Is Blastocystis a problem after all?

blastocystis is it a problem and how to treat it

Since publishing my experience successfully treating Blastocystis spp. (formerly Blastocystis hominis) I have been contacted by hundreds of people looking for help treating their Blastocystis infection. 

Lately I have been wondering if it is really necessary to completely eradicate Blastocystis at all. 

I know this isn’t going to be a popular post but hear me out.

My History with Blastocystis

I can remember sitting across from the doctor who found Blastocystis by running the standard PCR stool test that is commonly run when a patient complains from digestive health issues. 

He explained that currently Blastocystis is not a problem, that it was very hard to treat (read resistant to antibiotics) and it was up to me to decide if I wanted to treat it or not.

A quick google search revealed that Blastocystis was as issue (thanks dr. google) so I opted to treat the bug.

And so it started. 

Not only did the antibiotics fail to work, my symptoms actually worsened! 

Years and years of different herbs and still no luck. 

Finally one long and strong herbal protocol knocked out Blastocystis and Dientamoeba fragilis. 

I felt better so assumed that Blastocystis and Dientamoeba fragilis had caused my digestive problems. 

Then after 6-8 months some of my symptoms started to creep back. 

Even though I had successfully killed Blastocystis and Dientamoeba fragilis I was still experiencing 

  • Significant bloating 
  • Constipation 
  • Constant headaches 
  • Food intolerances
  • Anxiety
  • Poor sleep
Anxiety is a common symptom of poor gut health

The root cause of poor digestive health

My mistake was immediately blaming Blastocystis for all of my digestive health issues. 

The internet (and even scores of scientific papers) informed me that it is pathogenic and should be removed at all costs. 

I think this is because Blastocystis is easy and cheap to find on a standard DNA based stool test that your doctor can order (most of the time for free).

Because it is easy to find I feel it often gets blamed for other, harder to find, gut issues.

If someone approaches me wanting to treat their Blastocystis infection I keep a few things front and center in my mind

Blastocystis may not be the problem here. It may not be the root cause of your symptoms.

Other root causes that may need to be ruled out first include 

That last point is incredibly important. 

Let me explain why.

Blastocystis has been shown to produce cysteine protease which some research points to as a cause of an inflammatory response and some of the symptoms that you may be experiencing. These proteases cleave our immune systems defences (sIgA) and allows Blastocystis to take up residence in the gut (1).

Here’s the interesting bit.

These protease enzymes operate best at a neutral pH and less so in an acidic environment (2).

Furthermore, the amoebic form of Blastocystis, often seen in symptomatic people, is associated with a higher level of protease enzyme activity (3).

Image taken from: Amoebic forms of Blastocystis spp. – evidence for a pathogenic role

A healthy gut is an acidic gut. 

Ensuring that the gut is acidic may reduce the pathogenic nature of Blastocystis. Prebiotics like lactulose are very helpful. The trick here is that lactulose (and a number of other prebiotics) can be contraindicated in certain SIBO cases.

Many of the beneficial bacteria produce short chain fatty acids such as butyrate, acetate and propionate. These lower the pH of the gut and, generally speaking, keep everything in balance. 

There’s a deeper dive on the subject of short chain fatty acids, dietary fibre consumption and all the befits here. Check it out.

Image taken from: Vecteezy

One great example of this (there are many) is the ability of an acidic gut, thanks to the short chain fatty acids, to keep Candida from converting from a harmless unicellular yeast into the pathogenic hyphal form.

Beneficial bacteria in the gut can also keep Blastocystis from spreading and taking hold (4).

This is a pattern that I have been seeing crop up again and again. It is why it is so important to assess the whole bacterial composition of the large bowel when working out how to help someone heal their gut. 

The ecosystem approach to gut health is key in the healing process.

But how do we determine your root cause?

History, history, history

Good case taking is all about the history of the patient. During my Bachelor of Health Science studies at ACNT one of my lecturers repeated ‘a good case covers history, history, history

What does this mean?

Everything that you have experienced leading up to your Blastocystis infection and the symptoms you are experiencing now is so darn important! 

On top of that is important to know everything that you have done to treat your Blastocystis infection to date.  

