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uBiome results

Discussion in 'The Gut: De Meirleir & Maes; H2S; Leaky Gut' started by searcher, Mar 11, 2014.

  1. alicec

    alicec Senior Member

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    The bacterial species in these foods are, for the most part, not ones that naturally colonise the human gut. This doesn't mean the foods have no benefit. Indeed there are many studies suggesting a variety of health benefits associated with them.

    It is probably for the same reason that many probiotics are beneficial. Most, if not all, don't colonise the gut but they have a wide variety of effects on the host as they transit through the gut.
     
  2. alicec

    alicec Senior Member

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    Why do you think that is more reliable than the uBiome testing?

    CSAs focus on a few species that are aerotolerant are readily cultured, but these are a tiny minority in the gut. These tests are incapable of detecting the vast majority of gut inhabitants.
     
  3. alicec

    alicec Senior Member

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    I for one was not convinced by your claims.

    No-one is suggesting that bifido in isolation is the solution to all problems. It is only one part of a complex whole. What about the balance of all the other things in your gut? - or maybe your particular problems are not especially associated with the gut.
     
  4. pamojja

    pamojja Senior Member

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    I do biannually lab testing due to serious medical conditions since 9 years. CBC, lipids, liver and kindney function, thyroid and other hormones, inflammation markers, electrolytes, etc. All in all pretty comprehensive and would come at multiples the price than the ubiome test, twice a year. But most often - even with worsening - also nothing actionable. Since I do already everything which could be done (without a doc) against. So in that respect microbiome isn't different to all other lab-testing, in that conventional medicine also only uses it for screening serious conditions, but not at all for optimizing a healthy metabolism (as functional medicine would try to).

    Therefore, with your one-sided assessment, you would also have to conclude regular lab testing useless. We all know it isn't.

    Not reliable yet, mainly because it is gradually less accurate from the phyllum down to the species level. In my case from 100% down to only 44% of all species identified (73% on the genus level). Now for example, I found 7.7% Spirochaetia present, not specified further than the class level. And 5.1% Clostridium down at genus level. Both could contain very nasty bugs I especially would want to know and expect to get from an accurate and therefore reliable microbiome test. However, we're definitely getting closer. And am rather excited by the potential of such testing once matured.

    For that end it definitely is meaningful to donate our samples..

    Also the time factor. Took 1 month from taking the sample till I got results - heard many are waiting much longer - in which the microbiome composition could have completely changed. Found these 2 examples who tested each day for a whole year:

     
    arewenearlythereyet likes this.
  5. MaximilianKohler

    MaximilianKohler

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    I don't want to be argumentative, but it looks like there's a slight misunderstanding.

    Here's a study from today that supports the previous ones I shared, plus my conclusions: http://www.biorxiv.org/content/early/2017/08/15/176677 - "Interactions between species introduce spurious associations in microbiome studies"

    This kind of thing makes the current 16s gut testing significantly more useless than blood tests. Also, if something shows on a blood test there is usually something you can supplement, or stop supplementing.

    Other things I mentioned previously are that there is huge variation from sample to sample, from company to company, and even from which part of the stool you sample from. Like I said before, these are some of numerous factors which make these tests mostly a waste of money.

    Also, my problems are 100% gut microbiome related. Messing with my gut microbiome is the only way I've gotten any results.
     
  6. alicec

    alicec Senior Member

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    It is true that the technique has inherent difficulties in discriminating between some very closely related species and thus that complete species identification is not reported.

    It is not true that there is a gradation in accuracy going from the phylum to the genus level. A genus result, or indeed a species result for those that can be reliably detected, is no more or less likely to be accurate than a phylum result. The limitations of the method apply equally to all results.

    I'm not sure I understand what you are saying here but I suspect that you misunderstand how the test works.

    A large number of short pieces of DNA are generated from the starting mixture of organisms. These are sequenced and compared with extensive databases to identify the organism from which the DNA was derived.

    These pieces of DNA correspond with different parts of the 16S rRNA gene which contains highly conserved and hypervariable regions. The universal highly conserved regions make possible the initial amplification of all bacterial DNA and allow for things like the very general classification as bacteria.

    Within the hypervariable regions, there is wide variation in conservation,with more conserved regions correlating to higher-level taxonomy such as phyla and less conserved regions to lower levels, such as genus and species.

