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Results: Comprehensive Stool Analysis + Organic Acids Test

Discussion in 'General ME/CFS Discussion' started by Arius, Nov 17, 2016.

  1. I just got results from two tests: a comprehensive stool analysis, and an organic acids test. I’m attaching them if anybody wants to look at them more closely. The evidence points strongly towards what I suspected all along, that a gut dysbiosis (presumably caused by stress, poor sleep, eating foods I am allergic to [dairy and soy], plus other factors) poisoned my mitochondria with hydrogen sulphide. Here’s what I’ve learned:

    I have low Secretory Immunoglobulin-A (sIgA), which is the GI tract’s first line of defense against parasitic infections and toxins. Stress could be a cause, but also I just learned that blastocystis hominis can lower sIgA levels, as can protein malnutrition (I was vegan/freegan for a couple years leading up to my illness… plus I think I have a serious problem with malabsorption).


    The CSA revealed that I am infected with blastocystis hominis.

    Dysbiotic bacteria:

    4+ citrobacter freundii
    4+ citrobacter freundii, complex 2

    C. freundii produce hydrogen sulphide (H2S), which is a potent neuro-toxin. My understanding is that these toxins can overwhelm the liver and enter the bloodstream, travelling throughout the body and wreaking havoc (ie resulting in symptoms such as headaches, poor memory, brain fog, fatigue [your liver alone uses 27% of your body’s energy], joint and muscle pain, etc). Crucially, H2S also poisons mitochondria.


    There’s definitely something wrong with my mitochondria – but I’m not sure how to interpret that part of the test. It says I have low Aconitic metabolites. So, something wrong with my Krebs cycle? It would be great to know what this means and if there are supplements or something I can take to help fix it. I’ve been taking 1000mg of Acetyl-L-Carnitine, plus a teaspoon of D-ribose and 600mg of Alpha Lipoic Acid daily to help with my mitos. (I’ve taken CoQ10 off and on, but it has no noticeable effect on my energy levels.)

    The OATs test also revealed low glycolic metabolites, but again I have no idea what that means right now.

    And here’s another piece of the puzzle I haven’t figured out: My neurotransmitters (dopamine, serotonin, and norepinephrine) are low. I’m wondering if this can be accounted for simply because I’ve been physically inactive and chronically ill for the past two years. I mean, of course I’m going to be stressed and depressed.

    Also, my quinolinic acid is low and my quinolinic acid/5-HIAA ratio is way off… though I think this could just be because of low serotonin(?).

    Oh, and they found absolutely zero vitamin C in my urine despite the fact that I eat organic local veggies all day and take a multivitamin every morning. What the heck?

    I suspect that I have low stomach acid (hypochlorhydria), but I don’t know of an accurate test for this. I’ve done two rudimentary home tests – the baking soda test, and the betaine hcl challenge. You’re supposed to burp within a few minutes of drinking baking soda in water, but I never burped at all. I did this test ten days in a row and had maybe two tiny burps after about 20 minutes or more. Then I took the hcl challenge. You’re supposed to get an acid reflux reaction after taking one pill. I got up to the maximum dose – 14 pills – without so much as a warming sensation in my chest.

    So I assume I have an issue with malabsorption.

    Anyway, it feels amazing to have some answers as to what’s going on inside of me. I feel validated – “look, there really is something wrong!” - and vindicated – “my theory [ok, it’s mostly dr myhill’s theory] is probably correct!” - and generally happy. It gives me some new therapeutic directions. I need to start taking L-glutamine again, and also grapefruit seed extract and oil of oregano.

    I had been frustrated for some time. After correcting my sleep pattern, meditating and incorporating other relaxation techniques into my lifestyle, following a very strict and limited diet of vegetables and meat, and learning to pace myself, I stopped declining and improved quite a bit. But then the improvements stopped. Now I have some idea why – I didn’t do anything to try to actively heal my guts or fight the overgrowth and parasitic infection.

    If anyone knows how to read the mitochondrial markers or get more nuanced info out of these tests, I would love your interpretation.


