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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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    I do, I've just never sorted them in the way you describe.

    You are correct - clearly my brain wasn't working at all that day - I completely overlooked the lower tabs.

    You are quite correct and I was wrong in what I said about 100% identification across the taxonomy tree - sometimes there is, sometimes there isn't.

    Your way of sorting the data is in effect giving an average of the capacity of the technique to give specific identification.

    I looked again at the breakup of the taxonomy tree on one randomly selected recent test to see where most of the loss of identification is coming from (just a quick survey - not exhaustive).

    For most of the phylla, there is 100% or very close to 100% identification down to the genus level.

    For what is commonly the second biggest phylum, Bacteroidetes, there is a small loss from phyllum to order and a further small loss in just one genus identification, the rest are virtually 100%.

    Where almost all the variation is coming from is within Firmicutes, in particular, within the order Clostridiales.

    Clostridiales is bewilderingly complex and badly in need of reclassification. Whole sections of it are lumped together into "Unclassified" or "incertae sedis" (of uncertain placement).

    So I think at least some of the problem lies in current inadequacy of the databases used for identification rather than in the technique itself.

    Because Clostridiales is just so complex identification within the grouping suffers from the same problem that limits species identification. The short lengths of DNA used in the 16S technique don't always include enough information for unequivocal identification.
     
  2. alicec

    alicec Senior Member

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    I don't think they are comparable. The enterotype study used Sangar sequencing (1st generation sequencing).

    uBiome is using 16S or next generation sequencing.
     
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  3. MaximilianKohler

    MaximilianKohler

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    If you do a blood test and it shows low vitamin D, for example, you can supplement with vitamin D. If you do a 16s test and it shows low Akkermansia you cannot supplement with Akkermansia.

    Not to mention all the resources I shared that showed the gut microbiome is way more complex than that, and even if an Akkermansia supplement was available, there are tons of other complex details which play a huge role (strain + gut microbiome community interactions). People who show low Lactobacillus, for example, are not necessarily going to see improvement by supplementing with a Lactobacillus probiotic or fermented food. They could absolutely get worse from it.
     
  4. pamojja

    pamojja Senior Member

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    One can see one's particular correlations. And they will be different for everyone. For example, I've no Lactobacillus present in my test, and I do see immediate improvements from supplementing (usually have very soft to liquid stuhl, temporarily firming up with one pill only).

    Also there are the opposite examples, from persons testing low in D3, but aren't able to tolerate any supplemental vitamin D3.
     
  5. pamojja

    pamojja Senior Member

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    Wow, you almost seem to have done your microbiome test with an other company. For me the breakdown from phylum to genus identified is the following:

    Code:
    Firmicutes         65,12 %   54,96 %
    Bacteroidetes      20,76 %   16,31 %
    Spirochaetes        7,68 %     0 %
    Proteobacteria      2,39 %    2,19 %
    Actinobacteria      1,96 %    1,9 %
    Tenericutes         1,64 %    0,37 %
    Verrucomicrobia     0,23 %    0,21 %
    Lentisphaerae       0,16 %    0,15 %
    Synergistetes       0,05 %    0,05 %
    Fibrobacteres       0,01 %    0,01 %
    Elusimicrobia       0,01 %    0,01 %
    
    Therefore from Firmicutes only a tenth of genus identification was lost, from Tenericutes 1/5, from Bacteroides almost a quarter. And from Spriochaetes none at the genus level was identified. Doesn't appear to be particularly compounded by Firmicutes only, in my test results.

    But beside that, how did your microbiome composition change over time?
     
    Last edited: Aug 25, 2017
  6. alicec

    alicec Senior Member

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    Not another company, another combination of microbes.

    There is not a universal ability or inability in the test to discriminate between organisms. It does very well with some, consistently detecting down to the species level: it does much less well with others. This is largely a property of the particular sequence in the DNA segment studied in the test - ie how similar or different it is from other sequences.

    Since there is considerable variation in microbiome composition between individuals, there will be considerable differences between individuals in % loss of identification in the kind of analysis you are doing.

    Also of course, since you seem to be trying to get estimates of overall loss of precision of identification, relative abundance is important. In your case, 1/10 of 65.12% (Firmicutes) makes more difference than 1/5 of 1.64% (Tenericutes) or even 1/4 of 20.16% (Bacteroidetes).

    In the example I gave of my analysis, the contribution of Clostridiales was even greater since this constituted almost my entire Firmicutes count.

