Lipkin's Monster ME/CFS Study: Microbes, Immunity & Big Data
The Microbe Discovery Project outlines an ambitious new study by top researchers that has collected patient samples, but needs desperately funds to complete the work.
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Surprising (Scary!) results from new gut pathogens GI test

Discussion in 'Diagnostic Guidelines and Laboratory Testing' started by Rich D, Jan 26, 2018.

  1. Rich D

    Rich D

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    I’ve been seeing a doctor who practices alternative medicine, and he had me take a test called GI-Map. It’s only been around for a couple of years now. It uses DNA maps to test your poop for a number of pathogens – including bacteria, parasites, fungi/yeast, and a few viruses. It does not culture but rather uses new technology to search for DNA, thus yielding far better results than a run of the mill stool or blood test.

    My results were pretty crazy. Here is the list of what was found in terms of pathogens (an image of the test results is at the bottom of this post):

    - C difficile Toxin B
    - E. coli
    - Cryptosporidium (single cell parasite)
    - Whip worms (eek, I have worms! A parasite)
    - H. Pylori
    - Pentatrichomonas hominis (a protozoa, possibly not harmful)
    .. and high levels of klebsiella, citrobacter freundii, streptococcus, and a few other bacteria that seem bad (though I'm not sure how problematic these are)

    On top of all that, I have low readings of some beneficial bacteria. The good news is I don’t have EBV or CMV (viral testing is limited to only these two).

    I haven’t talked with my doctor in detail yet about the results or a game plan. It is interesting to me that when I look these things up on the internet, almost always these seem to be things that people with a compromised immune system are at risk for.

    I’ve had two surgeries since being afflicted with CFS, which might explain the C-Diff and a few others. Not sure when I got worms! I also have had a couple of ‘stomach bugs’ in recent years. Further, when I first got ill with CFS, I did several rounds of antibiotics (plus I took more with the surgeries). That certainly could be partially responsible for bacteria getting out of balance and opportunistic pathogens taking hold.

    My doctor said that this is among the worst results he’s seen. It looks very bad compared to the results from others I’ve seen on the web, so I don’t think this is anywhere near normal.

    I have a few observations/ideas/thoughts, and I’m curious as to what others think:

    1. The pathogens identified in my test may not have been the cause of my CFS, but rather the result. One theory that fits this picture is that some kind of instigator – like an as yet unidentified pathogen – sent my immune system into chaos, and these other things took hold. This would be consistent with the anecdotes of outbreaks and of immune system irregularities. If each person’s immune system is compromised, everyone might get different pathogens taking hold and wreaking havoc. For me it might be bacteria, for someone else it might be viruses, etc. Thus each person would have a unique response to the initial event, leading to disparate symptoms.

    2. Antibiotics may have made things much worse. My gut bacteria seem way out of whack, and this seems like the likely source.

    3. Treatment? My doctor is going to try to treat these in some kind of order and we shall see the results. He gave me a yeast/bacteria killer supplement (plant tannins) early on and I had an amazing improvement that was subsequently lost after a few months. Perhaps one kind of pathogen was killed off, leading to temporary relief, but then something else grew to fill the gap and caused more symptoms. This might explain why people get temporary relief with various anti-viral or anti-bacterial treatments.

    The test is $430, and is typically not covered by insurance. It must be ordered by a doctor, but there are folks on the internet who will order this for you (for a fee, I think). It seems like we should all be doing a test like this if we can afford it. I think over time they will add more pathogens to the list.

    What do you all think? I wonder if any of you have thoughts about how this fits with Lipkin’s work?
     

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  2. juniemarie

    juniemarie Senior Member

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    @Rich D Wow sounds like an amazing test. What was the yeast/bacteria supplement?
     
  3. Runner5

    Runner5 Senior Member

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    On the Animal Planet show, "Monsters Inside Me" -- they have a lot of Cryptosporidium. Whip worm doesn't sound pleasant either. Whoa.

    Keep us updated on how treatment goes. Glad you found out!
     
  4. Murph

    Murph :)

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    This DNA sequencing of gut bugs is the future. It's called 18s RNA sequencing and anyone still doing culturing of gut bugs to find out who's in there is only going to discover the ones that survive in a petri dish.
     
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  5. Rich D

    Rich D

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    It is called Tanalbit. You can find it on Amazon. I took 3 capsules twice per day between meals.
     