    Attached Files:

    Last edited: Nov 17, 2016
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  2. alicec

    alicec Senior Member

    A few general comments on your stool test.

    The parts of the CDSA which I consider to be useful, namely measure of digestive capacity, SCFA production, indicators of inflammation etc, look good.

    There are no obvious problems with digestion, sufficient pancreatic enzymes, you have good levels of SCFA production in good proportions and there is no obvious inflammation.

    Low sIGA is the main measure which suggests need for improvement.

    As for the parts of the test which rely mainly on culture of organisms, these are the least reliable since they give a completely distorted picture of what is going on in the gut.

    The technique selects only for aerotolerant organisms which can grow in culture. Until relatively recently, this was the only way to study the organisms in the gut but DNA sequencing techniques have now revealed that these techniques have missed the vast majority of the species in the gut - they are looking at only maybe 10% of the inhabitants.

    Personally I would be very cautious about undertaking drastic treatments based on so-called overgrowths detected by culture.

    At the very least I would be ordering a DNA based test (such as those you can order yourself from uBiome and American Gut) to get a proper picture of the full range of organisms in your gut.

    uBiome has just started offering a DNA-based gut test which provides interpretation, ordered via your doctor. I don't know the cost but it is worth considering.

    RedLabs has been offering such a test for a while

    I am familiar with the uBiome analysis offered in parallel - namely the citizen-scientist type project which provides the data to you and you have to work on the results (much like the 23andme project for SNPs).

    This does require a fair bit of work so the new test could be a useful shortcut though I imagine it is more limited and more expensive.

    As for the potentially problematic organisms identified in your test, consider the following.

    There is no definitive evidence that B. hominus is necessarily problematic - it may be but if so you would expect to have noticeable symptoms.

    Removal of this organism is not easy - the suggested flagyl treatment simply doesn't work and may create resistance. Effective treatment protocols have been developed here.

    C. freundii is an opportunistic pathogen - it is a normal gut constituent which doesn't necessarily cause problems. Rather it takes advantages of problems with the host - other illnesses, immunosuppression etc. If you had an opportunistic infection you would know about it.

    It may be that if levels in the gut are highish you could be affected by the H2S production but I would be checking by DNA whether levels are really abnormal.

    A few comments about the OAT test.

    Here is a thread discussing Rich's interpretation of a Nutreval test - not the same as your test but there are many elements in common and his discussion of energy pathways may be helpful to you.

    Here and here is some info from GPL on interpretation of the OAT test.

    The dysbiosis markers suggest there is no serious imbalance in your gut. The highish arabinose marker might be interpreted as associated with Candida but this is controversial. In the absence of other fungal markers and the results from your stool test, fungi don't seem to be a real problem.

    The highish hippuric in isolation could just reflect dietary influences.

    You don't appear to have an oxalate problem (the low glycolic is nothing to worry about - high values are a problem). The highish oxalate value probably reflects dietary intake. The other two markers, when high, are indicative of a potentially serious problem with endogenous oxalate production. You would also expect to see marked derangement of several B vitamin markers, most notably B6, biotin and B1, which you don't have.

    Your energy pathways - both glycolysis and Kreb's cycle are not functioning well. This is a very common finding in CFS/ME. As for what to do about it - well there is a whole slew of supplements that people have tried to try and boost these pathways - some have had at least a little success - unfortunately there is no easy answer. With trial and error you might hit on some combinations that help a bit. It is usually enzyme cofactors like B vitamins and minerals, maybe some amino acids, CoQ10, carnitine etc that are helpful.

    The very low aconitase is also a common finding and probably reflects the fact that this enzyme is very susceptible to the effects of oxidative stress.

    The highish 3 methylglutaric could reflect problems with leucine metabolism. There are rare genetic disorders which cause this (you would know about it by now if this were the case) but it is much more likely that the marker reflects poor mitochondrial function, consistent with your Kreb's cycle results.

    Your low neurotransmitters could just reflect a generally low metabolism but could also reflect poor availability/uptake of precursors. Supplementation with these amino acid cofactors could be worth trying along with B vitamin and mineral cofactors involved in the synthesis pathways.

