American Gut or UBiome Results?

[snowathlete]

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!).

I too, went through the email back and forth in order to get access to the beta link. I don't think they have an automated means of telling people yet?!

My results were very interesting.

 

[Sasha]

I too, went through the email back and forth in order to get access to the beta link. I don't think they have an automated means of telling people yet?!

My results were very interesting.

They seem to think that people will be happy to have their results shown graphically on a scroll-down computer screen, which is a very poor way of looking at a summary of your results, IMHO. I want a spreadsheet! I'm going to have to do it myself, though.

Glad you got interesting results! I still haven't done the work on the uBiome results to extract everything in usable form.

 

[aimossy]

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.

Are you doing this with Ubiome Searcher? Can I get this done form in NZ?
I am so in if I can be!

 

[snowathlete]

They seem to think that people will be happy to have their results shown graphically on a scroll-down computer screen, which is a very poor way of looking at a summary of your results, IMHO. I want a spreadsheet! I'm going to have to do it myself, though.

Glad you got interesting results! I still haven't done the work on the uBiome results to extract everything in usable form.

Yes I think that's their primary thinking. The raw data you can download is incomplete.
I'll point you to a spreadsheet I'm using, in a bit. Much easier.

 

[Nutritionnazi]

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.

Sparrowhawk,

I just signed up for this forum so I could respond to this older post of yours. My American Gut results are PRECISELY the same as yours, down to the percentages, at least for these "abundant" and "enriched" microbes. Seems very strange that this should occur. I too am from the West coast, if that has any bearing. I'm not Paleo or super low-carb, but am lower carb than most and eat only organic produce and wild or grass-fed/pastured animals. Lots of ferments too, though at the time I tested I was rebuilding my flora, after having inadvertently ingested water from the North Platte River, with cows standing in it! (our water filter broke), and had gotten sick enough to require antibiotics. I did this gut project test a few months after this episode.

 

[snowathlete]

Sparrowhawk,

I just signed up for this forum so I could respond to this older post of yours. My American Gut results are PRECISELY the same as yours, down to the percentages, at least for these "abundant" and "enriched" microbes. Seems very strange that this should occur. I too am from the West coast, if that has any bearing. I'm not Paleo or super low-carb, but am lower carb than most and eat only organic produce and wild or grass-fed/pastured animals. Lots of ferments too, though at the time I tested I was rebuilding my flora, after having inadvertently ingested water from the North Platte River, with cows standing in it! (our water filter broke), and had gotten sick enough to require antibiotics. I did this gut project test a few months after this episode.

If your results are the same, I'd say that is very unlikely to have happened by chance and I'd suspect AG screwed up somewhere. Just my opinion.

 

[Nutritionnazi]

You know, I had the same thought. I mean, if we're all unique -- and we are -- this is just too unlikely. At some point I think I'll test again and see what happens.

 

[aaron_c]

Hi Yall,

I just ordered a kid from the American gut project. According to their website, it should also give access to a more detailed printout of our microbiome that looks like this. Did I miss the part where people put those together? Do they exist?

 

[Sparrowhawk]

Yes I just got a postcard in the mail reminding me to go look and they had that chart plus a color set of graphs. The stuff they mailed me was incomprehensibile to me at the time (brain fog) but I looked at the report on their webstie and it was pretty straightforward. I want to sample again to see how things have changed since last time.

 

[aaron_c]

The more detailed printout seems like the more valuable tool in terms of comparison...although it probably won't be as simple as "people with ME lack some of these six bacteria," I can hope it will be.

I will post my results when I get them. Is anyone else willing to do the same? (@Sparrowhawk?)

 

[Sparrowhawk]

@aaron_c did you mean the long table with just the listings of gut microbe info, or the pdf of the color charts? I can post either one. What I found interesting is I wasn't really divergent from general population, even though I was pretty darn sick then. But I was quite different from the sample posted for Michael Pollen. Note I'm on a heavy fat, low carb, medium protein diet due to severe reactive hypoglycemia. I think anyone posting their info should at least include details of their average diet. Another would be to include a rough idea of geographic location.

That guy who posts about visiting the african tribe and eating what they eat, and then the impact on his microbiome -- mindblowing stuff. Check out his blog posts if you haven't read them.
http://humanfoodproject.com/rebecoming-human-happened-day-replaced-99-genes-body-hunter-gatherer/

 

[aaron_c]

Thanks @Sparrowhawk!

Both would be interesting, but the lists of gut microbes are most interesting in my mind. Those might be a departure point for further education.

