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American Gut or UBiome Results?

Discussion in 'The Gut: De Meirleir & Maes; H2S; Leaky Gut' started by acer2000, Dec 18, 2013.

  1. acer2000

    acer2000 Senior Member

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    Has anyone participated in either of these projects? If so, would you be willing to post your results? I think it would be cool if we could compare with each other and see if we can find any trends. I am expecting my American Gut results shortly.
  2. Sparrowhawk

    Sparrowhawk Senior Member

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    I got my American Gut results this week and have to say I'm confused. Was hoping to spend more time reviewing it this weekend to see if it makes more sense.

    I expected something that looks like the Genova labs, but this is much more general. Also they state very clearly "this is not for diagnosing any disease, etc."

    What I am confused by is that they sent paper results, a mini-poster and some regular printout pages, but the results on the printout not only don't jive with the "your results" on the poster, they are almost saying opposite things.

    All that said, I think the idea of a CFS/ME gut biome comparo is brilliant. Especially if we can help each other figure out anything meaningful from the results!
  3. Aileen

    Aileen Senior Member

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    The American Gut Project is for Americans only. But ... the uBiome one is international. Their website says people from just about any country can participate. Since I've had my genome tested (23andMe), maybe the next logical step would be to find out who I am co-habitating with. :alien:

    They present 3 options. In addition to just having your gut tested, you can have mouth, nose, skin and/or genitals tested as well. As I have many olfactory problems, I am thinking maybe having both nose and gut testing might be in order.

    "Also of interest from their faq:
    Is your project community-driven?

    Yes! We are involving the public in data collection, hypothesis-generation, and hypothesis testing. Our goal is to build a community around long-term sequencing of the human microbiome. We want to engage and involve you in the process. Let us know about your big vision, your awesome scientific idea, or anything we screwed up at support@ubiome.com."

    Well ... we are pretty good at the hypothesis-generation part. Having a way to test them out, even at a very basic level, might provide some interesting results. It's not like any researchers are lining up to do it for us.
    Jon_Tradicionali and Sparrowhawk like this.
  4. acer2000

    acer2000 Senior Member

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    OK well I got my American Gut results. It shows the following:

    Most abundant microbes:

    Taxonomy Sample
    Genus Bacteroides 27.2%
    Genus Akkermansia 20.7%
    Genus Parabacteroides 13.8%
    Family Lachnospiraceae 10.4%

    Most enriched microbes:

    Taxonomy Sample Population Fold
    Genus Ruminococcus 3.7% 0.92% 4x
    Genus Odoribacter 0.7% 0.10% 7x
    Genus Parabacteroides 13.8% 3.11% 4x
    Genus Akkermansia 20.7% 2.30% 9x

    Note says:

    Your sample contained 10 rare and taxa, including the following: Unclassified Family Methy-lobacteriaceae, Genus Methylobacterium, Unclassified Order Sphingomonadales, Genus Sphingobium, Genus Zoogloea

    The little bar graph shows what looks like higher Verrucomicrobia, and lower Firmicutes than the comparisons. But its pretty hard to read.

    Any clue as to what this means? Anyone else have similar results?
  5. acer2000

    acer2000 Senior Member

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    Yeah the presentation of the data is kind of different than the typical GI tests I have seen. FWIW you can get a PDF version of the poster by logging into the site and checking your sample number.
  6. consuegra

    consuegra

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    This is an interesting thread as it holds out some hope for the future. My daughter does the Metametrix test for identification of problems and also for tracking. Over time one can figure out what some of the items on this test mean. Most doctors are not much help. She also does repeat testing at RedlabsBE and this test is even harder to understand with only a few overlapping items with the Metametrix (and some diversion in results from the same sample). Over time I hope to learn to read this test better. I am in the process of doing the ubiome test on the five adult members of my family. I have written about the citizen science biome projects here-

    http://cfspatientadvocate.blogspot.com/2013/02/citizen-scientists.html

    Others of course will argue with this idea of a group of ME/CFS patients investigating the gut biome in this way, saying that this is a waste of time and money. I don't believe this and the more that we as a group - loosely bound - look at the gut biome and it's elements, the better. I am not talking of a short term solution necessarily but there are things that can be done now, given the proper information.

    I would be remiss to not mention the website of Ken Lassessen, chocked full of information.

    http://cfsremission.wordpress.com

    Chris
    Sasha likes this.
  7. Sparrowhawk

    Sparrowhawk Senior Member

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    Here is my test:
    Most Abundant:
    Taxonomy Sample
    Family Ruminococcacae 23.2%
    Genus Becteriodes 16.9%
    Femily Lachnospiraceae 11.5%
    Genus Ruminococcus 8.1%

    Enriched:
    Taxonomy Sample Population Fold
    Genus 02d06 0.6% o.1% 11x
    Genus Eubacterium 2.1% 0.2% 10x
    Family Mogibacteriaceae 0.4% 0.1% 5x
    Genus Glostridium 1.6% 0.3% 4x

    For ref my diet has been paleo-primal, very low carb, for about two years now.

    I feel similarly clueless as you do. Perhaps after American Gut Project gets further along they will be able to offer, or some subcontracting org will be able to offer, some sort of guidance based on these results.