    There was some loss in Bacteroidetes, though not to the extent you see (presumably reflecting the presence of different members of the phyllum in my gut) and as with your analysis, Proteobacteria, Acintobacteria, Lentisphaerae and Verrucomicrobia had very little loss.

    My first gut test was done after taking a lot of antibiotics over a long time. Actually it was not as bad as I expected (there were no serious overgrowths of potentially harmful microbes) but there was a clear lack of diversity and virtual absence of a number of known beneficial species which on average are present in relatively high amounts.

    I have concentrated on diet and consistent supply of a wide variety of concentrated prebiotics and have observed that, over time, diversity has increased and many beneficial species are returning. Star butyrate producers like Faecalibacterium and Roseburia established themselves fairly quickly and have remained consistently at good levels.

    Others like Bifidobacterium and Akkermansia took longer (especially the latter) and Bifido in particular is still very up and down for no apparent reason.

    One important genus, Ruminococcus, has never appeared and I presume I have lost it completely. Of course there is great redundancy in the microbiome and many organisms can fulfill the same function, but this is one I would rather have than not have, unlike, for example, Prevotella which I also don't have but don't care about.

    So I am pleased with that aspect of things, but there are others that I am not sure how to interpret.

    One noticeable aspect of the lack of diversity in my gut was the virtual absence of the minor phylla. While not much is known about the role of many of these organisms, it is thought their presence represents resilience, a store of possibilities to fill the gap if conditions suddenly change.

    A couple have appeared (Lentisphaerae and Verrucomicrobia) but the rest remain stubbornly absent.

    More worrying is the transitory overgrowth of a couple of members of Proteobacteria, viz Kluyvera and Thallasospira. The first time this happened with Kluyvera (present at 28% more than 8x average), I panicked. This is a member of the gamma Proteobacteria which contains many notable pathogens and the organism is known to be a rare opportunistic pathogen.

    I didn't have any particular symptoms so didn't think I had a serious infection but I was worried that this marked imbalance might eventually adversely affect gut function. Actually it resolved itself over a couple of months and I would have been none the wiser if I hadn't done tests at that time.

    This has happened again with Kluyvera and more recently with Thallasospira, a member of the alpha Proteobacteria about which little is known of its role in the gut. This took longer to resolve and again had no obvious ill effects.

    I don't know what to make of this. I wasn't doing anything obviously different, I don't know if this sort of thing might happen frequently or whether it is unusual and is flagging a potential problem. If the latter I don't quite know what I can do differently to deal with it. So I continue to contemplate this and still do fairly regular tests to follow what is happening with these potentially problematic organisms.

    Apart from that, I observe that my gut is fairly stable with the same grouping of organisms appearing in similar amounts most of time. There is a lot of variability at the lower levels but I think this just reflects the randomness of gut sampling.
     
    Last edited: Aug 26, 2017
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  7. pamojja

    pamojja Senior Member

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    Thanks for your detailed and interesting response. Also hunter/gatherer like the Hadza seem to have very strong variation between the dry season and the rest of the year. With a more omnivorous diet like in the west, their microbiome seems to become very similar to those of industrialized nations. With the end of the dry season their particular microbiota just reappears:
    http://science.sciencemag.org/content/357/6353/802
     
  8. Aubry

    Aubry Senior Member

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    Hmm weird... KDM really doesn't like if numbers of Bacteroides are high (has to be lower than 10%) ...
     
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  9. alicec

    alicec Senior Member

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    That is weird. Any reason given for this?

    In the uBiome community, the average for the phylum Bacteroidetes is about 36 and for the genus Bacteroides, it is about 22%.
     
    Last edited: Sep 10, 2017
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  10. Aubry

    Aubry Senior Member

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    See my results in attachment (Redlabs MSA stool test): very bad according to KDM
     

    Attached Files:

  11. alicec

    alicec Senior Member

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    I'd want to know a lot more about what is supposedly so bad and why.

    I see that your post above about Bacteroides needing to be <10 is based on the reference range quoted by the lab.

    I don't really know how they came to these figures and why they decided that some are < and some >. I can't see any rationale for this based on what I know about some of the genera involved, but you would need to get the lab to comment on that.

    I find the reference value very strange and restricted given what we know about the enormous variability between individuals when it comes to gut microbiome composition.

    With regard to Bacteroides here is a recent meta-analysis which has a somewhat different focus, being concerned with where stable enterotypes really exist or if there is a continuum, but gathers a lot of data on Bacteroides abundance since this genus is critical to defining one of the enterotypes.

