The Surprising Controversy of Blastocystis

by , | March 3, 2024 | Articles, Gut Health

parasite gut health

Written by Jonah Udall; Select sections of article researched, written by, and reviewed by Dr. Bojana Jankovic Weatherly.

If you’re like most people, the mention of parasites probably gives you the ick. You may think of severe gut infections from contaminated water, or maybe even scenes from a horror movie. Ew.

A “parasite” is an unwelcome organism that steals from its host. Many different species are lumped into the category of parasites, from single-celled protozoa to larger helminths, also called worms. Parasites can cause serious disease in the gut and beyond, and eradicating parasites can be an important part of natural healing.

But, what if we’re wrong about some “parasites”? What if some of these organisms can actually be beneficial for some of us—even just some of the time?

Not long ago, this same idea sounded far-fetched about bacteria. For most of the past two centuries bacteria were only the bad guys, but research on the gut microbiome has changed our tune. We now know that trillions of good bacteria live in our guts, and our health depends on them. While we know a lot less about the other organisms in our guts, research suggests that viruses, fungi, and even some “parasites” may be helpful players in the gut microbiome as well.

In this article, we’ll explore the latest research—the bad and the good—on Blastocystis, one of the most common and controversial parasites today.

What is Blastocystis?

Blastocystis is a microscopic multicellular organism that can be found in the guts of several mammals, including humans and rats. It is the most common parasite in the US, and likely the world.

Numerous studies have found that 5-30% of stool samples from healthy individuals in western industrialized countries have Blastocystis, while up to 100% of samples from healthy populations in rural countries are positive.1,2 Sanitization practices likely explain this difference. Blastocystis cysts shed in feces are transmitted more readily through unpurified drinking and bathing water in non-industrialized settings.

The dark side of Blastocystis

First, the bad news. Blastocystis is well-known to be associated with several diseases.

Blastocystis has been found in numerous case reports to cause reactive arthritis—otherwise unexplained joint pain that resolves when the parasite is eradicated. However, among parasites, Blastocystis appears to be a less common cause of reactive arthritis, despite being the most prevalent parasite globally.3

Numerous studies have found on average that people carrying Blastocystis have a 78% increased odds of being diagnosed with Irritable Bowel Syndrome (IBS).4 A meta-analysis of studies including over 100,000 participants found that carrying parasites such as Blastocystis increased the odds of anemia by 160% among pregnant women in particular.5 However, for both IBS and anemia of pregnancy, these observational studies don’t tell us what causes what. Blastocystis may take advantage of the gut conditions created by anemia and IBS, rather than contributing to disease.

There have been 23 reports published on cases of urticaria, or hives, that were resolved upon antiparasitic treatment for Blastocystis.6 In all cases, other more common causes of hives were ruled out first.

In two separate cohorts, individuals with Blastocystis had lower executive function scores on standardized cognitive tests.7 Fecal microbiota transplants from Blastocystis-colonized humans reduced cognitive function in mouse recipients, suggesting Blastocystis may be a possible cause of cognitive decline.

Lastly, in a study on people with Hashimoto’s thyroiditis, those carrying Blastocystis had clinically-relevant reductions in TSH (the main marker of thyroid function) and IL-17 (an autoimmune-related cytokine) when the parasite was eradicated.8

The hygiene hypothesis

Nonetheless, the widespread prevalence of Blastocystis in people without overt disease or symptoms has led to the suggestion that this “parasite” may be a normal, or commensal, gut resident.9 Some research also suggests that in many, if not most cases, Blastocystis is harmless or may even have benefits.

Our immune systems evolved to deal with all kinds of microbiological threats from our environment. The “hygiene hypothesis” is a widely accepted theory that reduced exposure to parasites and other microbes due to heavy modern sanitization is in part responsible for our modern epidemics of allergies and autoimmunity.10 Without parasites to keep in check, our immune systems may be more prone to overreact to our environment or our own cells. 

Indeed, rates of allergies and autoimmunity are far lower in the non-industrialized countries where Blastocystis is widely prevalent. Parasites engage the same immune system pathways involved in allergic responses, which may become hyperreactive without regular exposure to environmental parasites.

