Blastocystis hominis: Natural Herbal Treatments

blastocystis hominis natural treatment options byron bay herbalist australian naturopathic treatment for parasites

Anyone who has been reading this blog will know that I have been struggling with Blastocystis homins and Dientamoeba infections since contracting them, four years ago, in the Byron Bay hinterland. More on my story here.

Today I’d like to share my herbal treatment For Blastocystis hominis and the success in finally treating both Blastocystis hominis and Dientamoeba with herbal medicines.

Thankfully there are natural treatments for Blastocystis out there that work! I wasn’t convinced until I cleared them myself.

First Off What Is Blastocystis?

Blastocystis spp. (also known as Blastocystis hominis) is a protozoan parasite that can cause a range of different symptoms in people including abdominal pain, diarrhea, constipation, fatigue and skin rashes. Surprisingly there are some people that have a Blastocystis infection and show no symptoms (1).  

We have had some difficulties categorising this unicellular organism. At various times it has been classified as a cyst of a flagellate, vegetable, yeast, and fungus and finally landing on the protist classification (2). It also has the ability to take a whole range of different forms from vacuolar, granular, and ameboid, cyst, avacuolar, and multivacuolar (3) with the ameboid form suspected as causing the most symptoms in infected people (4).

Herbal treatment for Blastocystis blastocystis herbal treatment natural treatment herbal approach

Is Blastocystis really to blame here?

This is the million dollar question. I have spent a lot of time researching and speaking to experts on the subject of Blastocystis trying to get to the bottom of that very question. Originally I thought that Blastocystis was an outright pathogen and should be treated in anyone that came back with a positive stool test. After years of looking into it I now think that there is one of two things going on here.

Number one. You may have contracted a particularly virulent ‘strain’ of Blastocystis and this may be the cause of all of your gut symptoms. This is definitely possible and certain strains of Blastocystis have been found and do cause symptoms.

Number two, and possibly…maybe.. more likely. Blastocystis has come back on your stool test and you have blamed this particular bug for what is really some other gut condition hiding behind it. Things like bacterial overgrowths in the small intestine (SIBO) and large intestine may be the real issue here. Other things to be on the look out would be food intolerances (coeliac disease is a big one) and possibly leaky gut.

This second option makes Blastocystis a harder bug to treat because we aren’t 100% sure that it is causing your symptoms. A healthy approach to this particular conundrum would be to keep your mind open to other possible issues that could be causing your gut symptoms and not to focus solely on Blastocystis clearing as your main objective.

Ok. Now that little disclaimer is out of the way let’s cover how I managed to clear my Blastocystis infection.

Antibiotics for Blastocystis. Maybe not?

I have tried a number of different approaches to eradicate the bugs from my gastrointestinal tract.

The first attempt was the front line approach from conventional medicine. Metronidazole, brand name Flagyl here in Australia had very little impact on the gut infections. I am not a huge fan of antibiotics but I figured take them, get rid of the bug and then rebuild. Since then I have come across dozens and dozens of people that have tried Metronidazole with no success. There have been case studies showing an increase in the cyst count for Blastocystis spp. after taking it. I have been speculating on how this might come about. Antibiotic resistance is a real issue with gut infections. My thoughts are that many Blastocystis strains are resistant to Metronidazole and the antibiotic cleared the gut for them to take hold.

With such dismal results I turned to herbal medicine and changed my diet considerably (article on that part coming soon). Ok onto herbal treatment for Blastocystis hominis number one.

Herbal Attempt for Blastocystis Infection – Number One

For my first herbal treatment for Blastocystis I combined bereberine HCl with a herbal mixture which included a number of very obscure herbs from the Amazon. This was on the recommendation of a health coach who left me in the lurch when we discovered that it hadn’t eliminated the bugs. I definitely won’t be recommending him anytime soon.

After the herbal treatment I felt better, my gut symptoms improved dramatically. At that time I was already familiar with the importance of retesting. Lo and behold my stool testing came back showing both the two protozoan bugs were still there. Not only that but after about a month or two of feeling normal again my gut symptoms came back but this time with some non-gut related symptoms including

  • Brain fog
  • Irritability
  • Fatigue
  • Food allergies

At this point I was concerned with the state of my microbiome. I have seen a number of different cases where people continually blast their guts with antibiotics and strong antimicrobial herbs in an endless attempt to eradicate the infections.

