Natural Anti-microbial Supplements for IBD

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matt robinson

Matt Robinson lives and works in Washington D.C., USA.  He was diagnosed with Ulcerative Colitis in 2002 and has been living medication-free since early 2009.  FMT was one tool in his digestive illness toolbox and we published his FMT Success Story in 2012.. Matt is a health coach and blogs at Natural Digestive Healing, He has written a book called FMT Coach to help those with digestive illness tackle FMT and also provides one-on-one health coaching via Skype. This is an article he wrote on the range of anti-microbials than can be used as a gentler alternative to antibiotics.


Plants have been used as primary medicine for millennia. In fact, anthropologists have found medicinal herbs in the a 60,000 year old grave of a Neanderthal man. Cultures throughout the world have detailed plans and systems for using medicinal plants. What modern researchers are finding today, is nothing new. In fact, over 50% of the modern-day pharmacy is derived from plant material.

  • Unlike conventional antibiotics, there are few side effects. Most have none at all. This is a great relief(!), especially if you’ve been suffering through the side effects of steroids or immune suppressants.General principles for all natural antibiotics:
  • Unlike conventional antibiotics, they have multiple action (they work on microbes in and through many different mechanisms);
  • For geeks like me: In general, they are effective for both gram-positive and gram-negative bacteria, though there are always a few caveats…
  • Their chemical complexity prevents the formation of bacterial resistance, and is effective even with resistant microbes;
  •  Always, before you start a new treatment, tell your doctor, make a plan with your naturopath;
  • Always, always follow with probiotics for a minimum of two months after your last dose of natural antibiotic. (Consider taking probiotics concurrently with your antibiotic, but in smaller doses).
  • Take probiotics at least one hour after or two hours before your antibiotic.
  • Since antibiotics reduce the levels of bacteria in your gut, and since they reduce the levels of vitamin K, and vitamin K-dependant clotting factors in the blood, you should make sure you eat or juice plenty of leafy greens whenever you are on antibiotics. Leafy greens are the only significant dietary source of vitamin K.
  • There is strong evidence that IBD has an infectious origin. If this is true, then for IBD, you want to take the natural antibiotic until the infection is cleared.How will I know that? You will know that because your symptoms will lessen and/or (if you’re doing other things like diet and probiotics correctly) disappear. Take them for about 3-5 days after your symptoms get better.
  • Because microbes have a life cycle (bloom, recede, dormant (in some), bloom, …etc.), you may need to repeat the antibiotic treatment more than once. How much, how often, and how long you are on the antibiotic will depend on your infection: how long you have been infected, how thoroughly you are infected, what your diet is, which mix of microbes are your problem, etc.
  • It could take six months to a year to clear your infection, so be patient. You should see improvements along the way.

Oh, and did I mention they don’t encourage bacterial resistance? That’s huge. Bacteria can quickly (within a few generations) become resistant to modern pharmaceutical antibiotics.

There are many other natural antibiotics out there. I have chosen to write about these few, because I think they are universally the safest and the best for IBD. Others, like Wormwood, Uva Ursi, and grapefruit seed extract, may not be as useful, or safe to use in IBD (e.g., they may increase diarrhea or irritate the gut), so I have left them out; though I know there are people who use them with success.

One glaring omission here is garlic. It is a good antibiotic, but not nearly as strong as those listed below. While aged garlic is much more palatable than fresh, raw garlic, it irritates the gut so consistently in people with IBD, that I left it out. Sorry garlic lovers.

I list the antibiotics below in my order of preference. So if you’re looking for a place to start, start with a good Berberine complex and work your way down the page. If you decide to start natural antibiotics, remember that you may experience, in the beginning, some temporary die off symptoms. Remember, these are a good sign (as long as they go away in a week or so; if they don’t stop or get worse, call your doctor).

Some initial die-off symptoms you may experience are: headache, fatigue, achyness, nasal drip, increased diarreah, gas, bloating, moodiness. These largely caused by the toxins released as microbes die. It’s important during this time to drink plenty of water, get lots of rest, eat a clean diet, and most of all, don’t panic. The symptoms will pass. You can help your body during this process by eating lots of greens, either lightly steamed, raw (if you can handle it), and juiced (this is the best way). The vitamins, minerals, and other nutrients are good for you, and the chlorophyll will help rid your body of the toxins.

Using natural antibiotics and probiotics in healing Crohn’s and Colitis

In my posts on probiotics, I mention cycling natural antibiotics and probiotics as a good method of healing from IBD. There are two ways that I see to do this:

  • Take the natural antibiotic consistently (with 7-10 billion cfu of probiotics) until the infection is cleared; until your symptoms subside. Then continue with probiotics at higher doses after stopping the antibiotic. Repeat as necessary.
  • OR—use a four-week cycle. Four weeks of natural antibiotic, 4-6 weeks probiotic. Repeat.

