-organisms, aka pathogens, in your system.

Invasion by pathogens is an inevitable part of life. And, as pathogens are one of the top 4 root causes of most health problems, supporting your immune system in clearing these “bad bugs” is crucial to achieving and maintaining optimal health!

And natural anti-microbials of all kinds are a great way to do that.

What are Anti-Microbials?

Anti-microbials are compounds which kill pathogens. There are 4 main types of pathogens: bacteria, viruses, fungi, and parasites. And, correspondingly, the anti-microbials which are effective against each of these types of pathogens are called anti-biotics (which are anti-bacterial), anti-virals, anti-fungals, and anti-parasitics. Examples of infections and illnesses caused by each type of pathogen are:

  • Bacteria:
    • strep throat
    • ear infections
    • sinus infections
    • food poisoning
    • h.pylori
    • vaginal infections
    • bladder infections
    • UTIs
    • skin infections
    • whooping cough
    • bacterial pneumonia
    • bacterial gastroenteritis
  • Viruses:
    • influenza (flu), including Covid
    • herpes
    • meningitis
    • viral pneumonia
    • viral gastroenteritis
    • HPV
    • Epstein Barr
    • HIV
    • Type 1 Diabetes
  • Fungi
    • yeast infections
    • candida
    • mold illness
    • ringworm
    • athlete’s foot
    • jock itch
    • fungal pneumonia
    • fungal gastroenteritis
  • Parasites
    • malaria
    • giardia
    • toxoplasmosis

And as you can see from this list of examples, some types of illnesses can be caused by a number of different types of pathogens, such as pneumonia and gastroenteritis, which can make it difficult to determine the true cause of a problem. And that makes it harder to treat, at least with prescription medications.

But, one of the many wonderful aspects of natural anti-microbials is that they are very often effective against multiple types of pathogens at once – ex. antibacterial and antiviral and antifungal – without the many damaging side effects of pharmaceuticals (1). And, they can often work against drug-resistant strains of pathogens (2), making them powerful allies for your immune system.

Sources of Natural Anti-Microbials

Natural anti-microbials can be derived from mushrooms, animal sources, algae and plants.


Mushrooms are the fruiting body of Fungi, and are a big topic all on their own! The immune-boosting and other health-enhancing effects of mushrooms are well-known and wide-ranging, and mushrooms have – like plant-based medicinals – been in use by humans for many millenia. (3)

Animal Sources

Unfortunately, agriculture and livestock operations are a major source of antimicrobial-resistant strains of pathogens these days, making our quest for optimal health that much more challenging! (This is another great reason to only buy pastured animal products.)

But, animal-derived compounds can also be a helper in this quest, especially saturated fats that are sourced from organic, pastured livestock and wild animals.

Long maligned as harmful, saturated fats are actually protective and healing when they are properly sourced, and have strong antimicrobial properties (as well as raising levels of “good” cholesterol, HDL). (4,5)

This could help explain why, according to the PURE study (6), higher consumption of saturated fat (from animal sources and from coconut) reduces the risk of all causes of death by 14 per cent, and the risk of stroke by 21 per cent. Perhaps it is in part because of saturated fat’s anti-microbial, immune-boosting properties!


Part of the Protista kingdom, algae are present in huge numbers everywhere, and are predominantly aquatic – living on, in or near water. Many types of algae are highly nutritious, and have strong anti-bacterial, anti-viral, anti-fungal and anti-parasitic properties (7), including red, blue-green, and brown algaes, and all types of edible seaweed, aka sea vegetables: wakame, hijiki, dulse, kelp, nori, etc. And, the commonly used thickeners agar-agar and carrageenan, which are derived from algae, also contain many immune-boosting properties.

Plant-Based Sources

Anti-microbial compounds are found in many plant parts, including the flowers, fruits, leaves, stems, roots and bark, and come in many forms:

  • teas
  • spices
  • culinary herbs
  • medicinal herbs
  • essential oils
  • alcohol- and glycerin-based extracts

Plant-based medicinals – like mushrooms – have a long history of successful use for their vast health-enhancing powers, including their anti-microbial and immune-boosting properties (8), and the kinds that are easily and effectively used in or as food and beverages will be our focus for the rest of this article.

The Best Food-Based Anti-Microbials

There are sooo many wonderfully effective food-based anti-microbials! How do we even begin to choose which ones are “the best”?