    Many other substances have been discussed on PR for boosting neurotransmitters. As with energy metabolism, some people seem to hit on combinations which help a bit but trial and error is necessary.

    The high quinolinic/5HIAA ratio just reflects a very low 5HIAA - your quinolinic is not high.

    The highish uracil could suggest a functional folate deficiency.

    The non-existent ascorbate does seem odd. It could reflect poor absorption or excessive demand. It is easy enough to supplement further and many people find high dose vit c helpful.

    Some of your B vitamin markers are also low.
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  3. TigerLilea

    TigerLilea Senior Member

    Vancouver, British Columbia
    @Arius You should blank out any personal information on your test results (ie name and address) before you post them onto any public forum. :)
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  4. Oci

    Oci Senior Member

    Hi @alicec, Your comment on this comes at a good time. I had a Doctors Data CDSA done in June 2015 that showed...
    4+ Bacteroides fragilis group
    3+ Bifidobacterium spp
    1+ Escherichia Coli
    3+ Lactobacillus spp
    NG Enterococcus spp NG = No growth
    4+ Clostridium spp

    Commensal (Imbalanced)
    3+ Alpha hemolytic strep
    2+ Pseudomonas aeruginosa

    4+ Enterobacter cloacae complex
    2+ Candida Albicans

    Then this October my doctor had me do the Microbiology Profile part of the test because I was complaining of feeling tired and having more brain fog...itchy eyes, allergic reactions.

    Here are the results of the Oct 22 test.
    4+ Bacteroides fragilis group Same as last time
    NG Bifidobacterium spp Last time 3+
    4+ Escherichia coli Last time 1+
    3+ Lactobacillus spp Same as last time
    NG Enterococcus spp Same as last time
    3+ Clostirdium spp Last time 4+

    2+ Alpha hemolytic strep Was 3+ last time
    2+ Gamma hemolytic strep New
    1+ Pseudomonas aeruginoss Was 2+

    Dysbiotic Flora
    3+ Bacillus cereus New
    4+ Klebsiella pneumoniae New
    No yeast was cultured but there were "few" microscopic yeast which is considered "abnormal".

    I have been taking some silver and trying to figure out what probiotics and possibly prebiotics to use. I have not been thinking of doing anything drastic ie herbal antibiotics as my gut is very sensitive and cannot tolerate things like garlic, oregano, etc. I do use Candibactin BR and have done so for a long time to manage candida. Candibactin AR too strong.

    I have ordered some "SECURIL contains a unique and patented probiotic, two special strains of Propionibacterium freudenreichii, which produce propionic acid, a natural biological acid that benefits the bifidus flora."

    Interestingly Bifida were good first test. I also ordered Probiota Bifido from Seeking Health.

    I find it very curious that the Bifida just disappeared! I also wonder why NG for Enterococcus.

    My Integrative doc went to a conference recently in Chicago on the gut and is now keen on me doing an elimination diet for the next month. What timing! Just in time for the holiday season! It is the IFM diet and is very restrictive especially once I factor in the need for lower oxalates and lower histamine! First step is to get totally off caffeine!

    I agree that there is likely something going on in the gut affecting me... terribly itchy eyes and foggy head. He is also sending me to an allergist. Will see what that yields.

    On looking at the comparison of the 2 tests i came to the conclusion that the testing likely is not very accurate. I am not sure where that leaves me. I can do the Ubiome test but may not have any clear answers from it either. Steep learning curve too! BTW, the new test is not available here in Canada nor is it available in all the states yet.

    I guess all I can really do is to improve my diet (too much sugar of late and eating some dairy which doesn't agree), find appropriate probiotics etc. I have a problem with migraines and have always been negatively affected by fermented foods. They cause foggy brain too. I may have some SIBO...not generally a problem but can be when I start adding things like probiotics.