I prefer the former, having tried the latter without consistent success.

Natural Antibiotic Supplements


Berberine is a natural antibiotic which is found primarily in three natural herbs: Goldenseal, Barberry, and Oregon Grape. There is some controversy among practitioners over the dose and length of time berberine can be used, but there is little controversy anymore about its effectiveness.

Berberine is effective against antibiotic resistant infections, and works particularly well for bacterially induced diarrhea. It is known to be antibacterial, antihemorrhagic, antifungal, antiseptic, antiameobic, astringent, expectorant, diaphoretic (induces perspiration—a good thing for reducing fevers), a mucosal anti-inflammatory, mucosal stimulant, mucosal tonic, and is cytoxic to tumors (kills them; protects you from cancer).

Berberine is often used to treat severe systemic infections, and has been used successfully against, among other things, antibiotic resistant staph infection (the scary one). It has also been used to treat the also especially scary, antibiotic resistant E. coli, O157:H7, which causes bloody diarrhea and sometimes death. Berberine has been shown to surpass many pharmaceuticals in its dependency and effectiveness against diarrhea caused by enterotoxigenic (produces toxins in the colon) E. coli, and has been shown to minimize intestinal secretions in cholera and E. coli infections.

When taken internally, berberine supports the healthy functioning of the mucous membranes of the body (by promoting IgA antibodies; increasing macrophage activity), acts as an anti-inflammatory, as well as retaining its anti-microbial properties. Berberine markedly reduced inflammation in rat studies.

This is important (why I tried this one first): Berberine has been shown not to hurt beneficial flora, and does not promote bacterial resistance; therefore you can take this safely with your probiotic. It is also been shown to be highly anti-inflammatory. I’d still separate your berberine dose from your probiotic dose by one hour, though; but in theory, you could take them together.

Side effects and contraindications:

Berberine, in extremely high doses (way, way, more than the recommended dose) can interfere with B vitamins, cause liver damage, nervous tremors, and excessive drying of the mucus membranes. Do not use during pregnancy.

Caution: Berberine is not for long-term use. I use it for two-week courses only. Long-term and at high doses, it has been associated with thyroid problems, and can interfere with B vitamin uptake.


I recommend Integrative Therapeutics Berberine Complex. It is what my naturopath researched and suggested to me. I started it after re-introducing dairy (unsuccessfully) during my elimination diet. The yogurt worsened my symptoms, and I couldn’t recover. After ten days, I started the Berberine. 24-hours later, my symptoms settled down. Three days later, I was back to normal; symptom free. The dose of this brand is two caps, three times daily.

General dosing:

300-1200 mg/day, or 1-4 droppers of tincture, both with ample (6-8 oz.) water, for up to 14 days.

Berberine can be used in conjunction with Echinacea for short periods (don’t over-use Echinacea, or it can become ineffective in your body).

Comparable to Cipro.

Wild Oregano Oil

(for more on Wild Oregano see, The Cure is in the Cupboard, and The Miracle of Wild Oregano, both by Dr. Cass Ingram—Note: The former is a much better read than the latter, but you will learn from both.)

Wild Oregano Oil is probably the most comprehensive natural antimicrobial we know of today. I use the term ‘comprehensive’ because, while there are other extracts that are just as, or even more potent (such as grapefruit seed extract) than wild oregano, wild oregano has other broader properties that make it beneficial to the body. Those other substances, like sweet wormwood and grapefruit seed extract, do not demonstrate the myriad benefits (outside of killing bacteria) that wild oregano exhibits. They can also be toxic and cause, or encourage diarrhea.

In contrast, wild oregano oil is completely non-toxic even at extremely high doses, and, beyond the initial die-off symptoms, does not cause diarrhea or other side effects. It is anti-bacterial. It is anti-fungal. It is a burly killer of parasites. It is a powerful antioxidant. It has anti-inflammatory, and strong analgesic (pain-numbing; in this, one study found its analgesic properties to be about 66% of that of morphine) properties. And it helps kill tumor cells and prevent cancer. There are many more claims on wild oregano, but those are the ones I could verify.

Using Wild Oregano for IBD:

There are only two brands of wild oregano that I can recommend: (1) North American Herb and Spice; and (2) Joy of the Mountains. These are organic, wild, and diluted in high quality olive oil as a carrier oil. Make sure you’re getting a truly wild Mediterranean oregano, not a farmed or bred version from Mexico or Israel. Some brands even use a false oregano which is really another plant. There are at least five other plants commonly called oregano which are not. These can be downright dangerous. Only the whole, wild, Mediterranean plant holds value for us here.