 My Criteria for Choosing

Here are my criteria for how I picked my favorites:

  • Proven effective
    • there’s good science on their use as anti-microbials/immune boosters, and also, I’ve used them in my clinic and seen good results in a number of people
  • Low toxicity
    • buy organic whenever possible, and be aware that there may be environmental toxins like heavy metals in herbs & spices even in organic versions – this is a great reason to grow your own!
  • Minimal to no adverse side effects and contra-indications
  • Not an endangered species
  • Minimally processed, and DIY accessible/do-able for home use as food or drink
    • ex. grapefruit seed extract has shown strong anti-microbial promise, but is highly processed, is not something that can be made easily at home, and while it comes from a food, it isn’t a food
  • Readily obtained
  • Easy to use
  • Palatable (ok, mostly… :-P)

My Top 20

Based on those criteria, the following are my top 20 picks for anti-microbials to have on hand in the natural medicine toolbox, and to use in the menu as herbs, spices, teas and in foods:

  1. Alliums (garlic, onions, etc.) (9)
  2. Apple Cider Vinegar (10,11,12,13)
  3. Cinnamon (14,15,16)
  4. Clove (16,17,18)
  5. Coriander (19,20)
  6. Cumin (21)
  7. Curcumin (turmeric) (22,23,24,25)
  8. Eucalyptus (14,26)
  9. Gentian (27,28)
  10. Ginger (29,30)
  11. Green Tea (31)
  12. Horseradish (32)
  13. Lavender (33)
  14. Lemon (34)
  15. Oregano (35,36)*
  16. Peppermint (37,38)
  17. Rosemary (14,39)
  18. Sage (40)
  19. Tea Tree Oil (41) – for external use only!
  20. Thyme (42,43)

 *Oil of Oregano (vs. oregano herb) is a very effective anti-microbial, because it is very strong! If you are going to use it, dilute it with a good quality edible carrier oil such as EVOO (extra virgin olive oil) and use it very sparingly and with great caution.


An easy, efficient and effective way to harness the anti-microbial power of many of these natural substances is to consume mixtures of them, such as herb and spice blends, soups, and sauces that contain several of them at once. Here are some of my favorites, many of which get you not only several natural anti-microbials at once, but also some great digestion-boosting as well!

Food based:


Just in case supplements are easier, more manageable, or more appealing for you than the above options, here are 2 of my favorite supplements that each contain several of my top 20 food-based anti-microbials:

  • Biocidin – Independent lab testing has confirmed that this synergistic combination of several botanical medicines supports microbiome balance, and addresses microbial challenges throughout the body. And, as a nice bonus, it’s actually pretty tasty, too! 🙂
  • Ultimate Antiox Full Spectrum –  a unique antioxidant formula derived from a combination of some of nature’s most powerful herbs and spices, along with several classic and novel antioxidant compounds.

*These are both available through my online dispensary at Wellevate.


If you take too large a quantity or too many doses of natural anti-microbials too fast for your body – even as food – you can experience something called a die-off reaction, which is what happens when a large number of microbes die at once and release a bunch of toxins into your gut and bloodstream.

When a die-off reaction happens, there can be a worsening of your existing symptoms, or a resurgence of old symptoms, or you might feel immune challenged and “under the weather” like you are getting a cold or flu, or you could feel nauseous or have other digestive symptoms.

If any of these happen, drink lots of water with sea salt or electrolytes to help flush your system, and lower your anti-microbial intake, or have them less often, or stop them altogether until you feel better, then try again.


While using natural anti-microbials can be incredibly effective for improving health and healing a wide variety of health conditions, and it is often hard to truly heal the root causes of many diseases without them, it is absolutely possible to overdo it with anti-microbials (like with so many things, more is not always better, and balance is the key!)

What I typically recommend is taking anti-microbials in strong bursts, with longer periods of rest in between the bursts. My two most commonly recommended burst patterns are:

  1. A 2-month rotation, with 2 weeks on and 6 weeks off, and
  2. A 3-4 month rotation, with 1 month on and 2-3 months off.

These patterns are repeated, often for 1-3 years, while frequently switching up the types of anti-microbials used to avoid overuse and to get the broader benefits that you get from variety.

This type of rotation gives your body time to rest from the harshness of anti-microbials, and re-find its own balance.

I also recommend taking probiotic supplements (also on a rotation of types over time) around 1-3 hours after each dose of anti-microbial, to help restore some good gut bugs at the same time that you’re clearing out the bad guys.






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