The 12th Invest in ME Conference, Part 1
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Gut puzzle. Decoding the stool test results.

Discussion in 'The Gut: De Meirleir & Maes; H2S; Leaky Gut' started by Porke, Apr 26, 2016.

  1. Porke

    Porke

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    Hi,

    I finally managed to complete my gut testing with Genova and would appreciate some insights from any of the board members.

    Background:


    I have been struggling with CFS for about 8 years - digestive issues accompanying it all the way. However in the last 2 years I have spiralled downwards and gotten worse. This decline has coincided with a deterioration in gut function. My belief is that I could in the very least make some progress if I could only manage to sort out my digestive system.

    My symptoms have been:

    • Being quite thin, but still being able to gain some weight if I ate enough. However last 2 years has seen unexplained weight loss, with complete inability to gain any weight despite increasing calories. Probably a good 5-10 kg underweight
    • Started with some food intolerances and this progressed to severe food intolerances. Started with gluten and wheat, and now includes rice, corn, dairy and fructose.
    • Constipation has been ever present.
    • Complete intolerance of any probiotics. This is a mystery to me. For the most part they make me feel very foggy, spacey and out of it, and some give me heart palpitations. I have done VSL3, Homemade Kefir, Lacto Plantarum, Soil Based Prescript Assist, Saccharomyces Boull, Lacto 299v, Reuteri and Bifido Infantis (Align). Lactate free or not doesn't seem to make a difference either. Probiotics always make me feel much worse and I have completely given up on them.

    All other regular bloodwork is normal and in range, including thyroid function and adrenal ASI.

    Treatments:

    • I have tried numerous 'leaky gut' treatments to see if I could address the food intolerances. From glutamine, seacure, glycine, proline, zinc carnosine, marshmellow and aloe vera. All for extended periods without any noticable benefit.
    • Tried several digestive enzymes & betaine HCL to boost stomach acid. I'm really sensitive to supplements and both made me feel a bit off. Stayed on them for 4-5 weeks and pushed through. Digestion was a bit better, but it was no real solution.
    • I have done a general anti parasite protocol with Albedenozole and Mebendazole (Nothing seen in stools and no improvement)
    • Last year I was on a 3 week Xifaxan antibiotics course (for Sibo, but also general dysbiosis). Didn't notice much at all.

    Results:

    Anyways, here are my results:
    Organix Dysbiosis + GI Effects
    http://imgur.com/a/HZQsk

    Organix dysbiosis shows nothing out of the ordinary (This was one surprising, I was suspecting I could have some SIBO)

    GI Effects show no problems with candida, parasites or infections.

    However, I have numerous overgrowths of commensal strains. 9 of them are above reference range.
    I also have Alpha and Gamma Streptococcus which is listed as Non Pathogenic, but growth is high at +4.

    What is interesting is that one of the high strains are Methanobrevibacter Smithii, which is usually associated with SIBO overgrowth (the methane kind). Methane producing bacteria according to Dr Pimtel is what causes slow motility and leads to constipation. So there is one clue that fits my symptoms, however in this case it appears to only be in the large bowel, and not the small bowel as with SIBO. My understanding is that SIBO will show up on the organix profile test.

    Future plans:

    Unfortunately I do not have access to a SIBO breath test in my country, so I cannot do this test to rule it out absolutely.

    At this point it seems my only course forward is to persist with another round of antimicrobials, and this time adding in antibiotics like Flagyl - as recommended by Pimtel for Methane producing bacteria. (I hate using anti biotics, but I am at my wits end trying to fix my gut!!!)

    Something like:

    3-4 weeks of:
    Allicin (apparently good for methane producers)
    Candibactin Ar + Br

    2 weeks of:
    Another Xifaximin course, but this time with Flagyl for 10 days.


    Does anyone have any insightful comments on my gut tests that I am perhaps missing?

    Thanks!
     
