uBiome results

searcher

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Has anyone else gotten results from uBiome? I just received my results today and they were very interesting. My results seem to fit with the findings by De Meirleir.

The uBiome dashboard is still in beta so there should be more information soon, but the key chart compares my top 5 phylum % to the average user's phylum %.

Here are the top 5:
Firmucites Me: 74.99% Avg: 63.77%
Bacteroidetes Me: 11.86% Avg: 30.69% (matches De Meirleir's findings)
Proteobacteria Me: 6.22% Avg: 2.29%
Verrucomicrobia Me: 4.55% Avg: 0.68%
Actinobacteria Me: 2.08% Avg: 1.64%

I can also compare myself against a lot of different subgroups, including vegans, folks following a paleo diet and heavy drinkers. They all seem to have 30-32% Bacteroidetes so my numbers were significantly different.

http://www.ncbi.nlm.nih.gov/pubmed/23791918 has info on De Meirleir's findings. It should be interesting to compare results across our community.

There are a lot of other outliers but I don't know how significant they are until I can see more data; for example I have 160x less cyanobacteria than their average sample, but I don't know the total number of samples and how certain the results are below the five most common phylum.
 
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adreno

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Interesting. Are there more specific information in the report (species, strains aso)?
 

Thinktank

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Indeed interesting. I'm still waiting for my results from Ubiome and American gut project.
I've also done the MSA DNA stooltest from de Meirleir.

Mine:
Firmucites Me: 78.55%
Bacteroidetes Me: 16.14%
Proteobacteria Me: 0.05% !!! (i guess i need to have this fixed as well as nearly 0% bifidobacterium)
Verrucomicrobia Me: ?
Actinobacteria Me: 5%
Other: 0.26%

Does the Ubiome report mention anything else about low/high diversity and gram + / gram - ratio?
 

searcher

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@adreno , @Thinktank - The report does have some additional information but the beta interface is a bit limited. The diversity data says "Coming soon." I don't see a gram + / gram - ratio. There is a bacteria tree that goes below phylum but it doesn't show percentages yet. I will try to get some screenshots up somewhere soon.

Thinktank- It looks like we both had similarly low results for Bacteroidetes but very different results for the other phylum. It will be quite interesting if any of those differences correspond with different symptoms, although I suspect such a correlation won't be too straightforward.

I did a metamatrix report way back when and my bifidobacteria were also low. I can see my bifidobacteria under the Actinobacteria tree so it will be cool to see the percentages soon and compare it to other users.
 

searcher

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I checked again and they just added percentages for strains so they are rapidly adding features. For now you have to drill down each hierarchy to get individual data. It looks like my bifidobacterium is still at <.01% after years of attempting to improve my gut :( The average bifido percentage from their "healthy omnivore" samples is .16%. I'm looking forward to hearing reports from other folks who have sent samples to ubiome and the American Gut Project.
 
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searcher

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Hi @adreno - I have tried Richard Nikoley sized doses of Bob's Red Mill potato starch. I think it helped my sleep when I started taking it around 5 pm, but haven't noticed any other changes. I am really into trying to hack my microbiome- I have also tried a lot of Ken Lassesen's advice from http://cfsremission.wordpress.com/ and saw Chris Kresser about three years ago. My digestive system has improved over the last few years but it is just surprising that my ubiome results doesn't seem to reflect that. Of course, my results could have been worse four years ago.
 

acer2000

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I haven't gotten my results yet. I did the American Gut project and uBiome. It will be interesting to compare the results. How long did it take you to get them?
 

searcher

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@acer2000 - If you have a twitter account you can message @ubiome and ask if you see your results. I am able to see mine at beta.ubiome.com
I sent my samples in last October but I suspect they have already done the analyses for more recent samples but are waiting to do more testing before they release all the results at once.
 

snowathlete

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I had a test through De Meirleir, not part of his study, and have similar breakdown to you. My firmucites are an even higher proportion. I've used your reference ranges as my test didnt provide any for the phylums. My test shows subspecies and ranges, and suggests that the bacterioidetes being a low proportion might have more to do with the other phylums - such as Firmucites - being over represented. Will be interesting to see if your full results suggest the same or not.

Here are my percent breakdowns:

Firmucites: 83.09% Avg: 63.77%
Bacteroidetes: 13.94% Avg: 30.69% (matches De Meirleir's findings)
Proteobacteria: 0.75% Avg: 2.29%
Actinobacteria: 0.08% Avg: 1.64%
Other: 2.14% Avg: 0.68%

I'm willing to post my full results if anyone is interested in them.

I have to get tested again really because I have been on abx for 10 months since the test, and only recently stopped. So things are probably even worse now. I'm keen to try and fix my gut health now as having recently been diagnosed with ulcerative colitis, I need to focus more on my gut. Obiously, having UC may well mean my results are not entirely typical for ME/CFS. But I think the gut health may be related to both diseases.

