Ubiome Explorer +, Parasite Infections and CFS


Active Member
I was diagnosed with CFS/ME at Stanford's CFS Clinic in 2015. I helped fund Dr Naviaux's Metabolomics Study, was a CFS participant and it confirmed I was in the CFS/ME group based on my metabolomics profile. I have struggled with CFS and a wide range of ever worsening symptoms for more than 15 years. Besides chronic fatigue, my symptoms have always seemed to revolve around my gut IBS-C with sugars and carbohydrates being an obvious trigger/aggravator. Like most people suffering from CFS, I have seen 30+ doctors including ones at UCSF, Stanford, John Hopkins, Mayo Clinic, local integrative, internists and specialists. The doctors now look at my record and just blow me off. But that's another story for another time.

I've tried to search for diagnosis "leads" to my mystery illness on my own. One such effort is based on my hypothesis that my gut ubiota was at the center of my myriad of symptoms. These symptoms almost always flare while sleeping and especially when I eat any kind of sugar and to a lesser extent when I eat higher glycemic index foods. I have had high levels of IgE ( 300-1100) and erratic Eosinophilia ( up to 19%) for 20 years. This has always fueled my suspicion that a parasite could be part of my underlying problem. Five years ago, a Genova Labs gut test they said was using some kind of DNA analysis showed a positive for Hookworm and an "unknown parasite". I've also done the standard ova and parasite (O&P) stool microscopic evaluation a number of times which was negative. Its always bothered me that the CDC says due to a parasites life cycle, it requires as many as 9 O&P tests to achieve a reasonable sensitivity since eggs appear in a transient way making them difficult to reliably detect in stool.

I began the IL-5 blocker Nucala at Stanford for eosinophilic asthma in December which is one of the my more extreme and dangerous symptoms. Breathing and O2 is not optional. Since Nucala blocks eosinophil production, its contraindicated for anyone with a parasitic infection. Even its TV commercial strongly warns about "telling" your doctor if you have a parasitic infection. Seems like a catch-22 since its your doctor who would or "should" check or know if you have a parasitic infection. Some parasitic infections such as Hookworm can lead to a hyper-infection if the eosinophilic immune defense is suppressed. My symptoms took a major uptick about 3 years ago while on a 60mg/mo monthly prednisone taper which of course would have suppressed my immune system. My concern at the time was did the immune suppression allow some kind of underlying infection to spread and worsen.

So I have been wondering for years ( as did many doctors) if I had a parasite. Getting your doctor or any doctor to test for parasites using anything other than the O&P is impossible. Medical science simply doesn't have good "broad" and reliable parasite testing available unless one is in a research lab. There are some species specific antibody and PCR tests but given the thousands of different parasites, its absurd to think a doctor would guess correctly assuming they were willing to try. The Mayo Clinic ran one antibody test and Stanford ran the same antibody test based on my high IgE and EOS. Of course they were negative and that ended their effort.

When I learned that the company Ubiome was beginning to offer a Metagenomic sequencing based stool test, the "Explore Plus" last year that didn't just cover Bacteria and Archaea via 16S sequencing but also virus's and Eukaryotes, I ordered the 4 test kits for $399. Both Fungi and Parasites are Eukaryotes. Because of their wide variety and genetic breadth, using a marker sequencing via PCR just isn't effective as it is in Bacteria. Metagenomic sequencing has the incredible advantage that it doesn't assume or require guessing about "what infection you have" but simply reports all the organisms DNA it found and then a computer sorts out the "junk". Its far from perfect but it avoids the doctor "guessing" and testing.


In 2014, UCSF saved a young boy with a brain infection using Metagenomic sequencing. They like to brag about it but getting anyone at UCSF to use it is a joke!


So I did 3 samples since December when I began the Nucala IL-5 blocker and only got the results a couple of weeks ago. It was pretty shocking what I found. I'll focus on one parasite it found in all 3 samples over 5 months. A worm called Diphyllobothrium was in all 3 samples and it doubled in quantity between each successive sample. By mid April, it represented 1.5% of all the organisms found in my stool. This was up from about .4% in December when I started the Nucala. Diphyllobothrium is a fish tapeworm that can set up in a human host. Under-cooked fish is its typical source. I have had severe constipation for about 3 years. I have had bodywide pain similar to FM which became much worse after the prednisone. Diphyllobothrium can cause cysticercosis or neurocysticercosis during its larval phase where cysts build up in tissues throughout the body or worse in the brain. Neurocysticercosis can cause neurological symptoms just like I have while muscle and connective tissue cysticercosis can cause bodywide FM-like pain.


So rather than more testing, I began empirically treating it with albendazole and Praziquantel and both can cross the BB barrier. They are quite safe being used in the 100's of millions worldwide due to worm infections being common in the third world. On the third day, my constipation stopped like a miracle after 3 years of struggles. The bodywide pain declined in a near magic way. But the neurological symptoms flared including some new problems. Is it Neurocysticercosis? The Cysts are far more difficult to clear in the brain than elsewhere. The CDC says it requires 14-28 days of the anti-parasitics for Neurocysticercosis due to this difficulty.

So here I am after my first week on albendazole and Praziquantel and the changes are dramatic but the jury is still out. I thought I would share my experience here since I've seen so many people describe their symptoms as seemingly revolving around their diet, sugar and gut and IBS like symptoms. But these also include many non-gut such as fatigue, neurological and pain conditions etc..

So I wanted to get feedback on the parasite angle and alert people that the Ubiome Explorer Plus may be an important tool for looking at whats in their gut besides bacteria. One can see if there are any fungi or parasites that might be at the root of their problems living in their gut. After realizing Medical Science is so poor at finding parasites, I couldn't help but wonder how common long living parasite infections like the various worms are in the CFS/ME population? Love to hear your thoughts plus I'm curious if anyone has had the key markers of high IgE and Eosinophils that seem to be a glaring "hint" doctors just don't realize what it might mean. Humans developed both IgE and Eosinophils as a "worm" defense since early man had serious problems with worms. They have evolved into the "allergy" markers only in recent times. If you know you have high total IgE and odd Eosinophils popping up in CBCs', you should look into this. I'm not a doctor but this is something you should explore with your doctor as it appears to be a glaring hole only rarely discovered due to lack of doctor knowledge and extremely poor testing.

Good luck. Any feedback appreciated!


Active Member
That is great news. A turning point for me was reading Dr. Leo Galland concerning research about CFS and parasites. He is a top tier CFS doctor and his quote was the first thing he looks for in CFS is a parasite infection. He gave up on standard O&P tests since they are unreliable (but different now as you mentioned).

I did a multitude of testing and found a protozoa infection in one of the tests. For those who are unfamiliar with parasites, there are different classes, for instance pgrovetom had a worm (which has a few classifications such as nematode, cestode and trematode) while I had a protozoa infection (think of giardia, cryptosporidium etc). They are both parasites classifications but different in treatment strategies.

Education in the medical community is sorely lacking concerning parasites and testing is the big problem, but they are getting better. One of the laughable excuses I heard and read is that since you live in a developed country (US), therefore you cannot have parasites. This is simply false (think of global travel, imported produce etc). In fact, there was a big breakout in Milwaukee that was labelled as CFS. Turns out that cryptosporidium was found in the water supply.


I wrote a blog article that might be helpful (needs editing, so forgive me for the sloppy post).

Get Our Free ME/CFS and FM Blog!

New Threads

Forum Tips

Support Our Work



Shopping on Amazon.com For HR

Latest Resources