In fact, human clinical studies have shown that intentionally infecting people who have multiple sclerosis with worms may reduce autoimmunity symptoms and improve immune function.11 Parasites may help to regulate the immune system and reduce autoreactivity.9,12

A “keystone predator”

Microscopic parasites like Blastocystis may also play an important role in shaping our gut bacteria. Some microbiome researchers suggest that in the right context Blastocystis may act as a keystone predator—like the great white shark, or grizzly bear. Keystone predators can keep a whole ecosystem in balance, preventing any one species from overrunning the others.

Research has consistently found that people carrying Blastocystis have higher microbiome diversity, suggesting it may play an important role in maintaining balance in the gut.13–15

Blastocystis has even been associated with reduced fecal calprotectin—a marker of inflammation—in healthy individuals,16 and also in people with autoimmune spondylarthritis.17 Several studies have observed that people with inflammatory bowel disease (IBD)—characterized by extreme gut inflammation and elevated calprotectin—have far lower rates of Blastocystis than controls,15 while those who do carry Blastocystis have less severe disease.18 IBD is commonly associated with low microbiome diversity, which Blastocystis may protect against.

However, people with IBD who do have Blastocystis may be more likely to have a problematic infection. In one study, Blastocystis rates in IBD patients were far higher among those who were unresponsive to standard treatment.19 When the parasite was eradicated, these patients improved.

These examples show how the harms or benefits of Blastocystis depend on context—this organism can either help establish balance in the microbiome, or throw it off.

Testing and treatment

The tried-and-true method for testing Blastocystis is microscopy—simply looking for cysts in a stool sample under a microscope. Numerous tests use microscopy for Blastocystis, including Genova’s GI Effects and Testing multiple stool samples may increase the odds of detection, as cysts may not be present in every bowel movement. For this reason, when testing for parasites in stool, three samples are required. 

PCR can also be used to detect Blastocystis DNA, though less research has validated this method. Anti-Blastocystis antibodies are not reliably elevated in people carrying the organism.20–22

If you find you have Blastocystis, how do you know when you should treat it or leave it alone? Treatment of blastocystis is controversial. Future research may yield new tests that allow us to distinguish between commensal and pathogenic Blastocystis in a lab, but for now, the best approach is to rely on the clinical expertise of an experienced practitioner who can rule out other pathogenic organisms that may be causing symptoms, and determine if treating Blastocystis is appropriate.

If your symptoms match those commonly associated with Blastocystis—which may include loss of appetite, constipation or diarrhea, and otherwise unexplained joint pain or hives—or you have a condition known to be associated with Blastocystis, eradication may be warranted. Talk to an integrative or functional medicine internist or gastroenterologist about the right treatment for you. Otherwise, you may just want to count yourself lucky to have this keystone predator looking after your microbiome.


1. Asghari A, Sadeghipour Z, Hassanipour S, et al. Association between Blastocystis sp. infection and immunocompromised patients: a systematic review and meta-analysis. Environ Sci Pollut Res Int. 2021;28(43):60308-60328. doi:10.1007/s11356-021-16187-1

2. Popruk S, Adao DEV, Rivera WL. Epidemiology and subtype distribution of Blastocystis in humans: A review. Infect Genet Evol J Mol Epidemiol Evol Genet Infect Dis. 2021;95:105085. doi:10.1016/j.meegid.2021.105085

3. Zeidler H, Hudson AP. Reactive Arthritis Update: Spotlight on New and Rare Infectious Agents Implicated as Pathogens. Curr Rheumatol Rep. 2021;23(7):53. doi:10.1007/s11926-021-01018-6

4. Abedi SH, Fazlzadeh A, Mollalo A, et al. The neglected role of Blastocystis sp. and Giardia lamblia in development of irritable bowel syndrome: A systematic review and meta-analysis. Microb Pathog. 2022;162:105215. doi:10.1016/j.micpath.2021.105215

5. Taghipour A, Ghodsian S, Jabbari M, Olfatifar M, Abdoli A, Ghaffarifar F. Global prevalence of intestinal parasitic infections and associated risk factors in pregnant women: a systematic review and meta-analysis. Trans R Soc Trop Med Hyg. 2021;115(5):457-470. doi:10.1093/trstmh/traa101

6. Bahrami F, Babaei E, Badirzadeh A, Riabi TR, Abdoli A. Blastocystis, urticaria, and skin disorders: review of the current evidences. Eur J Clin Microbiol Infect Dis Off Publ Eur Soc Clin Microbiol. 2020;39(6):1027-1042. doi:10.1007/s10096-019-03793-8