  6. Learner1

    Learner1 Professional Patient

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    My insurance has been covering GI Map. I do a DNA stool test every 3-6 months. My daughter's and I are celiac and have a long history of gut issues...

    Things I've learned...
    • If you have a compromised gut, it'll be a magnet for bad actors, so yes, it can be the result of being sick, but it also worsens you health as these things snowball
    • The 4 R protocol is useful... Basically, you remove the bad stuff, heal your gut wall, and encourage good citizens to move in.
    • Prioritizing what to do in what order is important. A good doctor would be helpful with the list of things you've got going on.
    • Glutamine and glycine may help your gut lining.
    • Its not just probiotics. Insoluble fibers play a role, too, as well as digestive enzymes. Galactooligosaccharides were a recent good find that helped me.
    • A lot of folks with gut issues have food allergies. (And many of us have mast cell issues) Finding and dealing with these problems, avoiding foods that set you off, and taking things that calm your gut down are essential to gut health.
    • Avoid oral antibiotics unless you're in really bad shape. I'm currently on IV antibiotics for a chronic bacterial infection and my gut is ok - a year ago, I did oral abx and they killed most of the god stuff in my microbiome which took a year to get back.
    At least you know what you're dealing with. If you are serious about changing whatever you need to to fix what the test found, you'll be happy that you made those changes as your health improves. Resrarch is showing microbiome health is related to ME/CFS - fixing it may not totally cure us, but it can help a lot.
     
  7. Rich D

    Rich D

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    Thanks for your comments! So I’m curious - what did your tests uncover?
     
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  8. echobravo

    echobravo Keep searching, the answer is out there

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    Thanks for sharing this essential tip! So, taking the abx IV means it will not affect gut bacteria at all, i.e. nothing of the abx ends up in the intestines, for instance through bile or other mechanisms of “fluid excretion/exchange”?

    BTW, how does the GI-map test compare to uBiome? Ken Lassessen seems to recommend uBiome when he analyses people’s biotas.
     
    Last edited: Jan 27, 2018
  9. Prefect

    Prefect Senior Member

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    It's a gut, not a box of Kleenex, it's going to have things living in it. Most people have at least E Coli, a Strep strain, and H Pylori in their gut.

    I think way too much emphasis is put on a pathogenic possible cause for CFS, and time and time again patients are put on antibiotics, antivirals, etc, and they don't really improve.

    This disease is an abnormal HPA response to stress in my opinion, and the answer lies in pharmacology that re-sets the HPA axis. If CFS was cured by eradicating gut pathogens (unless it's something serious like Giardia) it would be in the papers.
     
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  10. Learner1

    Learner1 Professional Patient

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    I didn't say abx won't affect the gut at all. If they travel through the bloodstream, they will get to the gut.

    However, the effect will be less than sending them directly into your microbiome. That's my doctor's and my hope.

    My experience so far has matched the theory. Two months on azithro/rifampin a year ago gave me diarrhea for3 months, wiped out my diversity, and left me with no lacto or bifidobacteria, while on Xymogen ProBioMax 100 the entire time. It took months of careful rotation of high quality, expensive probiotics, along with insoluble fiber in sheep yogurt to get back to about 50-60% of the diversity I started with.

    Then, I started IV azithro/doxy/rifampin 3 days a week, staying on the same gut protocol if insoluble fiber and rotating probiotics for the past 3 months. I haven't done a stool test yet (I will right after finish the abx) but my output seems to be quite normal, nothing like the diarrhra I had with the oral antibiotics.

    No test is perfect. They all have their pros and cons. My doctor likes GI Map as it has viruses, bacteria, fungi, calprotectin, and antigliadin antibodies. I hear they just came out with a new version that tests more than it did in the past.

    I'm planning to do uBiome next. Ken seems to like it as it shows species that fit with the ME/CFS microbiome research. It also has a descriptive guide that tells you about each resident of your gut.

    There are also tests from American Gut, Thryveinside and Genova that hsvevpros and cons. I tried Thryve inside, which gave the longest list of bacterial species of any of the tests I've seen, but they didn't do fungi, and the reporting was terrible. Genova Diagnostics has less info than they used to, so I don't like it as well as I did.

