Blastocystis Hominis: What You Need To Know

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

Blastocystis hominis is a common gut parasite found here in Byron Bay, Australia and throughout the warmer climates of the world in general.

There is still debate on whether it is a problem bug.

If you are reading this then chances are you have found a Blastocystis hominis infection and are wondering what it is and what to do about it.

Read on learn more about this troublesome little gut bug.

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What is Blastocystis hominis?

Digging into the research it appears that Blastocystis hominis has been a tough nut to crack.

Originally it was classified as a “harmless intestinal yeast” only to be reclassified as a protozoan when researchers had the ability to sequence the RNA (1). 

It is extremely common in the human intestinal tracts and has been debated for over 20 years as to whether it is a normal resident or a problem.

That being said it is associated with many symptoms of illness (2).

Protozoan bugs are eukaryotic organisms making them much more complex compared to prokaryotes (bacteria and archaea.)

The headline for eukaryotic organisms is specialisation. Instead of a much simpler and smaller cell, eukaryotes have specialised internal organelles (3).

Blastocystis hominis original

Is Blastocystis Really To Blame? Please don’t skip this part!

This is the million dollar question.

Some clinicians and much of the research points to Blastocystis as a harmless protozoan that simple shares space in the gut with the rest of your microbiota.

Other research and many naturopaths and functional medicine doctors look at a Blastocystis infections as a problem that needs to be treated.

The answer may lie somewhere in the middle and possibly depends on you and the particular strain of Blastocystis (no not subtype here…the jury is still out on the relevance of different Blastocystis subtypes and their potential pathogenicity).

Before we move on I would like to leave you with one very important point.

Keep your mind open to other possible gut conditions before blaming Blastocystis completely.

It is a hard lesson and one that I wish I had learned before going on an all out campaign to rid this bug using very strong herbal antimicrobials. I’m sure I did more damage than good. This is why working with a clinician (naturopath, herbalist, functional medicine doctor, holistic doctor) that really knows the in’s and out’s of gut health and the microbiome is so darn important!

How Do You ‘Catch’ Blastocystis? – Routes Of Infection

The route of infection for Blastocystis is via the fecal-oral route.

Be cautious of any and all unfiltered tank water, especially in areas rich in wildlife.

It is quite simple to filter the parasite out so if you are considering living on tank water (as much of rural Australian’s do) then I would recommend a whole-house filter so that your shower, bath and washing up water is all properly filtered.    

Personal note: I will always be interested in Blastocystis. In my late 20’s I moving to the Byron Bay area and contracting it from contaminated tank water.

I spent three years battling the bug.

I finally cleared it, but still suffer residual gut issues from the infection.

There have been numerous visits to multiple doctors. The first doctor ran the stool test that came back positive for Blastocystis hominis and then suggested

A) not doing anything as many doctors don’t consider it a parasite
B) Taking an antibiotic that had roughly a 60% chance of success (his words not mine)
C) If all else fails that there a triple therapy that was showing good success formulated by the centre for digestive diseases. Basically carpet bombing your gut from what I could make out.

Symptoms and Health Issues In Blastocystis hominis Infections

The list of symptoms associated with a Blastocystis infection is long. Remember that any number of gut conditions could be causing these symptoms. Instead of blaming Blastocystis keep your mind open to other possibilities!

  • abdominal pain
  • discomfort
  • anorexia
  • bloating
  • cramps
  • diarrhea
  • constipation
  • alternating diarrhoea and constipation…the list goes on (1).

How common is Blastocystis?

A study performed in Turkey in 2015 sheds some light on that question.

The researchers looked at over 50,185 patients that presented to the Parasitology Laboratory at Yuzuncu Yil University. From that sample 0.54% came back positive for Blastocystis hominis.

Of those 0.54% (n = 275) 70.2% presented with symptoms associated with B. hominis (abdominal pain, diarrhea, anorexia etc) (4).

I would agree that there is the possibility that B. hominis is simply a commensal organism (natural/normal resident of the gut) that becomes opportunistic under certain conditions.

Along with the laundry list of possible symptoms (food intolerance is interesting here) there have been comments that B. hominis could be linked to IBS.

A few interesting case studies outline remission in both hashimoto’s disease (autoimmune hypothyroid) as well as ulcerative colitis (a type of inflammatory bowel disease) when Blastocystis hominis was eradicated (5, 6). 