  2. PeterPositive

    PeterPositive Senior Member

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    Welcome to the club, brother :rolleyes::)
    I have a similar history with, among other things, lots of digestive issues, inflammation and strong sensitivity to so many foods.

    Similarly I have done all sorts of tests, including several stool analysis such as those you have posted, with results not so different from yours. In other words, from those numbers and ranges it looks like your intesting is doing pretty well, except it isn't :lol:

    Similarly I have made several pharmacists pretty rich, going through the whole repertoire of classics... pre/probiotics, herbs, digestive aids, supplements, all sorts of dietary changes, relaxing techniques and autogenic training (for the "is all in your head" believers), etc... etc...

    I won't say that all amounted to nothing, I did find a small % of those to help a bit, but in the end I haven't solved anything. I just made my life 10% less miserable...

    As regards your questions on SIBO, I doubt that those tests you have done can tell you much about SIBO as SIBO interests the small intestine, while most of those lab's parameters deal with the colon.

    In any case it's good to know you don't have major dysbiosis issues, calprotectin is low (now IBD), etc... The fecal fat being high usually indicates a bit of malabsorption.

    Have you ever tested for H.Pylori?
     
  3. Porke

    Porke

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    It was an optional add-on that wasn't recommended by my functional medicine doc. He reckons many people test positive for it, and are simply carriers without any negative effects. He recommended one only tests for H Pylori when you have the classic symptoms of pain, burning, ulcers etc.
     
  4. PeterPositive

    PeterPositive Senior Member

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    Well, if you test for the presence of antibodies in the blood it's not a guarantee of an active infection. The breath test should be quite accurate, though.
    I did the blood test first, pretty convinced that it would come back positive since I had lots of the classic symptoms, but it was negative.

    Later I found some help using high dose zinc, B vitamins and L-Glutamine. These days the gastritis symptoms are kept to a minimum, but I still need to stay away from many foods.
     
  5. alicec

    alicec Senior Member

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    Before I make specific comments, by way of background, here and here are posts I made which compare some aspects of the Genova test with a full DNA sequencing test .

    I seriously question whether the attempt at quantification in this test means anything at all - and I find it difficult to imagine why you would want to take awful antimicrobials like flagyl to "fix" something which is unlikely to be a problem.

    There is a general problem with the PCR based part of the test. It is a poor attempt to dress up the very old CSDA test (which is based on culture techniques) in the new clothes of DNA based analysis of the gut microbiota.

    Presumably this is because it is now very clear that these culture-based tests have completely misled us about the composition of the gut microbiota. Because of their own technical limitations, they cannot detect the vast majority of the species in our gut.

    DNA sequencing has shown a totally different picture, but note that this is sequencing of all bacterial DNA, not just a few select species as this test is offering.

    The grafted DNA based analysis adds a few species or genera that the culture techniques miss, but is also unable to give a comprehensive picture of what is going on in the gut.

    Actually I think the whole test is a bit of a con - trying to convince us that we are getting a lot more than we actually are, that the test employs the latest technologies when it really doesn't.

    Then there is a specific problem with the attempt to translate the PCR results into the kinds of scales used in culture techniques in order to quantitate them - ie reporting a PCR result as cfu (colony forming units)/g faeces.

    They've dreamed up some calculation based on all sorts of dubious assumptions to report results this way, but it makes no sense to do it and I can find no reason to have much confidence in it.

    So before you start trying to "fix" the overgrowths in your gut, I think you should think seriously about what the results really mean and whether a proper DNA based test might give you a better idea of what is going on.

    I'd be thinking about diet and prebiotics to try to encourage a healthy population of gut bacteria. You've already tried the "nuking" route.

    As for other aspects of the test, as in discussed in my earlier posts, I don't have any confidence that culture-based detection of gamma strep at supposedly high levels means much.

    The high faecal fat suggests to me that you need digestive enzyme support. I know the pancreatic elastase marker is supposedly normal though I think their reference range is too low. Others think >500 is better.