Please do not use the oregano essential oil. It is not the same as wild oregano oil. It is too strong (needs dilution), and may cause you more harm than good.

In using wild oregano to treat Crohn’s or colitis, it is best to take the oil and also a spice mix oil, a separate product which is mixed with other antimicrobial spices, in pill form. Studies have shown that wild oregano oil produces, in vivo (in the lab), a 99% kill rate, even of antibiotic resistant forms of E. coli, strep, tuberculosis, etc. However, when the oil is used concurrently with other antimicrobial spices such as cinnamon, bay leaf, olive leaf, cumin, or sage, the kill rate is consistently 100%. You can take the spice mix either as an oil pill or as a crude spice mix pill. I prefer the timed release mixed oil pills.

It is important to understand, that wild oregano, unlike berberine, kills EVERYTIHNG—even good bacteria; so if you use it at a therapeutic dose, you also need to be taking a minimum of 10 billion CFU of a probiotic and supplementing with fermented foods (if you can tolerate them). You may need to slowly work up to 10 billion CFU before you start the antibiotics. The point is to take probiotics during and after a course of natural antibiotics, and to work up slowly with each to an effective therapeutic dose (see my post on finding your effective therapeutic dose of probiotics)

Wild oregano, like Berberine, in many cases has been shown to surpass conventional antibiotics in its effectiveness.

Dosages: (for North American Herb and Spice, Oreganol P73 Super Strength Oil. If you use regular strength Oreganol, or Joy of the Mountains, then increase the dosage to three times that which is recommended here.)

  • Sublingual doses are the most effective, but oregano oil is spicy, so judge this one for yourself. The spice is not very hot at all under the tongue, but once it hits your taste buds, it can be quite hot. Another option is to take it orally with water. See this video from Jini Patel Thompson for instructions on taking oregano oil with water.
  • Start with five drops under the tongue, 3x daily. Increase the dosage slowly as needed. Most authors I’ve read say that if infection is your problem, and oregano isn’t working, then it’s the dose, not the oregano itself, that is the problem—so take more. I’ve safely taken 10 drops, 6 times a day.  The same dose can be used orally, just take with water.
  • You may find that oregano oil ‘bites back’ at first. You may burp it, you may get some heart burn at first. These will pass as you get used to the oil. If you want to avoid these initial hiccups, take your oregano oil doses with a meal.

Comparable to Vancomycin, Flagyl.

Olive Leaf

Olive leaf is in the category of other antibacterial, antiviral, and antifungal spices. Olive leaf has been used in medicine for thousands of years, and is well-known for its potent antimicrobial action. In the 1800’s, scientists isolated an active component of olive leaf, oleuropein. This is just one of many active components of olive leaf. It has been shown effective on, E. coli, Klebsiella peumoniae, Bacillus cereus, Salmonella enteritidis, Staphylococcus auereus, Candida albicans, herpes, molds, and parasites.

It is also a potent antioxidant. Studies show that olive leaf can prevent the oxidation (break-down) of LDL cholesterol. Olive leaf has also been shown to increase macrophage activity by enhancing the nitric oxide pathway (gives more ammo to the good guys!).

Olive leaf is not spicy like Oregano Oil, so is easier on those with a sensitive palate, and is easier to give to children.

Olive leaf does not harm beneficial bacteria, and does not foster resistance.


500-3,000mg/day in divided doses (usually 3x per day). Try the Seagate brand extract.

Aloe Juice, Jel, or Freeze-dried Powder

See my posts on Aloe for more information on aloe and IBD.

Aloe not only has antimicrobial properties, but is a natural immune booster as well. It promotes healing in the gut and strengthens the GI immune system. There is evidence that bolstering, not suppressing the immune system is beneficial for treating Crohn’s and colitis. Aloe increases macrophage activity in the gut. Macrophages are immune cells which engulf and remove pathogens from our bodies. Aloe is great for soothing inflammation, can help stop intestinal bleeding, and can help with acid reflux.

Side effects and contraindications:

None; however, make sure you get an aloe brand with the laxative components removed. These laxative components, aloin and emodin, are from the rind. The pulp, or gel inside the leaf, however, contains no aloin or emodin, and is not a laxative.George’s Always Active Aloe Vera is the only brand I know of that has the laxative component removed. For IBD, do not use a flavored brand, or any brand that uses citric acid or sodium benzoate (as a preservative).