The bug is also linked to chronic skin disorders and there is the possible connection with mast cell activation, characterised by intolerances to high histamine foods.

These connections less studies but I figured they were worth mentioning.

Testing for Blastocystis – Recommended Gut Testing

You really need to properly test if you suspect a parasite infection. If you don’t test you’ll be shooting in the dark!

There are a number of different stool tests available to screen for parasites.

One tests, offered by many doctors, and covered by medicare is what is called a PCR (polymerase chain reaction) test. It is quite sensitive and can detect fragments of DNA from the top 10 major pathogens (Blastocystis being one of them). It will also screen for a parasite called Dientameoba fragilis which is a common co-infection often found with Blastocystis.

Combining this test with a comprehensive stool analysis (CDSA) will give you more information on other possible infections including bacterial overgrowths and fungal infections.

GI stool test PCR pathogen
Image: A PCR stool test ordered from the doctor showing Blastocystis and Dientamoeba infections

Conventional Treatment Options For Blastocystis hominis Infections

Conventional medicine first looks to metronidazole (aka flagyl) as the first line of defence against Blastocystis hominis.

At first look it seems promising but many studies have indicated that strains or subsets of Blastocystis hominis are resistant to this antibiotic (7, 8)

Personal note: In my case this was the treatment I was prescribed by my GP. I had spent over 6 months with stomach pain when I ate, diarrhea daily, bloating and flatulence.

Not pretty.

I have been resistant to taking antibiotics in my life, attempting to reduce my exposure as much as possible. Taking metronidazole completely floored me.

It was evident that serious upheaval in my gut was happening.

My symptoms never completely cleared but they subsided for a month and then returned to full symptomatic force within two months.

Researching Blastocystis hominis treatment it seems clear that metronidazole is a bit of a fingers crossed kind of treatment.

A placebo control treatment trial (a real gold standard in science) compared metronidazole and a placebo in 76 patients that had only screened for B. hominis (other patients that had multiple co-infections were removed from the trial.) 

Of the group that had been given metronidazole, 80% showed clearance of B. hominis from their stool samples.

Sounds great right!

A retest after six months found that only 48% (n = 40) of the group receiving the antibiotic had actually cleared the infection (9).  

Anecdotally I have seen this very case of clearance (or clearance of symptoms) for period of time and then a full relapse of symptoms in dozens of people here in Byron Bay area of Australia.

Personally I have experienced this as well. This is why it is so important to re-test after treatment.

Herbal Treatments for Blastocystis hominis Infection

Antibiotics scare me.

The more I learn the more I’d like to avoid them for anything short of absolutely necessary.

The drawbacks of antibiotic use but for the time being the headlines on why to generally avoid them include

  • Disrupted gut microbiome
  • Evolution of resistant super bugs when they are not 100% effective (remember the recurrence of blasto 6 months later from the study above)
  • They are quite taxing on your body (immune system and liver particularly)

Now that’s not to say that herbal antimicrobials don’t tax your system.

Anything that knocks back microbes is going to have some negatives. One point that is essential in my opinion is first building yourself back up before moving into the killing phase. It is common for people to want the silver bullet that they can take and fix their gut.

Often times lifestyle factors are not even considered. There are a few factors that I would seriously consider when considering a strategy to deal with gut infections.

  1. Remove all offending foods. You want to work on fixing your inflamed and possibly leaky gut before taking antimicrobials.
  2. Be sure that you are have at least one bowel movement each day. Constipation is a serious concern if you are killing off parasites. You need to be sure that you are eliminating waste from your body!
  3. Definitely eliminate all alcohol! This is a no brainer, but something that most people ignore. You don’t want to be drinking any alcohol while you are preparing and then going through the killing phase.
  4. Repair the gut with supplements and herbs recommended by your practitioner.

Depending on how you feel physically that could do it.

Personally I felt 50% better after removing suspect foods, eliminating alcohol and taking some soothing gut supplements. The main point is that you are focusing on reducing inflammation in your gut by foods that could be irritants, improving digestion and elimination, and working at repairing your gut before you attempt to eliminate the parasites.

Most conventional, and even alternative approaches go straight to the killing phase.