With this in mind I turned towards a rebuilding approach. I focused on different prebiotics including lactulose, fructo-oligosaccharides and different colonic foods like green tea polyphenols. I also began consuming more probiotics including Saccharomyces cerevisiae boulardii, Lactobacillus rhamnosus GG and Bifidobacterium lactis Bi-07

The rebuild phase is important. Building up my reserves and caring for my gut flora helped when I took the second round of herbal antimicrobials. Onto herbal treatment for Blastocystis number two.

Herbal Treatment For Blastocystis Number Two

Herbal treatment for Blastocystis number 2. At this point I was feeling pretty good. I still had issues with different foods including gluten and dairy but my digestive symptoms had improved immensely. This time I opted for a very different herbal approach.

Instead of taking berberine HCl I opted for herbs high in berberine and other similar alkaloids. The thinking behind this approach involves the drug-resistant methods that many infectious organisms use to avoid being killed by the antimicrobials. Berberine as an extract is one molecule. It is true that most of the research points to it as the most efficacious and ‘active’ but there are dozens of different berberine like alkaloids in different herbs. It has been suggested that these similar molecules have a synergistic effect, almost overwhelming the microbe’s ability to process them.

With that in mind I opted for herbs such as Goldenseal, Barberry and Coptis. Other herbs in the mix included Wormwood, Black Walnut and Garlic. The Naturopathic tradition has a number of overarching principles. One of these is to support the different body systems during a herbal treatment or intervention. Thinking along these lines immunomodulating herbs such as Cat’s Claw and antioxidants such as Olive Leaf are helpful.

Even with all this in mind my second herbal attempt failed to eradicate the two bugs.

GI stool test PCR pathogen

Onto herbal treatment for Blastocystis number three!

Continued Herbal Treatment for Blastocystis infection

At this point I was getting quite frustrated. I even spent some time considering another round of antibiotics (different ones this time). I had seen a number of people pursue the antibiotic route with no success. Some even ending up taking the triple therapy that the Centre for Digestive Diseases recommends in Sydney, Australia, still with no luck in eradicating Blastocystis.

Thankfully I stuck to the herbal antimicrobial approach. For the third time I repeated herbal attempt number two but I extended the treatment. I also changed a number of things including

  • Upping my garlic consumption – sometimes eating cloves of crushed garlic and at other times sticking to the garlic capsules
  • Lactulose – this prebiotic helps to acidify the gut. It boosts beneficial bacteria in the colon, increases short chain fatty acid production and reduces the ability for Blastocystis and Dientamoeba to produce their protease enzymes which protects them from our secretory IgA antibodies.
  • Probiotics – I focused on taking probiotics daily including, S. boulardii, Lactobacillus rhamnosus and Bifidobacterium lactis Bi-07
  • Biofilms – While I haven’t seen any quality research on Blastocystis forming biofilms this does not mean that they don’t. For the third attempt I threw everything I had into the mix. This included nattokinase, green tea polyphenols (high in catechins) and serrapeptase in rotation.

After the herbal treatment I was very keen to retest. Waiting the 4-5 weeks before retesting was difficult but as recommended by a number of different clinicians it is better to wait to let the dust settle.

Retesting after Blastocystis treatments

At this point I am well aware of the importance of retesting after treatment. I learned this very big lesson the hard way by thinking I had killed the infections and not retesting the first time. After a few months my gut symptoms came back with a vengeance. It still took another month or two to realise and get tested again!

After one round of standard antibiotics, multiple rounds of herbal treatment for Blastocystis, half a dozen tests and retests my last PCR stool test came back clean and clear for the two parasitic infections that I have been struggling with for the past four years! Hallelujah.

To Those Struggling With Gut Issues

If you have read this far then I’ll bet you are struggling with gut issues. Maybe you already know that you have a parasite infection and have tried antibiotics or a herbal treatment for Blastocystis. Many people have emailed me asking for help with their health issues. Currently I am still a student of herbal medicine (counting the days until graduation) and as such am unlicensed and can’t give any direct advice. It absolutely breaks my heart because I know how it feels. I’ve been there. I also find it incredibly hard to recommend a specific clinician to help. Most of the ones I would recommend are booked out and are not accepting new clients. Others are still take the nuke the gut approach which can be just as destructive as broad spectrum antibiotics.

What I can do in the situation I find myself in is keep researching the complexity of gut health and keep publishing articles. In this way I can share what I’m learning and hopefully help anyone out there that needs it. I now know that a herbal treatment for Blastocystis is possible and that gives me hope for anyone out there struggling with this difficult to treat bug.