    Look at fig 3 and the related discussion. The average abundance of the genus, from a large number of studies, is about 20% with a very wide range observed. The genus is the single most abundant genus in the gut for many individuals.

    I'd want to know exactly what the <10% reference is really based on, particularly in light of studies such as this one which show that lower levels of Bacteroides are associated with IBD.

    By defining the reference as <, they are in fact advocating for low levels - why?
     
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  12. Aubry

    Aubry Senior Member

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    Indeed... My thoughts too! Meirleir is keep saying the same too me: you are champion in high bacteroidetes this is bad because you have constant chronic immune activation. He also claims I have SIBO based on the test I put in attachment (no breathing test or so...). I see REDLABS also uses ratio's Firmicitus/Bacteroidetes etc and that is always too low in me...
     
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  13. Aubry

    Aubry Senior Member

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  14. Thinktank

    Thinktank Senior Member

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    My gut sample with ubiome is still processing.... it's been so for 11 weeks.
    I asked a question about it a week ago and only just received a vague answer.
    I'm suspecting they're giving priority to their physician "ubiome clinical" tests and let all the others wait. That or a shortage of staff.
    I will probably not use ubiome again until they've seriously improved their services. It's really a shame.
     
  15. mermaid

    mermaid Senior Member

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    Well mine finally arrived today. I sent it off in June I believe, and it was one of the free ones sent from the UK.

    Rather odd mix of results - a bit similar to someone else reported @pamojja I believe.

    Your ratio of Firmicutes to Bacteroidetes: 1.9 : 1
    Your percentage of Akkermansia: 0.00% (oh dear this is the one which helps you to keep slim).
    Wellness Match 96.6%
    Bifidobacterium compared to Selected Samples: 0.01x
    Lactobacillus compared to Selected Samples: 0x
    Diversity: 84% of all Gut samples are less diverse than your sample.
    Number of Very Elusive Bacteria: 6 - this includes one called Delftia which apparently can make gold nuggets!

    Doesn't sound too brilliant apart from the diversity. Incidentally I had had a colonscopy 6 months before, but in the meantime had used probiotics and eaten live yogurt.
     
  16. alicec

    alicec Senior Member

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    Doesn't sound too bad either - the wellness match indicating no essential difference from the gut flora of healthy people.

    Of course there is room for improvement. By concentrating on diet and addition of a variety of concentrated prebiotics, I have found that with time, known beneficial species such as Bifidobacterium, Akkermansia, Faecalibacterium and Roseburia have returned to something close to average levels.

    I wouldn't worry too much about Lactobacillus - our ideas of its importance have been greatly distorted by the probiotic industry and culture-based stool tests.

    Lactobacillus is much more important in the mouth, vagina and probably small intestine. Very few strains actually colonise the colon, most are just passing through.
     
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  17. mermaid

    mermaid Senior Member

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    Thank you @alicec
    Do you use prebiotic foods or supplements?
    I have looked at the list of foods and realised that on the whole they are the foods I avoid as they upset my gut. I have a very sensitive gut, and suffer from IBS and non ulcer dyspepsia so have tried to work out a list of foods that I can tolerate. That said, I could try to put the foods in, in small doses.
     
  18. alicec

    alicec Senior Member

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    Both.

    Initially I couldn't tolerate concentrated fibre sources so just concentrated on diet. Later I revisited the fibres and introduced them one at a time in tiny doses - 1/64 tsp. Now I regularly take several teaspoons of a few different fibres with each meal (varying the fibres).

    I sympathise with what you say about having problems with prebiotic rich foods. Way, way back I had that problem too. It took quite a few years of digestive enzymes, bile salts and things like glutamine before I could slowly expand my diet and eventually get to the point where I can eat most things.
     
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  19. mermaid

    mermaid Senior Member

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    That sounds very encouraging @alicec What I meant was whether you took prebiotic supplements. I presume that the fibres you mention are the foods rather than the supplements? I was just thinking that might be easier to start with as you can then use the tiny amounts that you mention. If you buy the foods then they will go off before you get to eat all of them I would have thought, using such tiny amounts?

    I do eat leeks which are prebiotic, almost every day, but I do cook them.
     
  20. alicec

    alicec Senior Member

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    No supplements such as raw potato starch, inulin/FOS, apple pectin, aloe vera, psyllium, benefibre, larch extract, artinisan (chitin glucan), acacia gum, baobab, PGX (glucomannan) - all powders which will keep indefinitely.

    Cooking leeks won't damage the fructans which are the prebiotic element.
     

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