    Any thoughts or comments from you or others would be much appreciated. Oci
    Last edited: Nov 28, 2016
  5. vision blue

    vision blue

    Thanks for posting the results - I always find comparing helpful. I haven't yet done OAT test but have done the comp stool analysis from doctors data and have ubiome experience.

    my biggest result was opposite of yours: very elevated secretory IgA. (I can attach the entire test result if you would find it useful) Suggests immune upregulation, whereas yours suggests downregulation. Have read, but not sure of credibility, that its not uncommon to start with elevated and eventually becomes too low. Same sources claim low secratory iga connected with leaky gut, which may go along with your allergic type responses to foods.

    note that i cannot eat fermented foods either; i am very intolerant of tyramines. but that's a diffeent topic and in fact maybe i'll start one on that since i just got back results on test for biogenic amines if i dont' run out of energy after i'm done with this message.

    for ubiome, i've tested my gut microbiome twice (and mouth once). The website only tells you up through the genus level, which is not very useful if youre trying to luck upon pathogenic species. But what it does let you do is to download species level data and then theres free programs where you can convert that to excel spreadsheet format. I may or may not have uncovered some lurking chronic salmonella that way, but its quite tricky and not especially trustworthy.

    That's because they only use sequence probes of about 72 positions in length. its hard to be sure of a species that way. So two different species could have the identical 72 length nucoleotide sequence- and it would only be if there were longer sequences that one would knkow which. In genetic sequencing, its the length of the segments that you pay for. test is cheap cause theyre only running thos 72 length sequences. so that's one issue- you miss alot because theres no way to be 100 percent sure its that species and you don't pick up alot (if you know a bunch about genetics, note i've also BLASTED the actual nucleotides but it was too much work).

    another problem is that you really don't know what to do with species where they find only a few in number. hard to know if they are real or artifacts. some are definitely artificacts. so one of mine for example is found, and only found, in the feces of caribou. And alot of people find marine organisms- they think it means something, but it does not. Its not clear why these one-offs occur, but their common in all sequencers- its not just ubiome. so really you don't know where to put the cutoff and how frequent what you find has to be before its real.

    there's also alot of hit and miss. so the website will give you percents of different classes compared to others or compared to yourself over time- but which bugs you pick up is largely random. been shown you can send in 2 samples from the same sample on the same day- and get very differetn results. its not that its a fraud, its that with so many bugs ina microbiome, what gets picked up is in part just random.

    so bottom line is you could get lucky, but more likely its a big time sink and you spend hours downloading, sorting the spreadsheet, cutting and pasting multisyllabic names in google with high hope and then realizing what youve just found is only found in lakes and streams in japan.

    but i don't know what their new clinical gut test is like. I" have not yet found a sample report anywhere. If they use the same technology, i don't see how they can get anywhwere, but maybe they fish for longer sequences and have much better software. would be very curious about that.
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  6. alicec

    alicec Senior Member

    I agree that at the low frequency end of DNA testing of the microbiome there is a lot of randomness.

    But then I couldn't see the point in spending a lot of time trying to understand the organisms present at <0.1%.

    At the higher end of frequency the data is a lot more robust and we can get a fairly good picture of the range of organisms which populate our gut.

    I think you exaggerate the variability of the test. Yes there have been reports of differences in tests done on the same sample but there are plenty of reports too about consistency. I have done 14 tests over about 18 months and am struck by the clear pattern that defines my gut - it is most definitely not random.

    The new test is a departure from the comprehensive sequencing approach I am familiar with. They are targeting and reporting on a limited range of organisms which are judged to be of particular value in defining gut health - ie ones we have considerable information about. These are all organisms present at moderate to high levels. It will be interesting to follow this test with time.

    As for the more usual comprehensive test, we should understand its limitations and not have unrealistic expectations.

    I think it is a very helpful counter to a CSDA which can give such distorted picture; it can help define a context in which to decide if there really are imbalances.

    For example, I had a CSDA and uBiome test in parallel.

    The CSDA claimed that I had an alpha haemolytic strep, E.coli and Klebsiella overgrowth. uBiome did not detect any Eschericia or Klebsiella, nor have either of these organisms been detected in 13 subsequent tests. I think it is clear that I don't have a problem with either of these organisms.