It is incredibly common for people to have taken 1, 2 and even 3 rounds of antibiotics. Many have even attempted the triple therapy with no success! How much damage has been done to the gut flora with these attempts? 

Even stronger herbal antimicrobials can lead to a disrupted gut microbiota.

An imbalanced or disrupted gut flora has a harder time producing the fantastic, amazing, beneficial short chain fatty acids to keep the gut acidic and healthy. 

Then, less than friendly bacterial overgrowths can sneak in and set up shop. 

Properly evaluating a patient

At the beginning of this article I mentioned that the doctor who discovered I had Blastocystis also mentioned that it may not be a problem.

What he didn’t do was comment on what possibly could explain my digestive problems.

I know how frustrating that is so I didn’t want to repeat that same process for you here. 

A proper evaluation for other possible issues includes (only when they are indicated from the history and presenting symptoms) 

One. Small bowel assessment – aka SIBO breath tests

These are indicated if you are experiencing 

  • Bloating 
  • Nausea 
  • Constipation 
  • Diarrhea 
  • Brain fog
  • Exhaustion

The real key here is how quickly you are experiencing any of these symptoms after a meal. If it within 2 hours of a meal (many times certain FODMAP foods can be triggers) then SIBO is a possibility and needs to be ruled out with more questions or a SIBO breath test.

Many times this will come back positive in patients with Blastocystis. Most of the time when the SIBO has been successfully treated people feel better. They still have Blastocystis.

Why is this? 

Research is still teasing out the details but I believe it is due to what we may soon recognise as post infectious SIBO. 

While this is early days, the thinking involves exposure to a number of different bacterial infections including, among others, Campylobacter jejuni, Salmonella, Escherichia coli, and Shigella. These, and many more bacterial infections, can cause acute gastroenteritis (5).

These bacteria can produce cytolethal distending toxins which the immune system recognises as an issue and creates antibodies to defend the body with. 

Image taken from: Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects

There is some cross reactivity and antibodies are formed against a protein found in the gut called vinculin. 

This process is outlining an auto-immune response triggered by infections! Something that should set off alarm bells for anyone that has experienced gastroenteritis and has never felt right since. 

Image taken from: Development and Validation of a Biomarker for Diarrhea-Predominant Irritable Bowel Syndrome in Human Subjects

The last part of this puzzle involving self-directed antibodies resulting in an autoimmune response is the functionality of vinculin. If the body has targeted this protein in the gut and is damaging it, what are the consequences?

Vinculin has a number of roles in the body. One of these roles involves gut motility. These self directed antibodies (an autoimmune response) impair the body’s ability to sweep the small intestine and prevent bacterial overgrowth (6).

Image taken from: Vinculin – a dynamic regulator of cell adhesion

So bringing it back to Blastocystis for a moment. 

You have some digestive upset. Maybe you have been overseas and experienced food poisoning or maybe, like me, you have been exposed to toxic tank water (very common in many places in Australia and overseas). 

A stool test reveals Blastocystis and you go on an all out campaign trying to rid yourself of the bug that is causing all of your digestive health issues when in fact this post-infectious autoimmune process is impairing the body’s ability to keep the small intestine clear and free from bacterial build up.

In this case I would 100% treat the small intestinal bacterial overgrowth and work on fixing the gut cells that have been damaged first. After this process we can circle back and reassess symptoms.

Two. Large bowel assessment 

The makeup of the large bowel almost always needs to be assessed.

The longer you have been sick and the worse your symptoms the more this is needed.

Ubiome was a popular was to assess the composition of the bacteria in the large bowel. Unfortunately they have since gone out of business. 

Other DNA based stool tests such as Thyrve have stepped in to fill the void. 

Image taken from: Thryve

Unfortunately a CDSA (as I previously suggested) doesn’t give you reliable, let alone enough, information. You need to know as much as possible about the balance and make up of your large bowel! 

These microbiome composition tests don’t screen for things like fungal overgrowths or worm infections. 

In very rare cases where someone has been sick for quite some time a gut test that specifically focuses on important infections and bacterial overgrowths may be required. 