    Thus each piece of DNA is independently assigned to a particular taxonomic level, depending upon its sequence. The end result is an array of classification possibilities.

    Almost nothing is known about Spirochaetia in the gut and I suspect that the reason they were identified only to the class level is that they are under-represented in data bases.

    The only pathogenic Clostridium for which we have good data in the gut is C. difficile. uBiome's SmartGut test does detect this along with other organisms for which there is good information about the role in the gut.

    Alternatively if you really want all the detail of what is in your gut, even if we don't understand what a lot of it means, there is the American Gut Beyond Bacteria test which uses shotgun metagenomic sequencing to look at all the organisms in your gut. It will detect bacterial species but also viruses and eukaryotes.

    Unfortunately it is very expensive.

    The inability to identify all species is inherent in the short lengths of DNA which are used in the Illumina sequencing technique. This will only change when alternative genomic sequencing techniques become as cheap and rapid as the current 16S technique.

    I'm sure this will happen eventually but it may take a while yet.
     
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  7. alicec

    alicec Senior Member

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    It doesn't show that at all.

    It shows that studies of the association of gut microbiome composition with different disease conditions may be confounded by interactions between individual bacterial species.

    It is not saying that the technique for detecting the bacterial species is faulty, only that the some of the observed association of species with disease may be spurious.

    They go on to describe a way of adjusting for the confounding inter-bacterial associations and apply this to a large data set on pediatric inflammatory bowel disease.

    They accept the gut microbiome information but propose a better way of analysing disease association.
     
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  8. pamojja

    pamojja Senior Member

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    No misunderstanding. But you are sort of stubborn ;). I just said that in 9 years of twice yearly comprehensive blood testing was for the most part useless, because I was already supplementing what I could, for many years. You said, even only one ubiome test confirmed your experience: better avoid certain probiotics which it showed you have already too many of. So it did instruct or confirm in your case what to stop supplementing.

    Did you take a look at those graphs just posted? (click to enlarge) With samples taken each day and frozen for a whole year? If that doesn't show consistency I don't know what.

    :confused:
     
  9. pamojja

    pamojja Senior Member

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    Thanks a lot for that detailed explanation. With inaccuracy I meant that with only 44% of species identified there could be a whooping 56% of pretty nasty ones. However, if I understand you right, than all species already known to be pathogenic, like C. difficile, would have been identified. Or my 5,1% Clostridium with no species identified means, C. butyricum, C. boltae, C. botulinum, or C. clostridioforme definitely aren't there? Left out are only those not yet identified, and therefore not contained in databases?

    Just came accross this article: https://theconversation.com/i-spent...o-see-if-it-would-improve-my-gut-health-78773
    Interestingly, my microbiome seem to have similarities to hunter/gatherer. And indeed, when younger traveled a lot, like for example in 1 1/2 years overland from north to south of Africa. Also 5 days with such beautiful people, the Pygmies of eastern Zaire.
     
    Last edited: Aug 18, 2017
  10. alicec

    alicec Senior Member

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    I don't understand where you are getting the 44% figure from, nor, in an earlier post, your claim that only 73% identification occurred at the genus level.

    I think you are misunderstanding/misinterpreting your results.

    The break-up of organisms is 100% accounted for down to the genus level for every uBiome test that I have looked at, and I have done quite a few.

    You may need to follow this on the phylogenetic tree to pick up the groups that you appear to be missing.

    Let me give an illustration. I just randomly picked one of my tests and looked at the counts attributed to the different taxa.

    If we follow the different phyla through their subclassifications of class, order, family and genus, the counts add up perfectly. There is no loss of identification going from phylum down to genus - 100% of the counts are assigned for each phylum.

    It is different at the species level because the short length of the DNA pieces don't always allow species identification.

    BUT THIS VARIES FROM GENUS TO GENUS. ie, there is no blanket figure for % of species identified (your 43% figure).

    As an example, in my randomly selected test, for the genus Bacteroides, 76% of the genus counts were able to be attributed to different species, 100% for the genera Phascolarctobacterium and Victivallis, 52.5% for Blautia, 21% for Alistipes, 0% for Clostridium.

    No I don't mean that. My comment about lack of information referred to Spirochetes.