    Streptococcus was detected at 0.05%, average being around 1%. I looked at the species analysis and found that the entire Streptococcus count was accounted for by S. thermophilus, a normal gut constituent. Subsequent tests have consistently shown Streptococcus at no more than average levels, again almost entirely accounted for by S. thermophilus. Again I think it is clear I don't have a problem with alpha haemolytic strep.
  7. vision blue

    vision blue

    If you had the test done 14 times, I'm not surprised you were able to discern the invariants. Most people will not be able to do that.

    Comparison groups at ubiome also problematic- they refuse to reveal how many people are in each comparison group, and if they come from the customers or elsewhere. It is most odd.

    The fact that none of your ubiome tests was able to detect the bacteria that grew in culture does not mean theyre not there. They may be species that do not have many if any unique codes in a short low res sequence of 78 nuclotides in length. If the culture shows the same bacteria more than once, youd want to do a PCR genetic test. This way, there will be a primer chosen exactly for that organism and youll know if its there or not. In general, I also trust DNA more than culture, but each has its advantages and in this case you can't rule it out with the ubiome shot gun approach.

    warning also to others- their website has a mistake in analysis of data, in one place showing its enriched, but in another saying that its much less than comparison population. Theyre not quite ready for prime time yet, though have improved.

    Do you have a link that can show a sample report and/or methodology used for the new clinical test? that would be interesting to see. Based on what you said, perhaps its very similar to already exisiting DNA clinical tests from mainstream labs that specifically look for a dozen or so pathogenic organisms

    Not saying one shouldn't do it- I did - but unless youre super lucky, other tests will likely give you more info for less time investment.
  8. alicec

    alicec Senior Member

    They may be there but they must be at a very low level - in other words not an overgrowth.

    Here is some info on the test, including the organisms targeted. I haven't bothered to try to get more info since I don't want to have the test.
  9. vision blue

    vision blue

    Thanks for the link; had been to that page, but think I had not gotten all the way to the end before; its an interesting list. The reference is useful as well as to what one can learn from the 16-S sequencing.

    Am not sure of that on the implications of "very low level". Problem is that the gut, unlike blood and CSF and even small intestine, is filled with so many different bacteria, that even when there's overgrowth , it still shows up as a small percent if one is doing a general fishing expedition. see for blood etc., they light up like a christmas tree (though even there you still need good software to filter out things. ). Anyway, i don't want to keep hijacking the OPs thread.
  10. paolo

    paolo Senior Member

    Interesting enough, in your glycolysis and Krebs cycle you have the same pattern that Whitney Dafoe has: both the glycolysis and the Krebs cycle are depressed. In the picture below you can see some metabolic values of Whitney
    that dr. Kogelnik shared during a conference in 2016. As you can see, he has low pyruvate and lactate associated with a reduction on all the metabolites in Krebs cycle, too. One possible way to expalin this pattern is a problem in glycolysis, with poor provision of pyruvate for the Krebs cycle.
    Last edited: Apr 29, 2017
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  11. Thanks so much for that info, paolo!
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  12. paolo

    paolo Senior Member

    This metabolic profile seems quite interesting, even if it offers 'only' 76 metabolites. It offers a good look at Krebs cycle.

    How much does this metabolic test cost?

    Did you repeat this test?
    Last edited: Apr 29, 2017
  13. I don't remember the exact figure right now, but the test cost about $300.

    I did not repeat it.

    It told me pretty much exactly what I expected it to, especially in combination with the comprehensive stool analysis. My plan is to treat the dysbiosis and parasitic infection, heal my presumably leaky gut while attempting to raise my sIGA levels, and then do things like hyperbaric oxygen therapy, glutathione injections, taking cold showers, and gradually increasing my exercise (at my own pace, not a doctor's) to hopefully get my mitochondria growing. I will know if there is any improvement in my glycolysis and/or Kreb's cycle if and when my energy picks up. Tests are nice, but expensive. I don't consider them more valuable than the information my body provides me with, and I get that for free.
    paolo likes this.

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