A major issue with this is the stress the antimicrobials (or antibiotics) puts on your body. If you have a leaky, inflamed gut on top of that stress it is a recipe for disaster.

Western herbal medicine has a long history of treating gut infections. Working with a herbalist or naturopath that specialises in digestive health is important.

Herbal Medicine For Blastocystis

Herbal medicines that help to treat Blastocystis hominis infections include the following herbs like:

  • Berberine rich herbs (Coptis chinensis, Barberry, Oregon Grape Root, Goldenseal)  
  • Oregano leaf and oil
  • Olive leaf extracts
  • Wormwoods (including Artemisia annua, Artemisia absinthium)
  • Cloves
  • Black Walnut
  • Pomegranate husk tincture
  • Probiotics have shown to be helpful as well. Especially the Saccharomyces cerevisiae var. boulardii CNCM I-745 strain.

For a deeper dive into the herbal antimicrobials that have been successful see – Herbal Treatment For Blastocystis

Those Living With Blastocystis hominis Infections 

I have spent the past two years battling Blastocystis hominis.

First I went the conventional route. It helped for a month and then my symptoms came back with a vengeance.

There was no chance of reinfection as I became overly cautious of the possibility and carried my own spring water everywhere.

It took three rounds of herbal antimicrobial herbs, a complete rehaul of my diet and a focus on biofilms to successfully treat Blastocystis hominis. 

It was hard.

To everyone out there in the same boat I feel your pain.

This infection (and the handful of co-infections) has completely changed my life. Now I am on the track to completing my Health Science degree in Western Herbal Medicine so that I can help others who are in the same position I was in and currently have a wait list for when I graduate in mid December.

As I am still a student all I can do is share what I have (and am) learning on Blastocystis infections and hope that it helps.

Now I want to hear from you. What experience do you have with Blastocystis or other related gut infections. Leave a comment in the section below.

References and Resources

Legal and Affiliate Disclosures: This post may contain affiliate links. That means if you decide to make a purchase through one of these links, I may earn a small commission at no extra cost to you. Learn more here

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  1. Thank you for this reasonably science-based article that is not too dumbed down.
    May I suggest that the reason your symptoms/parasites came back after a month may be because the antibiotics killed off all beneficial bacteria leaving the parasite free rein. Even supplementing with probiotics may not have been adequate.
    All the best in your quest.

    1. Thanks so much for your comment and excellent point! The more I look into antibiotics, and even the more heavy hitting antimicrobial herbs, the more concerned I am about our poor neglected microbiome. I’ve just found some solid information on nurturing and boosting our beneficial gut flora so stay tuned.

    2. Most likely the anibiotic killed most of blastocystis, but does not affect their spores/eggs as there is a claim that they are very resistant.

  2. I’m dealing with this currently and theres no one willing to treat it with anything other than Flagyl. I have extremely painful acid reflux and sore stomach most of the day that gets worse after eating. I also have left side abdominal pain and a feeling of hot glue stuck to my insides. I’m at the point where I feel I need antibiotics immediately but doctors wont prescribe any for me because they say Blastocystis isn’t pathogenic. I’ve had this for a year now but its progressing rapidly. Even more so after I took the Flagyl. Please help 🙁

    1. Hey Stephanie, sorry to hear about your predicament! I’ve been in a similar position. As I am still a health science student I can’t help directly. I’ve finally found a naturopath that I’m happy to recommend, she helped me with leaky gut after I cleared up my blastocystis infection! Shoot me an email and I’ll put you in touch.

        1. Hi Todd. I was diagnosed with Crohn’s disease a few months ago, but micro biome testing showed blasto and dientomoeba but none of the characteristic inflammation markers for inflammatory bowel disease. I’m working with a functional medicine doctor who prescribed paromomycin and a bunch of herbals 2 months ago. Recent stool pcr showed blasto still present. Most of my symptoms still present – gut pain, fatigue and brain fog less but constipation worse than ever. I’ve been vego most of my life but now an anti inflammatory diet means I am eating more meat than ever. No wonder I’m blocked up!
          I just got a script for flagyl. Not sure whether to take it? Apparently the paromomycin should have worked. Plus another round of herbals coming too. FM dr tests and supplements has cost $3k so far.
          Wondering if paromomycin ever got rid of it or if reinfection an issue. Do you know where I can get my tank water tested for blasto?
          Frustrated 😞

          1. Hi Jodie, Thanks for your comment. In most of my IBD patients I focus on bacterial balance rather than parasites like blastocystis spp. and/or dientamoeba fragilis first. A high animal protein diet can feed up less friendly, pro-inflammatory bacteria in some patients and wouldn’t be my first recommendation for anyone with an IBD diagnosis. Review your microbiome data and if there is an overrepresentation of Proteobacteria reducing/rebalancing them would be my first treatment goal.