7. Mayneris-Perxachs J, Arnoriaga-Rodríguez M, Garre-Olmo J, et al. Presence of Blastocystis in gut microbiota is associated with cognitive traits and decreased executive function. ISME J. 2022;16(9):2181-2197. doi:10.1038/s41396-022-01262-3

8. El-Zawawy HT, Farag HF, Tolba MM, Abdalsamea HA. Improving Hashimoto’s thyroiditis by eradicating Blastocystis hominis: Relation to IL-17. Ther Adv Endocrinol Metab. 2020;11:2042018820907013. doi:10.1177/2042018820907013

9. Rojas-Velázquez L, Morán P, Serrano-Vázquez A, et al. The regulatory function of Blastocystis spp. on the immune inflammatory response in the gut microbiome. Front Cell Infect Microbiol. 2022;12:967724. doi:10.3389/fcimb.2022.967724

10. Garn H, Potaczek DP, Pfefferle PI. The Hygiene Hypothesis and New Perspectives—Current Challenges Meeting an Old Postulate. Front Immunol. 2021;12:637087. doi:10.3389/fimmu.2021.637087

11. Fleming J, Hernandez G, Hartman L, et al. Safety and Efficacy of Helminth Treatment in Relapsing-remitting Multiple Sclerosis: Results of the HINT 2 Clinical Trial. Mult Scler Houndmills Basingstoke Engl. 2019;25(1):81-91. doi:10.1177/1352458517736377

12. Gazzinelli-Guimaraes PH, Nutman TB. Helminth parasites and immune regulation. F1000Research. 2018;7:F1000 Faculty Rev-1685. doi:10.12688/f1000research.15596.1

13. Kodio A, Coulibaly D, Koné AK, et al. Blastocystis Colonization Is Associated with Increased Diversity and Altered Gut Bacterial Communities in Healthy Malian Children. Microorganisms. 2019;7(12):649. doi:10.3390/microorganisms7120649

14. Lappan R, Classon C, Kumar S, et al. Meta-taxonomic analysis of prokaryotic and eukaryotic gut flora in stool samples from visceral leishmaniasis cases and endemic controls in Bihar State India. PLoS Negl Trop Dis. 2019;13(9):e0007444. doi:10.1371/journal.pntd.0007444

15. Tito RY, Chaffron S, Caenepeel C, et al. Population-level analysis of Blastocystis subtype prevalence and variation in the human gut microbiota. Gut. 2019;68(7):1180-1189. doi:10.1136/gutjnl-2018-316106

16. Nieves-Ramírez ME, Partida-Rodríguez O, Laforest-Lapointe I, et al. Asymptomatic Intestinal Colonization with Protist Blastocystis Is Strongly Associated with Distinct Microbiome Ecological Patterns. mSystems. 2018;3(3):e00007-18. doi:10.1128/mSystems.00007-18

17. Chaparro-Olaya J, Morales L, León Falla MD, et al. Decreased fecal calprotectin levels in Spondyloarthritis patients colonized by Blastocystis spp. Sci Rep. 2022;12:15840. doi:10.1038/s41598-022-18308-3

18. Kök M, Çekin Y, Çekin AH, Uyar S, Harmandar F, Şahintürk Y. The role of Blastocystis hominis in the activation of ulcerative colitis. Turk J Gastroenterol Off J Turk Soc Gastroenterol. 2019;30(1):40-46. doi:10.5152/tjg.2018.18498

19. Tai WP, Hu PJ, Wu J, Lin XC. Six ulcerative colitis patients with refractory symptoms co-infective with Blastocystis hominis in China. Parasitol Res. 2011;108(5):1207-1210. doi:10.1007/s00436-010-2164-8

20. Kaneda Y, Horiki N, Cheng X, Tachibana H, Tsutsumi Y. Serologic response to Blastocystis hominis infection in asymptomatic individuals. Tokai J Exp Clin Med. 2000;25(2):51-56.

21. Nagel R, Traub RJ, Kwan MMS, Bielefeldt-Ohmann H. Blastocystis specific serum immunoglobulin in patients with irritable bowel syndrome (IBS) versus healthy controls. Parasit Vectors. 2015;8:453. doi:10.1186/s13071-015-1069-x22. Zierdt CH, Zierdt WS, Nagy B. Enzyme-linked immunosorbent assay for detection of serum antibody to Blastocystis hominis in symptomatic infections. J Parasitol. 1995;81(1):127-129.


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