Gel may be better for chronic gut problems (1/2-2 tsp per day). Aloe powder, 1/2-2 tsp. Per day in water. Aloe juice, 2 oz. 2-3 times per day. Take on an empty stomach.

A quick note on other cool natural substances…

Raw Wildflower Honey

Honey? Yep, honey. Natural, unpasteurized, raw wildflower (not clover) honey is antibiotic, antiviral, anti-inflammatory, anti-carcinogenic, helps with allergies, isa good tonic, is antifungal, and is an immune stimulant.

Honey is the concentrated nectar of flowers gathered and partially digested by honey bees. This digestion alters the nectars slightly. When the nectar is regurgitated by bees in the hive, it is mixed with their digestive enzymes, which fosters the nectar’s transformation into new compounds. In the hive, the honey is further concentrated through evaporation. Because the bees peruse many, many different species, and because many of them are medicinal (e.g., elder, Echinacea, wild geranium), the properties of those flowers are present in the honey. Wildflower honey is best.

Unpasteurized honey contains a complex mix of enzymes, esters, antimicrobials, minerals, proteins, hormones, organic acids, vitamins, and carbohydrates. Do not feed raw honey to children under two years old.

One study of a group of 58 boys of the same age and general health showed promising results. Half were given 2 tablespoons of unpasteurized honey daily for one year. The other half were not. All boys received the same diet, rest, and exercise. At the end of the year, the honey-eating half of the study showed an 8.5% increase in hemoglobin, and an overall increase in other measured vitality, energy and health indicators.

Honey has been effectively used to treat ulcers in third-degree burns; using honey reduces or eliminates the need for skin grafting. It has also been shown to be more effective than pharmaceutical antibiotics in the treatment of stomach ulcers, gangrene, and many more conditions. The caveat here, is that I don’t know what doses they were using for stomach ulcers and gangrene. The burn study used a topical application.

Though high doses of sugar in any form are known to suppress the immune system, in small doses raw wildflower honey is a good immune stimulant. I take 1-2 tablespoons/day; one in the morning, and one in the evening. Any more than that, and you’re an addict (it tastes fantastic).


Ginger has antibacterial, antiviral, circulatory stimulant, anti-inflammatory, antispasmodic, antifungal, analgesic, antitussive (anti-cough), and many more beneficial properties. Ginger has a long history as a food additive, especially in warmer areas of the world. Traditionally used to treat colds and flu, it is especially useful with children and is safe in large quantities (for gut-normal people; for us with IBD, we always have to test a new food or supplement—always test something new to make sure it doesn’t exacerbate your symptoms). It contains a powerful digestive enzyme with the unfortunate name of zingibain (where do they come up with these things?)

Ginger can increase the digestion and uptake of other foods, spices, and herbs (like turmeric). It’s anti-cough properties rival codeine, and it has strong expectorant and antihistamine properties that are especially helpful with colds and other respiratory infections. It reduces inflammation, stimulates immune activity and sweating (good for reducing fevers), and is a good pain reliever.

It’s antispasmodic (anti-cramping) properties can help with diarrhea, though this in unconfirmed in IBD.

Best taken fresh:  1 oz. Of fresh root steeped in water for 8-10 min. 1-2 cups per day.


Licorice is in a special category. It has strong antimicrobial properties, but has equally strong immuno-stimulant, and anti-inflammatory properties, so I struggled with writing about it here, where I list natural antibiotics, per se. I might write more about it in the future. Licorice is well documented, and well-studied. It is an immuno-stimulant herb which also has antimicrobial activity. It also augments the effects of other herbs. It is especially good at colds, flus, upper respiratory infections, and aiding in the repair of ulcerations in the gut (esp. the stomach). It can also be used to restore adrenal function (good after a round of prednisone or other steroid), and is known to increase general vitality. Evidence shows that it stimulates the thymus gland, increases white blood cell generation and activity, stimulates interferon activity, and enhances antibody formation. It is also known for its anti-stress and anti-fatigue properties, and there is evidence that it has immunomodulating properties.


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1 reply »

  1. Hey Matt,
    had parasites real bad and wiped them out with massive dosage of abx, on two occasions, 100 caps in 10 days, and via colonoscopy. This wiped out all microbiome and cannot tolerate the smallest amount of probiotics, fermented foods. also severe food issues, salicylates, phenols etc.
    I have tried small sprinklings of probiotics over 12 month period and just cannot bear the gas and bloating, particularly during the night. all path tests indicate no bacteria or pathogens. Can tolerate apo lactoferrin and foot baths with Mag Sulfate, an taking enzynes and hci but still large bowl bloating/gas only at night kills.
    any clues?

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