The 12th Invest in ME Research Conference June, 2017, Part 2
MEMum presents the second article in a series of three about the recent 12th Invest In ME International Conference (IIMEC12) in London.
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DNA/PCR stool testing

Discussion in 'The Gut: De Meirleir & Maes; H2S; Leaky Gut' started by zzz0r, Jul 23, 2017.

  1. zzz0r

    zzz0r Senior Member

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    Hello everyone,

    I would like to ask which is the most reliable DNA/PCR stool testing

    I have found two tests from different labs:

    1. GI MAP from Diagnostic solutions
    2. GI effect from Genova diagnostics

    Do you know the differences and which one is the most reliable. Also if anyone has done it could would please let me know the price. Also why have you done that test? I want to try it for SIBO
     
  2. Oberon

    Oberon Senior Member

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  3. alicec

    alicec Senior Member

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    The two tests are not really comparable.

    I was not familiar with GI MAP so read up about it. It is almost entirely DNA based, with a couple of useful gut markers thrown in. It concentrates on gut pathogenic species (bacteria, fungi, parasites and a couple of viruses) plus throws in a couple of less problematic bacterial inhabitants.

    The GI Effects test is essentially an old fashioned CDSA test with a little bit of DNA -based analysis grafted on to make it appear to be an up-to-date test.

    There are a few useful markers reported in a CDSA, such as SCFA's (which aren't reported in GI MAP), but I think the culture-based analysis and the parasitology are largely a waste of time. The former technique selects for aerotolerant organisms which are easy to culture, but these are a small minority of the gut inhabitants; the picture given of supposed overgrowths is completely distorted.

    See this post.

    Furthermore, many parasites are fragile and are not preserved by the CSDA collection technique.

    The selection of genera/species chosen for the DNA based analysis is also a bit puzzling - there doesn't seem to be much reason for choosing those particulars ones.

    So the GI-MAP test is more sensitive and reliable for the species that it tests for and seems like a good test to have if you suspect that you have some kind of gut pathogen. It does not, however, give a comprehensive picture of what is going on in your gut.

    DNA-based tests like those offered by uBiome.com (the explorer test) do attempt to sequence all bacteria and archaea in the gut so give a comprehensive picture, though understanding what the results mean is something that needs work. See this post and this thread.

    uBiome has recently started offering a Smart-Gut test which focusses on specific gut bacteria for which there is good background knowledge. It is worth some consideration also.
     
  4. zzz0r

    zzz0r Senior Member

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    @alicec I can not find an example of the results that you get on their site...

    Does it indicate the pathogenic bacteria or does it give you the bacteria in general?

    Does it have any other markers that indicate the general health of the gut or is it just bacterial population?

    What is the difference between the explorer and the smart gut test?
     
    Last edited: Jul 26, 2017
  5. alicec

    alicec Senior Member

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    Here is some info from the website on the Smart Gut test. If you scroll down to the bottom of the page you will see the list of bacteria tested. It includes both beneficial and problematic species and your doctor will get a report about what is known about the contributions of the organisms to gut health/problems. There is a link to a more detailed scientific publication on the test.

    The SmartGut test is limited to genera/species for which there is considerable experience/knowledge about the role in the gut. It needs to be ordered by a doctor and results are sent to the doctor.

    The Explorer test is a citizen scientist initiative. Anyone can order the test but it is up to you to interpret the results. This test is attempting to get an overall picture of the bacterial species in the gut and sequences all bacteria in the sample. Archaea are also detected though these are usually very minor constituents.

    Here is info from the website about comparison of the two tests.
     
  6. zzz0r

    zzz0r Senior Member

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    Plus you need to be in the US to do the SmartGut as it is stated on their site
     

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