    Microbiome manipulation is in its infancy. No one knows what the ideal gut looks like. Scientist have looked at microbiomes of aboriginal peoples and found they vary depending on diet, though they're more diverse than people on a SAD (Standard Western Diet). And glyphosate, eating white food, and taking antibiotics are all known to dramatically impact the gut.

    Avoiding antibiotics and eating a wide variety of organic food, especially vegetables, plus probiotics and insoluble fiber if you need it, seems the best way to ensure gut diversity.
     
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  11. Learner1

    Learner1 Professional Patient

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    I have improved quite a bit with antivirals and antibiotics. There's a lot of research showing the drugs help when they're applied to the right problem. (Montoya, Lerner, Stratton, etc.)
    After thorough testing of my HPA axis, and fine tuning pregnenolone, progesterone, hydrocortisone, DHEA, testosterone, estriol, testosterone, levothyroxine, liothryonine, and melatonin, while on thyroid and adrenal support nutrients, I was still quite sick.

    Finding my immune system was dysfunctional and helping it and going after 7 infections has dramatically improved my functionality. I'm not cured yet, but I'm starting to see glimmering of normal life on some days.

    Across the globe from one another, Maureen Hanson and Chris Armstrong have both published work showing disrupted microbiomes in ME/CFS patients.

    While I don't believe fixing the gut alone will cure us, having a compromised microbiome is going to be an impediment to getting well.

    Scientists have come a long way in defining the role of the various bacteria in converting the food we eat onto the biochemicals our bodies need to function, such as B12, neurotransmitters, etc.
     
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  12. Lipac

    Lipac Senior Member

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    @Rich D good thread!

    #1: I'm curious where you're getting good alternative medicine? ( You can pm me if you'd rather)
    #2: Crypto has been a huge problem in many cities. Whipworm is not that uncommon- it's just no one looks!
    #3: I also had a serious reaction to an antibiotic , Chloramphenicol- rushed to ER and tested for CDiff. Didn't have it, but started all sorts of gut therapy through a Functional med Dr. He said that reaction was common in CFS ( and Lyme, which I have)
    #4: I was investigating how fecal transplants were rapidly helping patients with MS. Other chronic disease respond as well.
    It's been all over the medical shows on TV, the relationship between normal immune function , chronic illnesses and gut dysbiosis.

    #5: I can only fight this by trying to suppress/alter things with massive doses of good bacteria.
    Unfortunately, the literature on fecal transplants doesn't name the effective STRAINS they found.
    * I just found a few unique strains, one directly for antibiotic induced dysbiosis one found in healthy infants and some adults in foreign countries that have no chronic illness, and a 250 billion with multiple strains of each bacteria.
    #6: the products Im using ( no bad reaction so far) are :
    - L. Reuteri ( protects stomach, kills h. pylori) from Microbiome PLUS+.
    -Renew Life " extra care, Ultimate Flora 150 billion ( many more strains than a typical probiotic)
    (Both helps my stomach, severe bloating, stools)
    - AOR Probiotic-3- Enterococcus faecium, Clostridium butyricum, Bacillus subtilis.
    (I think this might be the most effective product... Says eliminates pathogenic bacteria and viruses, supports survival of healthy bacteria...Hoping)
    I'd bounce it off your Dr.

    Parasitology was an interest of mine since college. It's a huge unaddressed problem.
    So many people are told they have " IBS", when it's a parasite or pathogenic gut bacteria.

    They kill bees if they get immune dysfunction- so it can certainly attack our weakened bodies and create havoc as well.

    The gut and brain are so complexly linked. To focus only on the brain or muscle dysfunction or viral infections, ignores IMPORTANT Co morbidities.

    My patients were Mexican, and no one but me was thinking ' parasites', so I found MANY with the help of the City microbiologist who'd studied around the world ( all the hospital Labs were crap),.

    And patients got better.

    Unfortunately, I can't find anyone like me around.
    I'd really like to get the test you mentioned.
     
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  13. Prefect

    Prefect Senior Member

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    Antivirals and antibiotics have multimodal effects, so the causative component may not be their pathogen fighting mechanism at all. Some people here have gotten worse on these drugs.

