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Stool Analysis - Recommendations?

Discussion in 'The Gut: De Meirleir & Maes; H2S; Leaky Gut' started by Journeyman, Feb 5, 2018.

  1. Journeyman

    Journeyman Senior Member

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    Hi everyone,

    A year ago I did my first Organic Acids Test (OAT) via the highly recommended Great Plains Labs (GPL) site. I found it extremely useful as the included report showed a recurring theme of bacterial overgrowth, alongside higher than normal levels of commensal bacteria AND a high HVA/VMA ratio (excessive Dopamine (DA) to Serotonin (5HT) ratio). Original post with results here

    In analysing the OAT to make positive changes to my health, I learnt that many of the bacteria I was found to be high in from the OAT all tended to have a suppressing effect on the DBH enzyme that is responsible for converting Dopamine to Norepinephrine, I quickly found myself implementing a SIBO diet. Low and behold I experienced significant improvements in energy/concentration and realised that my gut was constantly distended from what must have been the bacterial overgrowth. I also went onto supplementing Relora to reduce what appeared to be excessive DA levels (though someone mentioned theres actually a DA deficiency in the brain when someone exhibits the elevated HVA/VMA ratio??))

    I'm still not where I need to be in terms of health and energy (frequent upper respiratory infections, ongoing anxiety and PEM) so I'm interested in taking the next most useful step which I'm informed would be stool analysis. Particularly as I'm also interested to know what the state of my gut microbiome is now that I've now done 3 SIBO herbal antibiotic regimes. Particularly as I spend a lot of money on probiotics alongside the usual methylation supplements.

    I've found a couple of highly relevant threads here in these forums such as here and a great link (at least it appears so) here and its all quite depressing. Firstly it appears that half of the tests are useless (culture based testing) because they only show a relatively small proportion of the gut bacteria that exist in the gut, and their proportions might be misrepresentative because of the method of transportation (stool is stored in some kind of nutrient broth to keep the bugs alive for analysis which is unlikely to resemble your unique 'in vivo' gut environment)

    Whilst the other more modern tests done using PCR (DNA based analysis??) don't appear comprehensive enough to allow one to see an overall pattern of bacteria or parasitology that could be actionable in terms of taking certain pro or prebiotics? Or are they? Diagnostic Solutions seem to have quite a bit of useful information but @alicec I think you found from tests done in late 2014 they didn't report half of the specimens that they were able to find in a simultaneously submitted and supposedly inferior culture based analysis of the same stool sample through a different company?

    Have things perhaps improved since late 2014 with the Diagnostic Solutions testing? If so what might the improvements be?

    Also, what of uBIOME who seem to really great what with its emphasis on citizen scientists and providing information that might actually allow for useful actionable report information?? (Seems I'm limited to their 'explorer' test given my location outside USA)

    Also what about Dr MeLeir... I see him mentioned as some kind of guru for gut testing... Can anybody comment on the usefulness of the above options or perhaps new ones that I havent mentioned? Is he horrendously expensive?

    One key question I have is whether any stool sample is going to give useful results taking into account my location here in Sydney, Australia meaning most samples will undergo 48 hours transit times overseas before analysis even begins.... Will PCR based tests be more reliable given the transit time?

    If not, then do I need to find an Australian based stool analysis provider who can offer something as useful as Diagnostic Solutions PCR and if so do I need the test requested through a Dr and if so how can I do it without costing myself an arm and a leg.

    Please, if you have any information or better still, information and experience from your own gut based investigations I'd love to get your input..

    Regards

    Journeyman
     
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  2. alicec

    alicec Senior Member

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    The Diagnostics Solutions test is not intended to give a comprehensive picture of the gut. It describes itself as a comprehensive pathogens test - it concentrates on gut pathogenic species (bacteria, fungi, parasites and a couple of viruses) plus throws in a couple of less problematic bacterial inhabitants.

    It appears to be a sensitive test for the species that it identifies and is certainly superior to culture-based tests, but it doesn't attempt to identify everything.

    If you have symptoms which suggestive of the presence of some gut pathogen, it would be a good test to get.

    If however you want to get an overall picture of what is in your gut, then you need a test like the uBiome Explorer. Dr de Meirleir uses a similar type of test available from RedLabs in Belgium.

    These tests sequence all bacteria present in the gut - archaea may also be reported at least by uBiome, though these are very minor constituents.

    Bacteria are far and away the most dominant gut constituents but eukaryotes (fungi and parasites) and viruses (which infect bacteria) are also present.

    uBiome has just announced a new test, Explorer Plus, which tests for these eukaryotes and viruses, as well as bacteria and archaea. They are offering half price for a while, but be warned, even this reduced price is substantial (USD 399).

    American Gut has offered such a comprehensive test for some time.

    Microba is an Australian company based in Brisbane which is intending to offer a test covering bacteria, eukaryotes and viruses. They don't say exactly when they will start, nor what the cost will be. You can sign up for updates.