    Anyhow you could try some pancreatic enzymes. High doses of Creon was one of the best things I ever did for food sensitivities.

    The high glucuronidase activity suggests that you might need some support there too - supplement with calcium glucarate.
     
    PeterPositive likes this.
  6. Crux

    Crux Senior Member

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    @Porke , It looks to me like more than a few titres are out of range, plus, you are feeling poorly - unable to sustain weight - the most telling.

    I'm not trained at any of this, but, I've had a similar experience, especially trying so many natural ways to battle the bacterial overgrowths that rob nutrients, leaving us undernourished.

    It doesn't have to be sibo, it seems now it's being called BOS, bacterial overgrowth syndrome. Anyway, there're too many.

    M. smithii is high, and has been shown to cause constipation among other things :
    http://www.nature.com/ajgsup/journal/v1/n1/full/ajgsup20126a.html

    A sulfate reducing bacteria, D. piger is high, which could be furthering the constipation, along with producing hydrogen sulphide, which, in excess, can be neurotoxic :
    http://www.medscape.com/viewarticle/732378_10

    E.coli is high, as are some other so called commensals. Even commensals, (friendlies), can become pathogenic if overgrown.
    http://www.uiweb.uidaho.edu/micro_biology/250/Week10.pdf

    Intolerance of probiotics is common here. Overgrowth of lactic acid producing bacteria is a suspect.
    Your test results show no lactobacillus, but there are other LAB that could be causing the symptom. Bacteria compete with each other, producing antibiotics as weapons.

    I agree that antibiotics are problematic, the side effects can be very painful, etc., but after trying to remedy my own gut with diet, probiotics, prebiotics, etc., for most of my life ; the use of abx. was what has shown the most improvement in my case.

    Metronidazole has been shown to inhibit methanogens, sulfate reducing bacteria, C. diff., etc.
    Rifaximin inhibits E. coli, and even C. diff., etc.

    I hope whatever choice you make works.

    https://www.gdx.net/core/interpretive-guides/GI-Effects-IG.pdf This may help a little.
     
  7. satori

    satori

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    Alicec-what would be a proper DNA stool test and where would you get it? Thanks.
     
  8. alicec

    alicec Senior Member

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    There are three, from American Gut, uBiome (both in USA) and RedLabs Belgium. All use similar techniques.

    The first two are crowd funded enterprises which anyone can order from and have similar prices (around USD 99 for a gut test, though uBiome often offers 3 for 1 specials).

    If you live in the USA there is not much to chose between them. If you live outside the USA, then uBiome works out cheaper because of different transport requirements (they preserve the sample differently and so it can be sent back in the regular mail).

    The RedLabs test is much more expensive and a doctor's name is needed on the order form. Results are sent to the doctor.

    All three tests measure only bacteria, so the archaeon M. smithii would not be detected (nor eukaryotes such as yeasts and parasites).

    American Gut does offer a fairly expensive test which sequences everything in the gut - ie all the above plus viruses. I am seriously considering having it but haven't yet got around to it.

    I should add that having the test done is the easy part - knowing what it means is more problematic. There is a great deal of redundancy among the gut species (different species can fulfil the same function) and a lot of individual variation. In other words there is no single "correct" pattern that we should all aspire to.

    Still it is the only way to get a proper perspective on supposed overgrowths and problematic species detected by culture. In my experience, results from the Genova test bear little resemblance to what is identified by DNA sequencing.

    Here is one thread about uBiome.
     
    Valentijn likes this.
  9. CCC

    CCC Senior Member

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    I'd say welcome to the club, but it's a club no one ever wants to join.