    Gut microbiota can impact HPA axis, and vise versa. Dysfunctional HPA axis can dysregulate gut microbial balance. Stress can increase intestinal permeability. Psychopharmacology that addresses mental illness can reduce stress and improve gut permeability. They've found gut inflammation in mental illness. But there is no proof which causes which. It's possible gut dysfunction is observed in people with major depressive states, not necessarily because the former causes the latter, but it may be depressive states can cause imbalance in the gut. The gut could just be a symptom and not the cause. When I first came down with this in 1997, candida was the craze. That conversation seems to have gradually died off now. And for good reason.

    These hormones should only be treated if there is a clinically diagnosed case of HPA axis dysfunction (Hypopituitarism, Cushings, etc). Exogenous hormone introduction can in fact further suppress HPA axis due to negative feedback. People with Major Depressive Disorder, PTSD, and CFS have been observed to display HPA axis dysfunction in very accurate research settings. But if any of these people walk into an endocrinologist's office and get tested, the doctor will refuse to diagnose them based on the marginal results.

    In fact some research has gone into treating HPA axis dysfunction and low daytime cortisol in PTSD patients with hydrocortisone; the problem is this doesn't solve HPA axis dysfunction created through negative feedback, it can in fact exasperate it. These hormones are only useful when your HPA is suppressed enough that there's no chance of getting them back up (addison's disease, secondary hypopituitarism due to tumor, etc) I believe the way to deal with marginal negative feedback caused HPA axis dysfunction is psychopharmacology that can re-set the HPA axis.

    The problem I have with integrative medicine is the proponents accuse the pharma industry of corruption. And they possibly are to an extent. But the former don't seem to hold themselves to a fraction of burden of proof that the latter are subjected to through blind clinical trials and meta analyses. They site mainstream medicine trials when it suits their argument and discount them when it doesn't. I find this VERY ironic.
     
  14. Lipac

    Lipac Senior Member

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    I'm sorry but I was trained in very good allopathic medicine. What Endocrinology, GI Specialists, Immunologists , et Al won't " treat" or Deem " marginal" amounts to treating individuals on large population ranges of normal; not the individual patient and response.
    ( t.e. Elimination of signs / symptoms of hypothyroidism with low doses of T3 for elevated RT3 )

    I remember in Med School in 1985, the older specialists with EXCELLENT physical diagnosis skills ( that few know or do anymore) would BLAST US in lectures, saying we relied on tests rather than clinical skills in diagnosing patients.
    Saying " YOU ARE TREATING NUMBERS AND IMAGING RESULTS; NOT THE PATIENTS ENTIRE CLINICAL PRESENTATION".

    WOULD that we still had that generation of Physicians left.

    I was TREATED to learn Physical Diagnosis at a " Dr House" type of level.
    And yes, Big Pharma controls what Drs learn- most of the CME , research, textbooks are funded by pharmaceutical companies. THAT'S NOT A FRINGE URBAN MYTH OR CONSPIRACY THEORY. It's easy to find the reports.

    HONESTLY , WHEN I GOT ILL, MY COLLEAGUES WERE NO HELP.
    I FINALLY began having educated conversations with younger, VERY WELL TRAINED Naturopaths from the NW, who are practicing genomic medicine, or Functional Medicine Drs who had re educated themselves.

    I HATED Naturopaths for 12 years in the NW. Seemed every patient had one.

    Till got sick .

    BTW- I have gotten the BEST orthopedic and neurologic exams and tests from Acupuncturists and NDs. I know how to do an exam. They were looking at physical signs I had not seen in clinical practice since 1990.

    I still don't do Homeopathy or bother with herbal protocols. I tried, they didn't help.

    PRP, trigger point injections, and acupuncture takes care of my chronic pain.

    But hormone replacement based on very good tests, drastic diet changes, ( Autoimmune Diet) and supplements like PQQ for example, have taken me from narcotic dependant and bedbound to " remission, " or at least not entirely bedbound, not overweight, no digestive issues, etc.

    I don't understand the bias against alt med ( by that I mean clinically very good, not money making scams) ;
    unless you have no need for anything but drugs and trust allopathic Drs implicitly.
     
    Last edited: Jan 27, 2018
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  15. Rich D

    Rich D

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    I am seeing a doctor in Ithaca, NY named Richard Cohen. He is an MD, but practices as a chiropractor. He sees a lot of patients from all over.
     
  16. Lipac

    Lipac Senior Member

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    @Rich D ... Yeah. Ok. No one in the Great Lakes area seems to have anyone.
    They are all East Coast, some in the South ( Atlanta and FL) or West Coast.