 

[Sparrowhawk]

They just took the site down, will have to post later:

" We are taking the American Gut and British Gut websites down in order to move the resource from the University of Colorado at Boulder to the University of California, San Diego. We anticipate bringing the sites back up March 12th, and we apologize for any inconvenience this interruption may have caused. "

 

[Sparrowhawk]

OK @aaron_c here you go, sorry I can't get the table better aligned. Not my diet was high fat, medium protien, very low carb for the period last year that this was tested:


Kingdom Phylum Class Order Family Genus Relative Abundance (%)
Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides 58.13
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Faecalibacterium 10.54
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae --- 6.57
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae --- 3.67
Bacteria Bacteroidetes Bacteroidia Bacteroidales Rikenellaceae --- 3.48
Bacteria Firmicutes Clostridia Clostridiales --- --- 2.66
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Roseburia 2.33
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Coprococcus 2.01
Bacteria Verrucomicrobia Verrucomicrobiae Verrucomicrobiales Verrucomicrobiaceae Akkermansia 1.80
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnospira 1.54
Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Parabacteroides 1.49
Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Dialister 1.15
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Blautia 0.93
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Oscillospira 0.89
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae [Ruminococcus] 0.73
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae Clostridium 0.39
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Ruminococcus 0.24
Bacteria Proteobacteria Deltaproteobacteria Desulfovibrionales Desulfovibrionaceae Desulfovibrio 0.21
Bacteria Firmicutes Clostridia Clostridiales Clostridiaceae --- 0.21
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Dorea 0.18
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae Coprobacillus 0.12
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae --- 0.11
Bacteria Firmicutes Clostridia Clostridiales [Mogibacteriaceae] --- 0.10
Bacteria Firmicutes Clostridia Clostridiales Peptococcaceae --- 0.08
Bacteria Bacteroidetes Bacteroidia Bacteroidales Prevotellaceae Prevotella 0.08
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae --- 0.06
Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae --- 0.05
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae Holdemania 0.04
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Collinsella 0.04
Bacteria Firmicutes Clostridia Clostridiales Ruminococcaceae Anaerotruncus 0.03
Bacteria Proteobacteria Gammaproteobacteria Pasteurellales Pasteurellaceae Haemophilus 0.03
Bacteria Firmicutes Clostridia Clostridiales [Tissierellaceae] Anaerococcus 0.01
Bacteria Firmicutes Clostridia Clostridiales Veillonellaceae Veillonella 0.01
Bacteria Firmicutes Clostridia Clostridiales Lachnospiraceae Lachnobacterium 0.01
Bacteria Bacteroidetes Bacteroidia Bacteroidales Porphyromonadaceae Paludibacter 0.01
Bacteria Actinobacteria Actinobacteria Actinomycetales Corynebacteriaceae Corynebacterium 0.01
Bacteria Proteobacteria Gammaproteobacteria Thiohalorhabdales --- --- 0.01
Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter 0.01
Bacteria Proteobacteria Gammaproteobacteria Pasteurellales Pasteurellaceae Aggregatibacter 0.01
Bacteria Proteobacteria Epsilonproteobacteria Campylobacterales Campylobacteraceae Campylobacter 0.01
Bacteria Firmicutes Bacilli Lactobacillales Streptococcaceae Streptococcus 0.01
Bacteria Actinobacteria Coriobacteriia Coriobacteriales Coriobacteriaceae Eggerthella 0.01
Bacteria Actinobacteria Actinobacteria Actinomycetales Micrococcaceae Rothia 0.01
Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Pseudomonas 0.00
Bacteria Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Sutterella 0.00
Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Saccharibacter 0.00
Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Rhizobiaceae --- 0.00
Bacteria Firmicutes Erysipelotrichi Erysipelotrichales Erysipelotrichaceae [Eubacterium] 0.00
Bacteria Firmicutes Clostridia Clostridiales [Tissierellaceae] Finegoldia 0.00
Bacteria Firmicutes Clostridia Clostridiales Christensenellaceae --- 0.00
Bacteria Firmicutes Bacilli Lactobacillales Carnobacteriaceae Granulicatella 0.00
Bacteria Firmicutes Bacilli Bacillales Staphylococcaceae Staphylococcus 0.00
Bacteria Bacteroidetes Sphingobacteriia Sphingobacteriales Sphingobacteriaceae Sphingobacterium 0.00

 

[alicec]

I've only just caught up with this thread. Did a uBiome test Dec 2014 and spent quite some time trying to figure out what it meant. The web based reporting format is not very helpful so I summarised my results in table form and added what info I could find about the various bacteria. Actually for most there is not a lot to be found.