        2. Hey friends I’m Nat and have just read allll these comments and finally feel less alone. Xxx

          I’ve been working with my naturo for years to calm my gut inflammation down, so $$$ to keep it up, but have been doing my best… have had low ferritin (2!!) and have been GF and DF for years – fructose makes me look 7 months pregnant and gives me suchhhh pain.

          A few months ago I noticed major bloating and pain after urinating and 💩 — am insanely fatigued ALL the time, just tested pos for Blasto yesterday. Dr said nothing is wrong with me everyone has some amount of it (FFS!! Doctors grrrr!!!) Seeing my naturopath Thursday – I’m in so much pain, bloating and so fatigued. I cried after having a shower today as I was so exhausted 😩

          Anyway, at my wits end!! I took a risk and moved from Melb to Bris alone at 44 this year, to chase my musical dream and study full tome and it’s all so intense 🤪🤪🤪😭😭😭

          Anyway thanks for this forum Todd it’s much appreciated.

          Nat 🙂 ☺️☺️☺️

    2. Hi Stephanie, did you end up clearing your Blasto? I just got diagnosed today and got put on 3 different antibiotics over a 10 day period. My integrative doctor said Flagyl does not work.
      I’m in Sydney if you need an amazing doctor.

      1. Hi Gabriela, I just got prescribed the same 10 day course of 3 antibiotics by my gastroenterologist. Just wondering how your experience was and if you have any tips? Is it worthwhile to add in some natural remedies at the same time do you think?

  3. Hi, thanks so much for your article it was really helpful. I got Blastocystos and entoameba while I was in indonesia 5 years ago. I treated them there with antibiotics and the tests where clear. 2 years and a pregnancy after i started to have problems and exploring I found out I had Helicbacter and the parasites where still there. I got flagyl for the parasites and a triple protocol for helicobacter without success. I changed doctor and discovered I also have SIBO. Since then I have been reading about it. I dont see the points of doing more antibiotics as that is probably the reason why I have SIBO but I am unsure how to sort this and what to tackle first.

    1. Hi Eli.

      It sounds like you’ve had quite the experience! Often times testing too early can show false negatives (you have cleared these parasites when you haven’t). What you are describing (the SIBO connection, multiple infections, possible large bowel dysbiosis) is very common, especially in people from tropical climates (this is what happened to me!).

      First priority would be tackling Entamoeba (assuming it is histolytica). The herbs here are very strong and might help on the SIBO front as well. Then SIBO would be second. Finally if you are still symptomatic Blastocystis would possibly need to be addressed as well.

      Drop me a line if you would like to be placed on the wait list –

      Happy to answer any follow up questions here too 🙂


  4. Hi there. My partner has just been diagnosed with blasto and I am waiting to hear if I have it also. I have just finished a radiotherapy and chemotherapy treatment and have had persistent nausea and burping that will not resolve ever since. Our whole house runs on well water which we have been assured is safe, but has never been tested. Obviously we are pretty upset about this, as my partner has been very sick with diahorrea and extreme fatigue for ages, and I have a very compromised immune system. We have bought spring water for drinking, but I want to know if it is safe to cook with, and to drink if it has been boiled, and also is it safe to shower in, wash dishes in etc. signed worried and sick.

    1. Hi Darielle. In most folks I now see blastocystis as just one part of an imbalanced gut ecosystem (especially if you have symptoms). Chemo can really knock your gut microbiota around so this could help to explain your symptoms as well (bacterial imbalances and overgrowths as well as the blastocystis infection).

      There is evidence to support boiling water as a treatment. If blastocystis is in the well water then showering, washing your dishes and brushing your teeth will all be vector points for infection. The cyst form is incredibly resilient.

      Reach out if I can help in any way!