Here the GI-MAP (or in Australia the Complete Microbiome Mapping test) is bar far the most comprehensive test. If this test didn’t cost over $350 dollars I would be inclined to order it more frequently. As there is information that is far more important that the GI-MAP doesn’t cover I only reserve it for specific cases

Three. Parasite assessment 

As always only if indicated. 

Things like Giardia and Entamoeba histolytica are known pathogens and need to be treated. 

While I am hesitant to pull out the big guns, herbally speaking, for Blastocystis, parasites such as Giardia, Entamoeba histolytica, Cryptosporidium and bacterial infections such as Campylobacter, Salmonella and Yersinia all need to be dealt with, and quickly. 

Finally Helicobacter pylori is always front and centre when people have symptoms such as upper gastric pain, a feeling of uncomfortable fullness after eating and signs of low stomach acid. 

Most of these tests can be ordered by your doctor (and are hopefully free/covered by your insurance). It is important that they are DNA based tests (the PCR test is commonly used). For H. pylori, a stool antigen test is the most accessible and reliable. 

Three. Other commonly missed gut disorders

One of my mentors, Dr. Jason Hawrelak, recently presented at a conference on a particular case study. The patient he had diagnosed 12 years ago with Blastocystis eventually managed to eradicate the bug with antibiotics and round after round of strong herbal antimicrobials only to find that his symptoms did not improve. 

The same patient returned to his clinic (12 years later) and, using his updated knowledge and understanding (instead of simply blaming Blastocystis) Dr. Hawrelak discovered he had coeliac disease and SIBO. 

Keeping the ‘diagnostic net’ wide when presented with a Blastocystis case is so important.

Blastocystis may not be pathogenic in most

So we have covered a few bits and pieces around not always blaming Blastocystis.  

In exploring the possibility that Blastocystis could be harmless in some (or even many) people, some research has shown that this particular bug increases bacterial diversity and evenness of the gut flora (8).

Image taken from: Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies  

The other important thing to note is that Blastocystis is extremely common in both industrialised and non-industrialised countries, even in healthy, asymptomatic people. 

One study on a population of healthy individuals in Ireland found Blastocystis in 56% of the 105 people that were sampled (9).

I can almost hear you asking…’but what about pathogenic subtypes?’

The same study noted that a range of different subtypes were present in the healthy people that had Blastocystis. There doesn’t seem to be an agreement on whether one specific subtype of Blastocystis is worse than another and the research is mixed. 

Image taken from: The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota

The authors speculated on the possibility of pathogenic strains of Blastocystis or even intra-subtypes. 

Finally, it is worth thinking on the evolutionary context of Blastocystis. Microbes are everywhere. It seems almost impossible to think that Blastocystis and Dientameoba haven’t been hitching a ride alongside humans for eons and may contribute to immune system regulation in many asymptomatic people (10).

This reminds me of both Helicobacter pylori and worm infections (helminths to be precise). 

Helicobacter pylori may have been a gut resident in humans since the dawn of our race. Over time we have been systematically eliminating it (see the graph below). The decline in Helicobacter pylori has been marked by a significant increase in asthma, obesity, gastroesophageal reflux disease, Barrett’s oesophagus and adenocarcinoma of the esophagus (11, 12). 

Are these linked? Possibly.

Image taken from: Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism

While Helicobacter pylori can cause a range of different (and serious) gut diseases, many people don’t appear to suffer from any issues from this bacteria. Infection in developing countries is high, but in certain places, such as Africa, Malaysia, India, China, Colombia and Costa Rica, the rates of gastric cancer are low (13).

Blastocystis may be an issue in some

I think it is important to rule out any other digestive health issues (SIBO, dysbiosis, other parasite infections) before blaming Blastocystis for your symptoms. 

With that said, there may be pathogenic strains of Blastocystis out there that may need to be treated with long and strong herbal antimicrobials or even antibiotics combined with herbal medicine.

Seeing as both of these options are less than ideal it is important to keep them for last resort options for regaining your digestive health. 

When other common gut conditions have been ruled out and it appears that Blastocystis is the problem then herbal medicine can play a strong role in helping eliminate or reduce this particular microbe. 

Do you have any thoughts on Blastocystis? Share them in the comment section below. 