    I'm glad you have a good Dr. I know what a difference it makes- just having someone who believes you, isn't trying to get rich off your illness and is trying to find answers.
    I did once.

    Mine died, so can't be contacted by my current Drs, IF they would even have listened to him ( they get by because crap medicine is the " standard of care" here).

    I'm really glad you found hope and some answers
     
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  17. Prefect

    Prefect Senior Member

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    In 1997, I came down with this after a mysterious infection. Doctor put me on 25 mg of Fluvoxamine, saying he doesn't believe in CFS but thinks that's what I have.

    After a year I basically very gradually improved and entered a state that felt like remission as it gets until two years ago.

    18 years is a good run. The SSRI likely helped my sleep, increased slow wave stage sleep, and likely induced an increase in growth hormone, and very gradually may have re-set my HPA axis.

    So what?

    I can't prove Luvox "cured" me. That would be irresponsible. I don't go around telling people on this site who come down with CFS to try Luvox. But here we are, at the mercy of alternative medicine's anecdotally supported dogmaticism. Though trying out a "suggestion" based on personal experience is well worth it, but I find anything beyond that not suitable.

    My "remission" was likely a form of adaptation We all seem to adapt to the new us after a couple of years and think we're improved, and attribute it to something we happened to be doing during that time.
     
  18. Learner1

    Learner1 Professional Patient

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    After conventional, western medicine failed multiple family members, I learned about functional medicine, which looks at the body as a system of interacting systems, just as you pointed out in a couple of your examples, @Prefect .

    I've attached a white paper that describes it, found on the site of the Institute for Functional Medicine, which has courses for conventionally trained doctors so they can learn about functional medicine. They have a Find A Doctor feature to help patients find doctors who practice it.

    The Cleveland Clinic, one of the top hospitals in the US, believing they were missing something, approached Mark Hyman a few years ago to start a Functional Medicine clinic that is so busy today, the current wait is about 3 months.

    I live in Seattle, where there are many high quality functional medicine MDs and NDs. They do not practice by dogma or formula, but are curious, take the time to get to know patients to tease out the sources of their illness, and use standard and specialty lab work to confirm problems before prescribing a comprehensive treatment plan that may include drugs, hormones, botanicals, nutrients, diet, mindfulness, and physical interventions, like prolozone, massage, and acupuncture.

    I have seen many conventionally trained MDs who have been unable to help my ME/CFS, and in the past, suffered as MDs missed celiac disease, Hashimotos, estrogen dominance, candida, and arsenic and mercury poisoning. I ended up with stage 3 cancer, which doesn't just drop out of the sky and land on unwitting victims, but develops as a result of metabolic derangement over time. And the aftermath of chemotherapy and surgery led to my ME/CFS.

    As a patient, having doctors who look at each of the body's systems and optimizing the function of each and the interaction between them, gives many patients a better chance at wellness, rather than by practicing cookbook medicine and handing out pills according to ICD10 codes.

    Its tedious and expensive, and takes a toolbox of tools, but can lead to health rather than just bandaiding the problem at hand.
     

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  19. Lipac

    Lipac Senior Member

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    I WHOLEHEARTEDLY Concur. The BEST Drs I worked with , now are getting certified in Functional Medicine.
    The bulk of Drs 40 and under want a 9-5 job that's no more challenging than being an accountant all day.
    I'm not being insulting... This came from discussions with Drs 50-60 who cannot find younger Drs to replace them, or to take Chronically ill patients.
     
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  20. Lipac

    Lipac Senior Member

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    @Learner1 ...
    Every time I read your posts I wish I could find a provider like yours. I didn't realize how much it helped having a doctor who read research in the NW, till I lost him .
    Now that I live in a " medical desert" I can't convey how much UNNECESSARY STRESS there is- it's a Full Time Job on the phone with Medicaid , trying to get a PCP, running out of meds, having undereducated people IN CHARGE ( medical assistants in charge of figuring out prescriptions , not a nurse...I don't think it's legal, and they can't do the math, but...).

    You are getting so much better care than people in the " midsection" of the country.

    I burned through $200,000 in 8 years, because I had no insurance and couldn't get any in the NW. I can't afford to return.

    If you can afford your Dr, labs and treatments, there's Hope.
     
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