References and Resources

  1. Oh my aching gut: irritable bowel syndrome, Blastocystis, and asymptomatic infection
  2. New Insights on Classification, Identification, and Clinical Relevance of Blastocystis spp.
  3. Blastocystis hominis revisited.
  4. Predominance of amoeboid forms of Blastocystis hominisin isolates from symptomatic patients

You may also like


  1. Hi Todd,

    My son has Blasto and I have Fragilis. I have done a similar protocol to you – did it for 5 weeks but stool sample said not erradicated. I have had Blasto before and erradicated it with the triple therapy from the CDD in Sydney you mention without any health problems. But antibiotics are still such a question for me in regards my 7 year old son. So, was wondering, on your third attempt, how long did you do the antimicrobial treatment for?? And dose? Cheers! Lara

    1. My successful protocol took 3 full months. I made sure to support my gut flora with prebiotics and probiotics during and after the herbal antimicrobials.

      It is thought that children respond well to herbal medicine and especially probiotic therapy for gut infections. That may mean a shorter protocol but you can never be 100% sure with these things.

      Let me know if I can help with anything else.

  2. Thanks Todd for that – ah, 3 months is double what we did, so that makes sense why we were unsuccessful perhaps. We also took pre and probiotics, and immune support. We took almost the same antimicrobials as you mention but in rotation. Perhaps we should stick with a selection of antimicrobials for the duration and not rotate. With the Goldenseal, Barberry and Coptis, did you simply follow the directed dose from the manufacturer? Did you use tinctures or tablets? Thx again for sharing your experience with us!! Lara

    1. not a problem at all. Happy to help where I can!

      I stuck to the one formula in capsule form. I am still waiting to hear back from a very experienced clinician who deals with these infections daily on the tincture vs. capsule debate. I know for sure that tinctures (coptis, pomegranate, propolis etc) work very well on other protozoan infections (giardia, cryptosporidium) and bacterial infections (H. pylori, klebsiella) but Blastocystis seems to be an unusual little bug. Some strains appear to be very resistant.

      I did find that lactulose was incredibly helpful with my symptoms
      again that may be strain dependant – some Blastocystis strains are impaired by the low colonic pH that prebiotics create while other strains just power on.

  3. And did you follow the manufacturer directions for dose? Thanks for the lactolose tip (we were taking galactooligosaccarides and beta glucans). And looking forward to reading your article regarding tinctures or tablets when done!

    1. Sorry on the delay! Dosage was per manufacturer. All of the herbal medicines have a therapeutic range and I wouldn’t want to take more than the recommended dose for such a long time (short term treatments you can up the dose)

  4. Hi Todd! I have been battling BH since I learned I had it along with C. Diff. The latter has since cleared however, BH has not. I have gone through 2 months of Biocidin/Antimicrobial tx, changed my diet, getting rid of all the sugar bug eating foods however, I still have symptoms. I plan to start round 2 soon, I understand cycling treatment with the moon will better my chances to rid the parasite. What are your thoughts? I understand you can’t give prescriptions, but can you provide suggestions as I remove into round 2. Much appreciation!

  5. Hey Todd,
    My wife has been suffering with blasto for over a year now (long story – seems very similar to yours!), with multiple therapies having limited effect. I was wondering about the doses of your “final” treatment regiment….it would be very helpful to know what they were and also the brand of products you used. Others might also find this helpful…


  6. Hey bud,

    I’m in the process myself seeing a bioresonance therapist to treat BH coming up to 5 years now. The root cause and low success of herbs so far likely to have been high stomach ph which was caused by helibavtor pylori. I’m waiting for my PCR results this week so will share my story if successful with my track, but sounds like I’ve got a next phase of artillery with your final protocol if needed. Great to see your success. As per Kevin, would be great to get some brands etc of lactulose etc.

    1. Hey Kevin, thanks for your comment and sorry to hear you’ve been struggling with blastocystis too. It seems like a very common story.

      I decided not to post the brand or doses intentionally. After years of self-experimenting with high dose antimicrobial herbs I’ve come to the opinion that the treatment of this particular bug should be done under the care of a gut savvy clinician.

      I get that my answer can be frustrating but from my own experience I may have done more harm than good with the antimicrobial treatments. A more balanced approach with prebiotics and targeted herbs may be more indicated if blastocystis is the issue.

      This is the main driving force for me going back to university and studying to be a herbalist so I can help to provide people with the care they need with these complicated gut issues.