References and Resources

  1. Recent advances in Blastocystis sp. research 
  2. Protease activity of Blastocystis hominis
  3. Amoebic forms of Blastocystis spp. – evidence for a pathogenic role
  4. The influence of probiotic bacteria and human gut microorganisms causing opportunistic infections on Blastocystis ST3
  5. Assessment of Anti-vinculin and Anti-cytolethal Distending Toxin B Antibodies in Subtypes of Irritable Bowel Syndrome
  6. Autoimmunity Links Vinculin to the Pathophysiology of Chronic Functional Bowel Changes Following Campylobacter jejuni Infection in a Rat Model
  7. Vinculin – a dynamic regulator of cell adhesion
  8. Microbial Eukaryotes: a Missing Link in Gut Microbiome Studies
  9. The microbial eukaryote Blastocystis is a prevalent and diverse member of the healthy human gut microbiota
  10. Eradication of blastocystis in humans: Really necessary for all?
  11. Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism
  12. Helicobacter pylori: a beneficial gastric pathogen?
  13. The enigma of Helicobacter pylori infection and gastric cancer
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  1. Hi Todd,

    Great info – thanks!
    You point out that, after SIBO, it is important to fix the gut cells that have been damaged, in order for the MMC (gut motility) to work properly.
    How does one fix the gut cells?

    1. Yes indeed that is the big question. There are very helpful herbs that can improve the damaged cells. Iberogast comes to mind (I’m not sure if it is available in the states). Improving gut transit time and dealing with bacterial overgrowths really helps to move the needle too. Finally we want to improve gut permeability (leaky gut) if present.

  2. Todd, thanks man for putting this out there, including your experiences. I’m in the midwest/US, have dealt with some mild gut and inflammation issues through the years. was diagnosed with blasto few months back, with some slightly out of balance gut flora…naturopath did herbal protocol – combo of garlix, berberis, and intestibal with parasite formula for 40 days. tested and still there. in the meantime, during that protocol I developed some nasty upper GI stuff (discomfort, burping, acid reflux), including globus sensation (lump in throat) and some pain in and around ears. honestly kinda scared me. but i read you stuff on mast cells which resonated. i just now am starting to feel it go away…big relief, but still have some discomfort. in the meantime, he’s recommending flagyl for the blasto….just doesn’t seem worth it based on what i’ve seen/read. think i’d like to focus on other gut matters. any thoughts you have on that are appreciated. also, did not see any suggestions on colonics, curious about your thoughts on that (but that obviously goes away from the herbal methods being discussed). if this is asking too much i’m happy to discuss with you in a separate venue.

    1. Hi Mike.

      Thanks for the kind words!

      Is blastocystis an issue, thats the big question. Good on you for keeping your mind open to other issues.

      I would want to explore the out of balance gut flora. An incredible amount of research has been coming out over the past 5 years showing that large bowel imbalances can be a root cause driver of gut health issues and even more serious diseases. SIBO is also massively under recognised (that may or may not be your issue and symptom presentation might hint at that).

      In regards to the symptoms during the protocol I would want to explore whether you were having an allergic reaction to the herbs. The pain around the ears is a big flag for that. Was there anything in there that may have triggered a reaction?

      On the flagyl comment. I have heard from dozens and dozens, possibly hundreds of people that have not had success with this antibiotic. That is not saying it won’t work for you if you choose to go down that route, just something to consider.

      Colonics wouldn’t be a part of my approach but may help if you are significantly constipated. Depending on test results I would prefer to focus on rebalancing.

      Feel free to get in touch if you prefer to chat over email –

  3. Todd,

    Thanks so much for the prompt response.

    Your question about whether or not there was anything in there that may have triggered a response…I just don’t know. To a large degree, I feel like trying to sort through that is a ‘needle in the haystack scenario’…one of the herbs may have triggered it, the capsules the herbs were in may have triggered it, the combined components of the protocol might have triggered it (i.e., gut deals with all of them fine individually, but it was the combo that caused the reaction)….at least that’s just my take on it.

    I have certain IgG food sensitivities/reactions according to my blood test, but I’m still mixed on how accurate I view those.
    My doctor and I concluded I have some leaky gut issues based on some of my GI discomfort and occasional minor breakouts (few pimples) after certain meals (mostly containing dairy and/or gluten).