    There is plenty of information in databases about Clostridium , though DNA sequencing technology has shown that the genus, and indeed much of the Clostridiales, needs to be reclassified.The current uBiome technology used in the Explorer test can't discriminate between most Clostridium species. That will not change until the technology changes.

    I was really making a passing comment about the known gut members of the genus. A couple are known to be problems if they overgrow, but most are just part of the normal gut flora.

    In other words, don't get overly concerned about potentially pathogenic species and definitely don't make the assumption that all the species not identified could be the nasty pathogenic ones. These are rare.
     
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  11. Thinktank

    Thinktank Senior Member

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    My latest sample from exactly 8 weeks ago is still not done processing....
     
  12. alicec

    alicec Senior Member

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    Could it be a failed sample? This does happen from time to time and they will send you a free replacement kit.

    My most recent sample (a few weeks ago) was processed within 2 weeks.
     
  13. Thinktank

    Thinktank Senior Member

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    I'm not sure, the last sample also took 8 weeks or so to process.
     
  14. pamojja

    pamojja Senior Member

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    Most came from the mind-map taxonomy tree, confirmed by the raw data. Painfully copied and pasted into the spreadsheet I linked too. Species details are found in the raw data only.

    Okay. Then my initial assessment of ubiome not being accurate yet, was right then. Since it isn't able to identify most species, as they also transparently admit.

    To help understand how I arrived at the percentages pertinent to my ubiome test result only, please take a look at the linked to spreadsheet at the end of my first post, reposted below. Then it may become self-explanatory. Included are all breakdowns and raw data:

     
  15. alicec

    alicec Senior Member

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    None of that shows when I look at the spreadsheet. Most of it is blank.

    But in any case, in all the many tests I have done, if you follow all the subclassifications, there is 100% accountability from phylum to genus. There is no loss of "accuracy" as you describe it.

    Nor does uBiome report a figure for overall species identification in the raw data. If you compare the species list with the genus list, as I noted already, there is great variability. For some genera, all the species can be identified, for some none, plus various possibilities in between.

    If you have averaged these to get your 43% figure it doesn't mean a lot, but in any case, it is readily acknowledged that complete species identification is not possible with the technique as it stands.
     
  16. pamojja

    pamojja Senior Member

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    Sorry. Because you read already so many ubiome results I thought you already knew what the columns in the raw data sheet mean. Of the columns tax_name, tax_rank, count, count_norm, taxon and parent - count_norm gives the percentage of each bacteria, one just has to divide it by 10.000. Just added a further column with that calculation for you. To see the exact percentage of one taxonomy rank one just has to sort the column tax_rank, so that all of the same rank are close to each other. Then mark all percentages of that rank, and the total sum shows in the lower status-bar of google spreadsheet. Repeat that with all percentage of the other ranks, and you will see yourself that the 100% identification at the phyllum rank gradually reduces down to 43% at the species level. Leaves 57% unidentified.

    On the genus level still 23% are unidentified. There is this loss of accuracy as I described.

    The same results can be found in the mind-map taxonomy tree in your ubiome account. If you don't click, but hover above a node, a popup opens, which show the exact percentage of each compound of a rank. Going down a taxonomy tree, the more the total percentage decreases from the family rank increasingly downwards genus rank. As already mentioned, species aren't included here, but can be found in the raw data.

    You must have overseen the additional tabs in the lower status-bar, where beside the intro, you also could find the tree, compare, bacteria, function, biotics and data tabs, which lead to their respective pages.
     
    Last edited: Aug 20, 2017
  17. pamojja

    pamojja Senior Member

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    Just read this paper, which suggests that ubiome's 100% identification on the phylum level also may not mean exactly that much:
     
  18. mermaid

    mermaid Senior Member

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    Mine is also about the same length of time so far, but at least I know they received it safely as I had an email to say so.
     
  19. MaximilianKohler

    MaximilianKohler

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    There was definitely still a misunderstanding/lack of understanding of the info I shared. So I'll just ask a question:

    What are the beneficial outcomes you expect people to have from paying $90 for a test like this?
     
  20. pamojja

    pamojja Senior Member

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    The same as with all other regular blood testing for the same price: Either much, or little, or nothing. Most often nothing, exactly the same as with regular blood testing.

    For example in your case, you got a little ..even for free, by having found the reason why you don't do well with certain probiotics.
     

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