    Sending DNA samples doesn't have the same constraints as sending live organisms. The stool sample is collected into a preservation solution. With uBiome that I am familiar with, preservation is such that the DNA is stable at room temperature for several weeks.

    You return your sample to the USA in the normal mail.
     
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  3. Bob

    Bob

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  4. Journeyman

    Journeyman Senior Member

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    Hi Bob,

    I have considered it as far back as a year ago, but it was quite expensive and I'd already started a SIBO antibiotic protocol so I didn't want to go wasting money to get a false negative result. The improvement in abdominal symptoms, energy and concentration were all sufficient to vindicate the findings from my OAT where numerous different markers were suggestive of bacterial overgrowth of the stomach.

    Regards

    Ash
     
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  5. Journeyman

    Journeyman Senior Member

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    Glad I called you in on this one @alicec A veritable treasure trove of information as always!.
    The American Gut option has really caught my interest and I've taken a look at their various options per here
    It seems too good to be true that for $99 (+ about $25 for postage from here in Australia?) I could get a DNA based (PCR) stool analysis, but I noticed looking further down the list of options (appears on right of my screen) that its not till you pay *deep breath* $2500 USD for their 'beyond bacteria' product that you get the fungi, viruses and eukaryotes identified.

    This will be my first stool analysis. I'd like to get as complete a picture as possible. Particularly with a view to being able to take action on the results (probiotics etc.) However it also seems that unless I'm willing to pay a fortune I may have to get a DNA based Bacterial only analysis. The question is: how important is it to get the eukaryotes/fungi/viruses included in a stool test when you already have IBS or SIBO which I believe is indicative of these??

    Regarding: "Bacteria are far and away the most dominant gut constituents but eukaryotes (fungi and parasites) and viruses (which infect bacteria) are also present." I'm thinking Its one thing for bacteria to be the main constituent but is it possible that the fungi/viruses, whilst making up a relatively small proportion could be massively important in their functional effect on the body?? (causing dysfunction of the migrating motor complex/ abdominal symptoms etc.)? If I want to get both a complete picture and something reasonably useful to treat a potentially long standing gut issue it seems I'd be far better off getting a stool analysis that includes the fungi/viruses/eukaryotes?

    You mention that UBiome's new product - the Expolorer Plus will give me not only the bacterial analysis, but also the fungi, viruses and eukaryotes along with ALL archaea which for $399 USD seems like a relative bargain compared to the American Gut 'Beyond Bacteria' offering.. How comprehensive is the fungi/virus/eukaryote analysis or is it like the Diagnostics Solution test where it only picks a select few markers??

    Regards

    Journeyman
     
  6. alicec

    alicec Senior Member

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    It is comprehensive - ie it is trying to sequence everything that is there.

    The Diagnostic Solutions test just targets selected organisms.
     
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  7. vaer

    vaer

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    Thoughts on Viome?

    Viome uses transcriptone technology. ......While uBiome, DGL etc. use 16S technology.
    It reports down to strain level and and reports only those that are active (not dead or dormant)
     
    Last edited: Feb 12, 2018
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  8. alicec

    alicec Senior Member

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    Yes well someone will always come up with some new variation on things and blacken the alternatives (some of the things they say about uBiome and American Gut for example are oversimplifications of just not true) and tell you only the good things about their own brand new test in order to entice you in.

    You would need to evaluate the reliability of their technology from a source other than themselves.

    I don't have any experience with this test.
     
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  9. renski

    renski Senior Member

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    @Journeyman, I wouldn't do more stool testing.. not really going to tell you anything useful with your issues, you can rerun the OAT test to see if the SIBO protocol helped by looking at the bacteria markers.

    OAT test doesn't come close to giving the full picture, have you been tested for other things like Bartonella? Or Lyme
    Some of your B vitamins are possibly bit low, B12, B2, B6 for example. The biotin marker is off as well, that might be a deficiency. Have you checked your minerals? (hair, blood, RBC etc)
     
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  10. Journeyman

    Journeyman Senior Member

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    @renski, I'm feeling torn between whether to do another OAT follow up or the stool test now. I think I'd be able to choose more confidently if you could clarify exactly why you think a stool analysis would be no use for me?
    Also you mention not doing more stool testing but this would actually be my first, and from what I've learnt the gut is actually where its all at in terms of your overall health with both your body and brain being a reflection of the state of your gut...

    As for RBC I did get some basic bloods done in Dec 2017 which confirmed borderline low RBC count which suprised the hell out of me and is partly why I'm already 3 weeks into a strong Methylation protocol with all the cofactors modelled on fredd's treatment.
     
  11. Journeyman

    Journeyman Senior Member

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    Any ideas how long the Gut Explorer Plus is available for at that discounted price? I'm guessing it will be quite open ended but you never know.... I'm so torn between doing this or just getting a follow up OAT.
    PS I just saw someones post in another forum (not this site) from the end of Jan 2018 advising that they're received a marketing email from UBiome suggesting to 'pre order' the explorer plus to ship from Spring 2018. Now I looked up 'spring 2018' in america (northern hemisphere) and it says 20/3/18 so does this mean it won't even ship till then??