    One thing is for sure, the graph shows me with many more Firmicutes than Bacteriodaetes versus the proportions of Average or Similar Diet. Oddly, my biom is closer to Micahel Pollan than to average. FWIW.
  8. snowathlete

    snowathlete

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    According to their site it is an international project, but the FDA aren't happy about them recieving poop from outside the US through the post so they are currently not accepting international customers. I guess that might change in time. But just as likely that the uBiome project will end up having to stop allowing international customers for the same reason, so if you're thinking of taking one of these tests and you're outside the US then you might want to get on and order while you can.
    Sparrowhawk likes this.
  9. Aileen

    Aileen Senior Member

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    Just sent mine away earlier this week. Given how minute the sample is, I think this is rather silly. If it is a concern, they could always require extra packaging. The courier companies have special clear plastic bags to put your sealed package in for certain types of items.
  10. Sasha

    Sasha Fine, thank you

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    Well, they just accepted my sample - posted it off a couple of weeks ago, just had acknowledgement that it's going into the poop-o-meter.
    snowathlete likes this.
  11. snowathlete

    snowathlete

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    That's reasuring. Maybe they have resovled the issue with the FDA and just havent updated all the bits on their site to reflect that. It's interesting the regulatory issues with all these citizen science projects. The stuff with 23andme is well discussed but they are also upseting companies like FTDNA who are a genealogical DNA testing company, even though their focus in not health related.

    I love these sorts of projects, they're brilliant. The question for me is which one to join, uBiome, or American Gut Project. I'm probably not going to join one for a few months yet, but I'm sure I'll be joining one of the other.
    Sasha likes this.
  12. Aileen

    Aileen Senior Member

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    @snowathlete I see you are in the UK. The American Gut Project is only for Americans, so you are out of luck there. uBiome is open to most countries. :)
  13. Sasha

    Sasha Fine, thank you

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    Yup, it's uBiome for me and you, @snowathlete!

    Disappointing that we can't take part in a UK- or European-based project of this kind. I'm surprised there's not such an endeavour over here.
    snowathlete likes this.
  14. Aileen

    Aileen Senior Member

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    @Sasha have you gotten your uBiome results? I finally saw them show up as "sequenced". Couldn't access any actual results though so I emailed them. They responded promptly. They are still using a beta version so gave me a link to use.

    I am now taking a look at my results. Now I just have to figure out what they mean. :nervous:
  15. SDSue

    SDSue Florida

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    This makes me want to run amok collecting e-coli for "personal use" lol. But seriously, it makes me much more excited about Dr. Lipkin's work!

    It also makes me wonder why we can't get our hands on Mutaflor. Anybody on PR with experience?
    Sasha likes this.
  16. consuegra

    consuegra

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    I too have received a beta version for myself - whatever that means. Six members of my family have done this including one ME/CFS patient and one type one diabetic. I am anxious awaiting more results in hopes that it might be the very beginning of a useful pursuit. I think Joey on healclick is assembling some early results and I applaud his efforts. One of the fellows running Ubiome was open to the idea of looking at a group of ME/CFS patients to see if something might be revealed in this very complex situation. It was difficult to get patients to tag into this at that time.

    http://cfspatientadvocate.blogspot.com/2013/02/citizen-scientists.html

    Chris
    cfspatientadvocate.blogspot.com
    Sasha likes this.
  17. searcher

    searcher

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    I have spoken with Ken about trying to collect results in a centralized location, so now that more people are getting results I will follow up on that endeavor. I put a few results in an excel spreadsheet but ubiome changed the information in their reports so it may make sense to wait until they get out of beta to start collecting all the results in a standardized way.

    Ken did an analysis of what probiotics make sense based on a few patients' results at http://cfsremission.wordpress.com/2014/03/16/gut-bacteria-testings-part-3-available-probiotics-to-address-test-results/

    There were some commonalities but we need a lot more data to try to draw any conclusions. One possibility is we all have different imbalances that lead to similar end-results (but would help explain the big difference in symptoms across patients); obviously it will be easier to identify and treat the problems if it turns out there are common patterns.
    Last edited: Jun 11, 2014
    Sasha likes this.
  18. Sasha

    Sasha Fine, thank you

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    Yes - I also accessed them via the beta version (after about a dozen emails back and forth explaining how to do it) and have asked for a file to download, which they've sent me but I didn't know how to open it - apparently it will open in Word so my next task is to try to open it (one cognitively-demanding task at a time!).
  19. Sparrowhawk

    Sparrowhawk Senior Member

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    Forgive me if I am repeating myself, but I received my American Gut project results, which are paper only. As much as I have slogged through microbiome information in the last two years, had Genova /Metamatrix tests explained to me, etc. I have to say I found the results completely incomprehensible and contradictory. The results were given on two sheets of paper, but the biome didn't match from one paper to the other. In fact they looked highly contrasted (what was low in one was high in the other). I prepaide for four tests, was going to do them over time, but now am not really motivated to send them any other samples. Would love to hear from others what their experience has been with that one and if I'm missing something here. Thanks.

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