I recently wrote a blog post on how the popular plant-derived product, berberine, is indiscriminate in its effects on killing microbes. Berberine kills undesirable microbes, but it also kills desirable microbes.

Berberine kills undesirable species that can overproliferate in the human gastrointestinal (GI) tract, species such as E. coli, Klebsiella, Enterobacter, and Citrobacter. This makes berberine useful as an antimicrobial for correcting colonic dysbiosis and small intestinal bacterial overgrowth, SIBO, widespread and profound disruptions of the GI microbiomes that spares almost no one in the modern world. Berberine is therefore one of the preferred agents to correct SIBO, e.g., 400-500 mg twice per day or as a combination product such as Candibactin BR containing 400 mg per capsule. Berberine, sometimes in combination with other factors such as oil of oregano or curcumin, can convert H2-producing SIBO to H2-negative within 10-14 days, while also reversing SIBO-related phenomena such as food intolerances, fibromyalgia, restless leg syndrome, and high blood glucose.

But berberine is also a potent antibiotic effective against Lactobacillus species. Since my original blog post from about a week ago, a number of people have come forward and said things like “I’ve been making the L. reuteri yogurt and experiencing none of the effects you describe: no improvement in sleep, skin wrinkles, musculature, mood, libido, GI habits, etc., and I’ve been taking berberine to treat my high blood pressure.” Well, no surprise: Berberine effectively kills L. reuteri. If you are consuming SIBO Yogurt, you will likewise experience none of the benefits of this combination of microbes because the berberine also kills Lactobacillus gasseri and suppresses Bacillus species (e.g., coagulans, subtilis), rendering this otherwise wildly effective SIBO solution ineffective.

Berberine is essentially an antidote that blocks all the beneficial effects of Lactobacillus reuteri and otherl Lactobacillus species. I’ve personally experienced this effect. As a chronic insomniac, sleeping only a few hours per night for decades, I now sleep a full 8-9 hours per night with rare interruptions by consuming L. reuteri yogurt or probiotic. If/when I take berberine (I’ll often take things to better understand their effects), I promptly revert back to severe insomnia: unable to fall asleep, frequent awakenings at 2 or 3 a.m., waking up at 4:30 a.m. and unable to fall back asleep, patterns that leave me fatigued and foggy the next day. Stop the berberine while continuing the L. reuteri, and I once again enjoy a full night’s sleep.

I am continually perplexed by the widespread failure to recognize these effects. Take, for instance, 500 mg of berberine and you pass 500 mg into the toilet—it is not absorbed. Yet there are plenty of data telling us that berberine can reduce blood sugar, blood pressure, reduce inflammation, and have other beneficial effects. But rather than acknowledge that these effects must therefore be mediated by effects on the GI microbiome or intestinal barrier, many have proposed that berberine metabolites must somehow be the effective factors, or that we must develop forms of berberine that force absorption, ignoring the fact that the non-absorbable form has already been shown to exert benefits.

So let’s be clear: Berberine kills the undesirable species of colonic dysbiosis and SIBO, effects that readily explain why blood sugar, blood pressure, inflammation and other phenomena improve because endotoxemia is reduced. In other words, reduced populations of fecal species such as E. coli and Klebsiella, species that contain lipopolysaccharide (LPS) endotoxin in their cell walls, are killed off, reducing their release of LPS endotoxin—that is why such benefits develop, no need to force absorption.

Take berberine if you must to correct colonic dysbiosis or SIBO. But NEVER take it chronically to, say, reduce blood sugar or blood pressure because its undesirable effects on beneficial microbes will impair your health. If you experienced positive effects by taking berberine, it is because you inadvertently and unknowingly corrected colonic dysbiosis or, more likely, SIBO.

As I often say, half of my job is batting down misinformation. And this is a case of widespread misinformation and misinterpretation that can have significant damaging effects on your emotional and physical health.