top of page

Why we don’t prescribe berberine

A popular supplement has now been shown to damage the gut microbiome, and yet it is still being widely used.

Growing in parks and gardens, Mahonia (Oregon grape) is currently fruiting in the UK, with long strings of tasty, blue-purple berries. But its root contains a chemical called berberine, that’s widely-used as an antimicrobial and weightloss supplement.

Berberine is freely available online, without a prescription. It's also commonly prescribed by many practitioners, especially those working within the Functional Medicine framework, for treating SIBO (small intestinal bacterial overgrowth) and IBS, even cardiovascular disease. It’s also getting a lot of publicity currently as a “natural metformin” in the treatment of Type 2 diabetes, and as weight loss aid alternative to Ozempic.

However it's important to note that berberine-containing herbs (such as barberry, goldenseal, Coptis chinensis) have traditionally been used very sparingly in Western and Chinese herbal medicine. Furthermore, in supplement form, berberine is isolated; with many of the microbiome-boosting polyphenols found in the whole-herb removed.

A few clinical studies of berberine have been published, and while several show positive health outcomes, there are now several studies showing it has harmful effects on the gut microbiome; killing beneficial species and even boosting inflammatory species, including Proteobacteria.

Unfortunately many practitioners prescribing berberine, often longterm, are using tests that detail only a small number of microbiome species (qPCR tests), so they miss the damage it can cause. At The Microbiome Group, we use whole-microbiome analysis (primarily 16S testing, and some shotgun metagenomics) so it’s possible to see that clients with a history of berberine treatment have very reduced populations of beneficial species.

Herbal antimicrobials are still a very useful part of our clinical toolkit. However we avoid not only berberine but also commonly-prescribed essential oils, such as oregano, that again seem to be far less selective in antimicrobial action than previously thought.

Rather than simply killing off bacteria though, we focus on addressing the depletion of beneficial bacteria usually underlying the conditions berberine is often used to treat. This is why our treatment plans include targeted prebiotics, polyphenol and food recommendations. Which brings us back to mahonia’s delicious, tart little berries — full of polyphenols to feed your beneficial gut bacteria.

Applying microbiome science in clinical practice is hugely exciting. It can be very powerful with potential long term impacts on our health, so that comes with responsibility to our clients to avoid risks and only using antimicrobial supplements very cautiously, staying up to date with the latest research.


Ming, J., Yu, X., Xu, X. et al. Effectiveness and safety of Bifidobacterium and berberine in human hyperglycemia and their regulatory effect on the gut microbiota: a multi-center, double-blind, randomized, parallel-controlled study. Genome Med 13, 125 (2021).

Zhang, Y., Gu, Y., Ren, H. et al. Gut microbiome-related effects of berberine and probiotics on type 2 diabetes (the PREMOTE study). Nat Commun 11, 5015 (2020).

Yang L et al. Efficacy and safety of berberine for several cardiovascular diseases: A systematic review and meta-analysis of randomized controlled trials. Phytomedicine. (2023) 112: 154716.

Li J et al. Effect of Berberine Hydrochloride on the Diversity of Intestinal Flora in Parkinson's Disease Patients. Contrast Media Mol Imaging. (2022) 8381870.

Zhang Y et al. Enhancing intestinal barrier efficiency: A novel metabolic diseases therapy. Front Nutr. (2023) 10: 1120168.

Viola Sampson BSc MCMA is a registered Microbiome Analyst, Founder and Director of the Microbiome Group practice. You can book appointments with her team of Associates here. (Viola's availability is by waiting list only – currently at least 18 months' wait).

155 views0 comments

Recent Posts

See All


bottom of page