    Our symptoms are similar enough to yours to offer two possibilities:
    1. How much fat do you have in your diet? This is an odd question, I know, but fats and fat digestion can affect motility and body weight. I mean unprocessed fats - milk, meat, coconut and olive oils, avocado etc.
    2. Have you had proper stool testing for specific parasites - a PCR test is currently the preferred approach? In our case, Dientamoeba fragilis has wreaked havoc. It's hard to detect, hard to kill, and causes almost all the symptoms in your list (see BadBugs and CDD for more detail than you'll ever want). Commercial probiotics can make things worse too - it's as if they feed the little beasties.
     
  10. alicec

    alicec Senior Member

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    PCR was used so titres are not measured. The attempt to "convert" to titres to align the two parts of the tests is highly questionable. I can't see that it means anything.
     
    Valentijn likes this.
  11. Porke

    Porke

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    Thanks AliceC, food for thought. I have looked into the UBiome tests, but as you say these did not seem as comprehensive and give a greater overall picture of gut bacteria, rather than specific strains.

    The GI Effects test might be imperfect, but actually seeing the result align with many of my symptoms, so I am inclined to believe that it is somewhat accurate.

    What I found very interesting was:
    • The high levels of methane producers (Methanobrevibacter smithii), explaining my battle with constipation. (According to Dr Pimtel). Perhaps also why Xifaxan didnt do much at all for me as this doesn't target the methane producers.
    • My complete intolerance for fructose where before my 'crash' I was able to still enjoy a somewhat moderate intake of fruits without any issues. This, at-least in my mind, is explained by so many overgrown strains as shown in the GI Effects. The fructose is feeding these buggers, and their by products are causing the issue.
    • Lastly, the general overgrowth of so many bacteria, coupled with my complete intolerance of any probiotics. After reading this rather convincing thread about a guy who finally managed to overcome his SIBO by ditching probiotics all together. His argument in a nutshell is that when you have an issue with overgrowth, whether in SIBO or elsewhere, you are simply adding fuel to the fire by adding more probiotics. I am now inclined to be in agreement with him, as it appears I have significant overgrowth, and it could explain why I do so terribly when taking probiotics http://www.ibsgroup.org/forums/topic/102286-after-5-relapses-now-cured-heres-how/
     
    Last edited: Apr 29, 2016
  12. Porke

    Porke

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    Thanks for the interpretive guide. I had a look through it, but it seems Genova only gives really useful information for the pathogenic strains and not much with regards to overgrowth of the friendlies.

    As for the abx, I have noted a few other threads where people have tried numerous natural approaches to their gut with not much success, and in the end an abx course for something completely unrelated ended up 'resetting' their gut and solving many of their issues. I am holding off on them as a last resort, but at this point im desperate enough to try anything to fix my darn digestive issues.
     
  13. alicec

    alicec Senior Member

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    uBiome actually does look at species but because it is not exhaustive, they are not shown on the website. If you download your raw taxonomy data you can sort by species.

    I routinely see 20-30 species identified in an analysis. Typically 50-100 genera might be identified.

    With the PCR part of the Genova test you get 11 species plus 11 genera and (probably) 1 family or order (I'm not sure exactly what they are measuring when they say Bacteroides-Prevotella group).

    Yes that is a unique part of the test you wont get from uBiome. I'm not sure that this single analysis warrants the increased cost over doing an old-fashioned CDSA.

    That is actually a report of the work of Henry Butt from Bioscreen Australia. I think the data are pretty meaningless because the culture-based test used to accumulate the info is seriously flawed. Here, here, here and here are some posts about the problems (written in a slightly different context).

    I don't think this test is capable of really showing that.

    You obviously have gut problems, I just think you should open your mind a bit more as to what might be causing them rather than relying solely on a very flawed test.
     
  14. Porke

    Porke

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    Alright, I will definitely look into doing a ubiome test as a complimentary picture of whats going on in my gut. It will surely be good to compare the two to see if there are any similarities or fresh insights.

    Can you explain why the vast majority of functional medicine docs still do CDSA or GI Effects tests if it is so inherently flawed? Or why a lab as large as Genova doesn't offer this more advanced DNA based testing if it was more accurate?
     