    Has anyone been able to proactively improve their health following an explorer or explorer plus kit?? I'd like to think that at a holistic level it would at least allow me to look at the ratio of one category of bacteria to another and then take probiotics which can promote or inhibit to rectify any imbalances (I think theres talk of firmicutes vs bacterioides?)

    I'm unable to look into the RED labs option (Dr Meirleir) in terms of cost or features. The best I could find (that actually brings up a website) was this. Where as this gives me nothing (banned in Australia??)

    Thanks as always for your input @alicec , @renski, @Bob and @vaer
    Regards

    Journeyman
     
    Last edited: Feb 13, 2018
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  12. renski

    renski Senior Member

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    CDSA's can provide some good data but you can't do much with it, you probably have gut issues. At least with the OAT test you can see how your b vitamin levels are, I'm running OAT test every 3 months while supplementing B's to see what is/isn't improving.

    RBC, as in mineral analysis in RBC (like https://www.doctorsdata.com/red-blood-cell-rbc-elements/).
     
  13. vaer

    vaer

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    redlabs = http://www.redlabs.be/ , click on 'intestinal dysbiosis - MSA'
     
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  14. Journeyman

    Journeyman Senior Member

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    All good now vaer. Turns out I just needed to load the page in a less secure browser (I have no script installed in my usual browser).
    I've sent them a msg asking for the price including postage to here in Australia as well as to confirm whether they test for anything like viruses or eukaryotes. I'm doing this because uBiome are absolutely hopeless in terms of customer service. Don't expect any kind of reply to your questions re: their explorer plus product @alicec just to let you know in case you too have had any experiences with them?
     
  15. Journeyman

    Journeyman Senior Member

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    I was really keen to do the stool analysis but with it being 2 weeks now without a response from uBiome and what must be getting on to a week after sending an online enquiry to Dr MeirLeirs (again with no response or acknowledgement) I'm thinking a follow up OAT would be more useful.....

    On this point, has anyone else made enquiries with either uBiome and Red Labs, and if so how long did it take to get a response (if at all?)

    If I do get another OAT I've considered local options and found I can get it done here in Australia but it works out at pretty much the same cost through Nutripath, and would obviously have different analytes than the GPL OAT making direct comparison less than perfect.. The only question is, if the urine sample deteriorates over the week it takes to get to and be processed in USA from my location in Australia, would it be much more beneficial to get the OAT done here in Australia??? Like I'm wondering whether the 'low amino acids' that someone observed from my original OAT thread was more the result of a deteriorated sample moreso than an actual low AA level because I was consuming a lot of protein in the lead up to the sample submission... Am wondering if it just deteriorated whilst in transit... @alicec @renski @vaer @caledonia thoughts?

    Regards

    Journeyman
     
  16. I think I would ask Great Plains what is the longest time a sample is reliable, and if you can freeze it and/or send it with an ice pack to make it last longer.
     
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  17. vaer

    vaer

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    I got a quick response from the ubiome explorer team however they Yes they don't seem to be giving anything away, even the date other than spring is approaching in USA...

    i am very tempted for it though at the pre-order price ~ $90 per sample x4 (using a coupoun readily available).

    Look at the ubiome thread in this sub, alicec has given a little though on explorer+ .

    Look at the sample report for Redlabs
     
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  18. alicec

    alicec Senior Member

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    I'm not sure what information not available from the various websites you think you need before you can make a decision.

    Last time I looked, if ordering from Australia, uBiome is the obvious choice. That will change when the Microba test comes online in June.

    The tests offered American Gut, uBiome (explorer) and RedLabs are essentially the same but there are associated differences.

    The RedLabs test must be ordered by a doctor and results are sent to the doctor. With the other two you can order yourself and receive the results yourself.

    The RedLabs test is considerable more expensive, the other two are a similar price.

    Both RedLabs and American Gut require the sample to be received in about 72 h. From Australia this means an international express courier which adds considerably to the expense.

    The preservation system used by uBiome means the sample is stable at room temperature for several weeks so it can be returned in the normal post for a few dollars.

    The recent addition of Explorer Plus is an additional plus for uBiome, though yes you will have to wait for a few weeks before the kits become available. The Microba test will be a little cheaper but while they are taking orders now, they are not sending out kits until June.

    These tests and an OAT test are not at all comparable. They identify the microbial constituents of your colon while the OAT looks at metabolites. It can certainly give helpful insights, but the dysbiosis markers, even if they were robustly backed by research - which they aren't - are at best suggestive. They are no substitute for knowing what is actually there.

    GPL provides instructions and timelines for sending frozen urine to ensure metabolites are stable. I would hope the Australian test also requires frozen urine carefully packed.
     
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  19. jason30

    jason30 Senior Member

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  20. alicec

    alicec Senior Member

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