    My bacteria/stool assessment showed no reading of Bifidobacterium and Lactobacillus in my gut (apparently a problem); showed little overgrowth of klebsiella pneumoniae and siccibacter turicensis, and little bit of candida. No readings of dysbiotic flora. This test was done just before the blastocystis herbal protocol. I’d invite any thoughts you have on that.

    I think my preference at this point is to prioritize other aspects of gut health…be it proper bacterial balance, increase stomach acid, etc… rather than a crusade to kill the blasto. And in doing so, hopefully minimize blasto’s negative impact, and perhaps slowly kill it with herbal remedies that may be more gradual.

    So, all that said, if you have any protocols/advice you’d point to based on data/preferences I’ve outlined, I’d really appreciate it.

    I am happy to compensate you for your thoughts on this. Thanks again for your willingness to tell your story, and the research you’ve done on the topic.

  4. Also Todd,

    I think you had mentioned it was VERY important for you to give up coffee (ouch) as part of your healing process. Sounds like you view that as pretty critical?…Any other items/foods you view the same way?

    1. Hey Mike,

      Yes indeed, intestinal permeability (leaky gut) may be a picture. That can also drive these IgG food sensitivities, which generally resolve when the gut has been healed and sealed.

      Leaky gut testing may be indicated. I have found it is very helpful to help explain why people are so symptomatic around food. Plus it really helps with compliance!

      As for the stool assessment it very much depends on what stool test you used. Many clinicians are still using the culture and microscopy used in CDSAs (drs data, nutripath CDSA, etc). I consider the results (particularly the parasite testing and the bacterial assessment) extremely unreliable. Nowadays many clinicians, including myself, have moved towards DNA based, culture independent tests (GI MAP, thryve, PCR parasite testing). These are much more reliable when assessing bacterial balances.

      When working with patients here at Byron Herbalist we will be focusing on other digestive health issues before targeting blastocystis specifically (SIBO, coeliac disease diagnosis, large bowel infections and overgrowths…). Blastocystis can be eradicated but it does take time and can cause damage to the gut ecosystem so I would prefer to avoid that if it isn’t a problem for the patient.

      Coffee for me was a major trigger. Caused headaches and sore lymph nodes. I believe it was a histamine reaction! This was possibly triggered by the leaky gut (confirmed via testing). Now that I have improved my gut health I can tolerate coffee but it was important for me to completely remove it for a period. Some patients may need to. It is a case by case process 🙂

  5. Out of desperation I had triple antibiotic infusion via colonoscopy late 2018. Things were great for the first 6 months but then I started to experience hair loss, my skin became itchy and reactive, chronic joint and soft tissue pain, chronic cough, fatigue, dry eyes, reactive gut etc etc. I went down the autoimmune rabbit hole without solution. I’m only now getting tested for protein malabsorption as part of a stool analysis. It’s now thought that the cure was worse than the cause, in my case.

  6. I found your ideas on Blasto very interesting. I had it two years ago and got rid of it with paracea forte over 2/3 months. I was very disapointed when I found out ( stooltest) that I have it again and can’t understand why when I only drink filtered water. My Doctor thinks my Billi water filtering system wouldn’t be doing it’s job. Do you have any ideas where you think most Blatos come from. I’m very healthy dairy and gluten free but have a mild case of Hashimotos.
    I will be starting the Paracea forte again. Thank you

  7. Hi there – we live on the Sunshine Coast on tank water. For the last couple of months our family (2 adults and 2 kids – 6 year old and 16 month old) have all bouts of diarrhoea. We’ve all tested positive to Dientameoba. On checking our water tank filter – the power box has been blown. So we’re not sure how long it hasn’t been working. Anyway all fixed now. Dr thinks we should give it another month to see if we’re all still symptomatic. My question is – if we’ve been drinking continuously contaminated water, now thats fixed and we’re not reinfecting ourselves – can the parasite clear on its own? Would you blame the parasite for our diarrhoea- or perhaps we’ve been unlucky with gastro bugs (given the ages of our kids). I just don’t know if I should treat us all or not! Hoping now our tank water has been fixed our symptoms improve.

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