  15. jepps

    jepps Senior Member

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    My last Ubiometest showed Eukaryota (Superkingdom, 0,004 %), this is according do this study a good sign, and increased diversity to 93 %. So microbial eukaryotas might be detected.
     
  16. alicec

    alicec Senior Member

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    Great - so far I haven't encountered that. They do seem to be continuously expanding their analysis.
     
  17. alicec

    alicec Senior Member

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    It was my comparison of the two that convinced me that culture based tests mean very little and that the quantitation offered in the PCR part of the Genova test was unreliable.

    You will certainly get fresh insights when you see what is really in your gut.

    Until relatively recently, CDSA was the only way to look at gut bacteria. Indeed culture-based tests were virtually the only way to study bacteria full stop.

    The revolution in DNA analysis that started with the human genome project has superceded this approach. All bacteria can now be studied, not just the few that are amenable to culture in a dish.

    This approach to studying the human microbiome is relatively new and we are still better placed to gather information than we are to understand it. The testing is still largely research-based and not to the black and white state that pathology companies like.

    RedLabs is a company offering various specialised tests, all of which they say are research-based. They do not interpret and hence send results to your nominated doctor. Unfortunately there would be very few doctors who would understand the first thing about the test. One exception is KDM who as I understand it works closely with RedLabs.

    This is highly commendable but for the rest of us, the crowd funded route of citizen scientists is the only option. Both American Gut and uBiome put a lot of info on their websites, including comparative info from the community using their services, but it is up to us to work out what our own results mean. This does require some effort - a bit like getting a 23andme analysis.

    Functional medicine docs keep using CSDA because they are used to it, think they know what it means and because the alternative requires considerable effort on their parts to understand. It also overturns all they thought they knew about the gut. Resistance to change is hardly a new phenomenon.

    CSDA tests have been bread and butter for many functional pathology labs for decades. DNA based analysis is a much more difficult proposition requiring considerable investment in sequencing instrumentation and big data processing. None apart from RedLabs appear willing to make this commitment yet.

    Genova have attempted to con us into thinking they are embracing the new technology by grafting on a bit of PCR to a traditional CSDA. It bears little resemblance to a full DNA analysis.
     
  18. alicec

    alicec Senior Member

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    I've just received new uBiome results. I don't show any Eukaryota, but I do show the phylum Euryarchaeota (archaeons) and the genus Methanobrevibacter at a low level (haven't had a chance to explore raw data yet so don't
    know if species identified).

    So it seems uBiome is ever expanding its testing.
     
  19. Oci

    Oci Senior Member

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    Very interesting and valuable information, @alicec.
    I was thinking of doing another Doctor's Data CDSA test. I did one about 9 months ago that showed 2+ Candida and 4+ enterobacter cloacae complex. Also only 1+ e coli and NG enterococcus spp. At the time I did have some candida going on and/or oxalate problem. Probably both!

    Those cleared up but I have an uneasy digestive system - likely SIBO. No diarrhea or constipation but often reflux and indigestion. I have had this off and on over many years.

    I have delayed in re-doing the DD CDSA test - feeling that perhaps I should instead do the Genova test...or that neither test held much value. My guess is that it is an ever changing scene in the gut. DD tests only a few of the bacteria. Perhaps I will try Ubiome but am not sure how that will help.

    You have a good point about finding the source of the problem. I have been withdrawing from Zopiclone (a pseudo benzo sleeping pill). If I reduce too quickly I get a lot of digestive problems as well as anxiety and very tight neck/shoulder muscles. And of course, anxiety was one reason for the sleeping pills in the first place.

    I've no idea what to do next other than slowly work my way off the sleeping pills and to live well.
     
  20. alicec

    alicec Senior Member

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    It is M. smithii so even that is no longer unique to Genova's test.
     

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