I think it is interesting that a lot of people with ME/CFS who have these tests, show a low, or zero bifidobacteria - I have zero too.
 

snowathlete

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Can anyone point me to reference ranges for 'normal' gut flora? (I know, 'normal' may be rather difficult to define, but still, based on the best data we have so far...)
I have some with my report from redlabs but I don't know what it's based on and would like to compare it to others. Also some of the ranges are a little general, for instance <50% for Roseburia - there might be a big difference from those with 0% compared to those with 49% yet both would be flagged as normal in this instance.
 

adreno

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Can anyone point me to reference ranges for 'normal' gut flora? (I know, 'normal' may be rather difficult to define, but still, based on the best data we have so far...)
There are no absolute reference ranges for humans. The gut microbiome composition depends on your diet. Here you can see typical profiles for european vs african subjects. As explained in the article, the differences in biome is caused by differences in diet. So if you want to change your microbiome, change your diet. First and foremost, you need fermentable fibers (like resistant starch) as this is food for your biome.




http://www.pnas.org/content/107/33/14691.full
 
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I checked again and they just added percentages for strains so they are rapidly adding features. For now you have to drill down each hierarchy to get individual data. It looks like my bifidobacterium is still at <.01% after years of attempting to improve my gut :( The average bifido percentage from their "healthy omnivore" samples is .16%. I'm looking forward to hearing reports from other folks who have sent samples to ubiome and the American Gut Project.
I recently did the Redlabs metagenomics stool test. My Actinobacteria is at 24.12%, with Bifidobacteria representing 23.7% of my entire gut microbiota. In the past I had low levels of Bifidobacteria on culture and metametrix stool tests. I think the increase is mostly due to my diet and prebiotic consumption. I eat some starchy foods (so resistant starch). I eat lots of colourful polyphenol and fibre-rich veg and fruits which boost Bifidobacteria. I eat a good omega3/6 balance which also influences the gut microbiota. I also took GOS, specifically B-GOS (i.e. Bimuno), for a long time; although was off supplemental pro/prebiotics for a month before the test. GOS is pretty selective for Bifidobacteria (far more so than FOS/inulin). B-GOS is even more specific since it is created by running Bifidobacterium bifidum-specific enzymes in reverse. It selectively promotes the growth of Bifidobacterium bifidum and Bifidobacterium longum, and has demonstrated beneficial effects on immune and metabolic parameters in humans. Note despite my apparent high Bifido levels I still have gut issues and ME/CFS; although slightly improved. My gut microbiota is still probably not ideal, I certainly have slightly low gut microbial diversity amongst other things. I will be trying more things to improve it further.
 
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acer2000

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@acer2000 - If you have a twitter account you can message @ubiome and ask if you see your results. I am able to see mine at beta.ubiome.com
I sent my samples in last October but I suspect they have already done the analyses for more recent samples but are waiting to do more testing before they release all the results at once.
Yeah I am talking to them. Their website isn't updating correctly for my account, but they are working on it.
 

searcher

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If anyone wants to share your results, Ken Lassesen (of http://cfsremission.wordpress.com) is collecting them to do some analysis. He did a 4-part series on what you get out of uBiome, American Gut, and some other labs at http://cfsremission.wordpress.com/2...sting-part-1-what-you-get-back-from-the-labs/ In the short series he also looked at how a few of our results compared with that of previous studies, and what probiotics could potentially help.

You can share your results in one of two ways:
1) Send them to Ken at Ken@Lassesen.com I shared them via screenshots but you can send them in whatever format is convenient. I took screenshots of the five levels on the compare screen (phylum, etc.)
2) Add them directly to the spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0AgfydlJUm1rAdGZJMFRBWjh0cXFHcngxTVNSR3YtWlE&usp=sharing

I put the groups in alphabetical order so it's easy to match with uBiome.

We'll come up with a better way of sharing results soon. I don't think there is an export yet so that somewhat limits how simple/automated we can make the process.
 

acer2000

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If anyone wants to share your results, Ken Lassesen (of http://cfsremission.wordpress.com) is collecting them to do some analysis. He did a 4-part series on what you get out of uBiome, American Gut, and some other labs at http://cfsremission.wordpress.com/2...sting-part-1-what-you-get-back-from-the-labs/ In the short series he also looked at how a few of our results compared with that of previous studies, and what probiotics could potentially help.

You can share your results in one of two ways:
1) Send them to Ken at Ken@Lassesen.com I shared them via screenshots but you can send them in whatever format is convenient. I took screenshots of the five levels on the compare screen (phylum, etc.)
2) Add them directly to the spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0AgfydlJUm1rAdGZJMFRBWjh0cXFHcngxTVNSR3YtWlE&usp=sharing

I put the groups in alphabetical order so it's easy to match with uBiome.

We'll come up with a better way of sharing results soon. I don't think there is an export yet so that somewhat limits how simple/automated we can make the process.
Great idea. I should be getting my uBiome results shortly. I have American Gut ones but I have no idea how to read them.
 
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searcher

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Awesome @acer2000 . I think Ken is also looking at American Gut results if you want to mail it to him.

I just found that uBiome has a raw data download. It's in json format in the sample dashboard and says "Raw Data." I am attending the ME/CFS conferences this week but will try to work with folks to start getting ME/CFS reports anaylzed once the conferences are over.
 

snowathlete

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I got my Ubiome results today. Had a major crash last week so not sure what i can do with that at the moment as my brain is dysfunctional right now. But I have them and figure I'll eventually figure out how to see all the genus level proportions. Right now I can see them in their dashboard thing but it doesnt give absolute values just shows different ized circles depending on the amount you have. I have the raw data file but havent looked at it yet. If anyone knows of a tool like there exists for 23andme, which takes the raw data file and tells you what it all means with a few clicks then do shout. cheers