      1. Hi Nick, definitely keep us posted on how you go. Herbs should be tailored to the individual so brands and doses were avoided (as per comment above too).

        Any lactulose brand should do. I have used lac-dol with good success. There may be a SIBO picture with many blastocystis cases so go low and slow with this particular prebiotic!

  7. Omg, thank you for this insight Todd. I have been suffering from gut health problems to the point of depressed life and loss of partners who couldn’t handle my depleted energy state and optimism, because of the fatigued adrenals. This gives mi much home because still have blasto.

    My naturopath suggested I should eat, cinnamon, cloves, black pepper garlic and nutmeg with every meal if possible. I just ordered tests today will see if it worked, if not I’ll try your approach.

    1. Hey Jure. The spices and herbs sound like a good approach, especially the cloves and garlic. Just remember to keep an eye out for other possible gut conditions that may be the issue. I have found people tend to blame blastocystis just because it is easy to find. Keep us posted on your progress!

    1. Hi David.
      I tried a handful of diets from ketogenic to low-fat (that one is more indicated for Giardia infection though). I’ve come to the thinking that it is very individual and depends on what else is going on in the gut. Avoiding alcohol is definitely a good idea and I found a lower refined carbohydrate diet to be helpful too.
      Hope that helps!

  8. Thanks Todd. I appreciate the advice. I’ll let you know how I go. One last question – do you think apple cider vinegar would perform a similar function to a lactulose prebiotic?

    1. No problem at all. Apple cider vinegar may help with certain digestive symptoms but it won’t work like lactulose. Lactulose has a very specific effect on the gut flora. I found it incredibly helpful when I was treating my blastocystis infection.
      Keep us posted on how you go!

  9. Hello Byron,
    I really appreciate your website. I have been struggling with natural treatments for blasto these last few months (mostly essential oils like oregano, cloves, cinnamon and thyme and anti-parasitic tinctures with wormowood, etc. and s. boulardii + l-glutamine) and although they make me feel a bit better, the parasite is still there and I still feel sick. I was also diagnosed with SIBO / dysbiosis via a breath test but have no further details regarding this as the drs here in France are very limited what concerns this diagnostic. I am now wondering if I should concentrate myself on treating SIBO and if then the blasto will disappear or stop creating other symptoms?

    I must say that I starting feeling bad about 8 months ago after an antibiotic treatment for an UTI and right after I did (my first) gastroenteritis… Your opinion is very valuable to me, thank you in advance!

      1. Hey Roxana,

        Thanks for taking the time to share your experiences.

        Gut conditions can be complex but I would place SIBO treatment well above treating a blastocystis infection. The good thing is that most SIBO treatments will help on the blastocystis front too! It seems like you are on the right track with the herbs (although we focus on whole plant herbs rather than essential oils as they can be very rough on the beneficial gut bugs!). Was your SIBO breath test methane dominant, hydrogen or both? All very important in the treatment and maintenance phase.

        Hope that helps!


  10. Thank you for replying, Todd!
    Unfortunately I don’t know whether I have dominant methane or hydrogen SIBO as the dr wouldn’t give me any details / no written diagnostic either. And this was the only dr in the area which does the breath test… He gave me some dietary tips and some natural treatment which doesn’t work. Are there herbs / natural SIBO treatments which work for both types?

    Wishing you all the best!

    1. No problem, happy to help! There are a few herbs that overlap but the approach is very different when treating methane vs hydrogen dominant SIBO. It is possible to take a guess at which one depending on your symptoms. Here is some info on methane dominant symptoms and general treatment approaches
      Hope that helps! Sorry I can’t give specific health advice.

  11. Wow! So glad I came across your site after receiving the news today I have BH. I’ve had all the classic symptoms for YEARS and told everything from ‘it comes with age’, you’ll have to live with bloating, etc, ‘it’s in my head’… After reading your own journey I’m not going to waste time on Flagyl and go herbal. Will keep reading and share information with my nutritionist / herbalist. Thank you!

  12. Thanks for the kind words dawn! The website has been a labour of love, lots of personal experience and countless hours of research and input from some very gut savvy naturopaths who have been mentoring me! I hope it helps 🙂

    Just a comment on blastocystis. I have started to see it as a proxy for some deeper gut imbalances (not saying it’s not an issue but just to keep your eyes out for other gut issues…SIBO, large bowel dysbiosis etc).

    Keep us posted on your progress and sing out if I can help!


Leave a Reply

Your email address will not be published. Required fields are marked *