At the same time I did a Genova GI Effects Stool test so made another table where I compared the PCR component of the Genova test with the uBiome analysis. I'll upload both of these for your information.

With best wishes
Alice

 

[Sparrowhawk]

Cool. The most recent NYT article on this stuff that I liked was titled something like "there is no perfect microbiome" so it is hard to see what to try to influence at any given time if we don't know what ours was before, say, we were dosed willy nilly with antibiotics as children.

I have also been following the Fecal Microbiota Transplant group on Facebook. While a lot of people have been helped for C. Diff with as little as one treatment (from a healthy donor, natch), it is not clear that it is helpful for Chrone's or UC without a lot of treatments and then perhaps it may not take. Very few reports of folks doing treatments even at a clinic with tested donors from OpenBiome, who later come up with Auto-immune issues that seem unrelated to their previous issues, and possibly linked to the FMT. So it is early days yet, but an exciting time for science.

Reference: http://www.nytimes.com/2014/11/02/opinion/sunday/there-is-no-healthy-microbiome.html

 

[consuegra]

I've only just caught up with this thread. Did a uBiome test Dec 2014 and spent quite some time trying to figure out what it meant. The web based reporting format is not very helpful so I summarised my results in table form and added what info I could find about the various bacteria. Actually for most there is not a lot to be found.

At the same time I did a Genova GI Effects Stool test so made another table where I compared the PCR component of the Genova test with the uBiome analysis. I'll upload both of these for your information.

With best wishes
Alice

Alice,

Thanks for your information.

I did the ubiome test on my adult daughter who has ME/CFS. I also had four other members of the family do this test.

There were notable differences between my daughter and the rest of the family. Many of the differences were along the lines of what you note in your tests - roseburia, faecalbacterium, clostridium (not you), ruminoccocus, bifidobacterium, all marvelously low.

What do you do to try to correct this? Or do you think any of it is correctable?

Regards,

Chris

 

[alicec]

@Sparrowhawk, @consuegra

Thought I'd just summarise my thoughts on the points you raise in your replies, based on my recent reading plus experience of trying to influence gut flora composition.

Absolutely we are dealing with a complex ecosystem where there is a great deal of redundancy - ie many different species can fulfil the same function and no one pattern is "right"

At the same time there does not appear to be an infinite number of possibilities. I was particularly struck by the work of a group of French researchers showing that there is a relatively small number of widely shared genera which they define as a likely phylogenetic core. http://www.scribd.com/doc/25339273/Towards-the-Human-Intestinal-Microbiota-Phylogenetic-Core.

More recent work has confirmed this notion and shown distinct pattern changes in disease states such as IBD and Crohn's. http://www.nature.com/nature/journal/v464/n7285/full/nature08821.html

Others have expanded on this notion that there are certain keystone species which play a critical role in making substrates available to a wider group of organisms and without which there is widespread collapse of diverse bacterial populations. While some of it is a bit speculative, I have noted the identity of many of these species in my tables.

The other striking pattern observed is the relative lack of diversity in Western populations compared with people eating traditional diets and within Western populations, the even greater lack of diversity in the gut of people with disease, not just gut disease but the "modern" diseases such as diabetes, obesity, metabolic syndrome, etc. My gut is a good example of this loss of diversity.

At this stage there is just too little information to come up with some "evidence based" strategy to try to direct change in the gut flora. This of course doesn't stop people experimenting on themselves, particularly the adventurous and determined lot who frequent Phoenix Rising.

The huge Resistant Starch Challenge thread is a wonderful resource for those who want to try a targeted strategy involving diet, prebiotics and probiotics. Be warned though that this can be powerful stuff and small changes can induce big responses, often adverse. Based on the experiences of people on the thread, it may be that the sicker you are with CFS/ME, the more likely it is that you will be an adverse reactor. I certainly was.

Rather than go into any more detail I'll upload another summary document that I prepared. I had to get my doctor to order the Genova gut test and of course she asked me what I thought about the results (knowing that I knew more about it than she did). I told her about the uBiome test which I had done at the same time and my gut plan so she asked me to write it down. In it I spell out the various possibilities I have gleaned from the Resistant Starch Challenge pages plus other places.

It is still early days for me but I am certainly noticing some improvements, provided I take things slowly. The response reported by people on the thread is mixed, but overall many have seen improvements. It is not a short term project however - probably a lifetime's work!

With best wishes
Alice

 

[alicec]

I've made a post here http://forums.phoenixrising.me/inde...e-been-looking-for.26976/page-165#post-601104 that may be of interest.