  5. Hi there, lve got blasto for the second time in 12mths!! Im wondering what the 3 antibiotics that some have been prescribed, lve done 2 rounds of flagyl and 1 on tindanazole.(l think these antibiotics are just feeding the disease) Im so over this.

  6. Bonjour je vous demande de l’aide svp on m’a découvert 2 parasites depuis 4 mois blastocystis hominis et dientamoeba fragilis je perd beaucoup de poids je suis très fatigué j ai comme une gêne lorsque je respire..j ai essayé plusieurs traitement en 1er :14 jours de flagyl,puis:10 jours de ornidazole,et pour finir:15 jours bactrim qui n’ ont rien les parasites sont toujour j ai contaminé mon fils de 7ans ..avec le dientamoeba fragilis. Aidez moi svp

  7. Hi there, I’ve had the dreaded blasto twice, once about 8 years ago, and more recently two years ago. I am pleased to report that I managed to defeat it – twice – by taking the triple therapy, known as the ‘triple cocktail’. Extremely harsh on the gut microbiome, but successful in eradicating blasto. It is a slow, arduous process then rebuilding the gut microflora and my digestion has most likely suffered as a result. It’s a bugger, for sure.

    1. Hi Heather, could you give me some info on how to obtain the triple therapy here in Sth Aust. My doctor has not heard of it & is not really interested in investigating the triple therapy. I have tried 3 different antibiotics which haven’t worked for my Blasto. Am getting desperate, thanks.

      1. Hi Ron,
        Could you please share the triple therapy and advise on the doctor who worked with you.
        Thanks so much.

  8. Hi Todd,
    Thank you for your article. I became very sick with severe left sided pain and constipation in India in 2000. In 2006 I was diagnosed with left sided ulcerative colitis and my blood tests showed Blasto as well. I’m from Victoria and hadn’t travelled to any other states so I think it must have happened India. I did some research and found that often people with colitis tested positive for Blasto. My doctor laughed at the suggestion. I still have colitis flair ups and after reading your article I am going to have another blood test and if Blasto is still there I am going to work on eradicating it.

  9. Hi from Canada, I’ve been dealing with treatment resistant DFrag and BHominis for several years. I came across this new promising tri-therapy enema treatment. I’m speaking with the Tropical Medicine Department of Toronto General Hospital but they are taking forever to get back to me…

    I would like to give it a try to maximize chances of eradicating my treatment resistant DFragilis and BHominis. I am comfortable administering this treatment at home.

    Any chance I could get a prescription (and buy it from from an AUS Dr you’d recommend?

    Best regards,


  10. Thanks for all this! Is there anymore info you have on the PCR and FMC test results? I had an FMC initially positive but returned negative upon flagyl and herbal treatment. A following PCR at the request of my dietician said Blasto DNA was detected though? Does this mean it’s clear or not?

  11. I am treating my second Blasto infection and am so grateful for people such as you who bring this to light.

    On a positive note. You will learn so much about your body through the treatment process

  12. I have been diagnosed with blasto 4 yrs ago after swimming in a mountain stream. I have had the symptoms go away several times up to a year and a half. All the while having about 10 ounces of red wine at happy hour daily. I have been trying to treat it with about two cloves of raw garlic, oil of oregano and a suggested pro biotic. I don’t eat sweets but do have carbs , brad, rice, crackers etc. my most current bout with it after being symptom free for about 18 months started with a loose stool. Not diahrea and with the garlic etc my stool is back to being very normal however many days I still have stomach constant mild pain. It goes away at night. I know drinking the wine is surely not helping. I have not lost weight and don’t have any of the other stated issues or symptoms. I did try one antibiotic, not flagyl two years ago which did not help and am afraid to try more after reading all the comments on failure to work. I see no blood in my stool which is good. My stomach constantly growls obviously after eating but for hours.

  13. I’m a senior here over 70 , and last year started to see fast weight loss 16 pounds when you are thin to begin with . Took metrondizole for 7 days 750 mg , just about devasted me .. felt so toxic as I just had finished amoxicillin for tooth infection. I was free of B hominis in Feb and now in July , it has returned .. Dr. wants me to take metrondizole again .. I don’t think i can . Will try oregano and eat more garlic and probiotics. Some say probiotic with S. boulardi may help .. will look into it

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