uBiome results

[jepps]

No, not a dummie at all.

In essence that is right, though a single bacterium may have more than one copy of the same sequence so it could get read multiple times. And I expect there are other complexities that I am unaware of that may interfere with the counts. But roughly, a sequence read means a bacterium, and thus you can find out which bacteria are more prominent than others. The real reason we can't extrapolate how many bacteria we have in our gut from this data is because it is just a single sample of the whole, and the sample size could be smaller or larger than another sample. I had my gut tested twice so far, and the first time I had a count of 49,740 and the second time a count of 203,027. It's tempting for me to think that this was due to the first sample being right after a long course of abx, and the second result being one year post abx, but actually most of the difference is probably just a how much material there was in each sample, with there being a lot more the second time around.

So I assume, the count shows a tendency, but we cannot relate it to the total number of bacteria in the gut. My friend also has a count of 50000 after a course of abx, I have much more, the next tests maybe show a tendency (or not).[/QUOTE]

Sounds like you're doing great, that improvement sounds like a massive win, so I'd just keep on doing what you're doing!

Thanks! The next topic are fermented foods (I adapt myself to a long time for potantial establishment) . I am curious, if Ubiome test shows changes in the gut with fermented foods.

You could email me the text file for sure, happy to give you my address over private message, but you may also be able to add the text file to the forum by first putting it in a zip file?

Thank you, Zip does not function, I send you a PM.

 

[snowathlete]

So I assume, the count shows a tendency, but we cannot relate it to the total number of bacteria in the gut. My friend also has a count of 50000 after a course of abx, I have much more, the next tests maybe show a tendency (or not).

Thanks! The next topic are fermented foods (I adapt myself to a long time for potantial establishment) . I am curious, if Ubiome test shows changes in the gut with fermented foods.



Thank you, Zip does not function, I send you a PM.[/QUOTE]

Good question about fermented foods. I have only tried saurkraut and that did not show up on my subsequent test. However, a small portion of the bacteria in the samples cannot be assigned yet to a match in uBiome's database and so it could, potentially, be hiding in there, though I think this is unlikely as the ones that are more likely to be unclassified are ones that research hasn't identified before, the more commonly known ones are likely to be classified - that's my take on it anyway. Most likely the species of bacteria that you get in sauerkraut are not the kind that establish in the gut. That may not be true of other species from other fermented foods though.

I'll go read your PM. Thanks.

 

[Avengers26]

It will be interesting to see what difference, if any, fermented foods make in the subsequent test results. I am not taking any fermented foods yet but plan to add them slowly in the future.

I remember reading about someone (richard sprague?) who regularly has ubiome tests & posts his results online. But, he doesn't have CFS to the best of my knowledge.

 

[jepps]

It will be interesting to see what difference, if any, fermented foods make in the subsequent test results. I am not taking any fermented foods yet but plan to add them slowly in the future.

Yes, I am also very interested, with fermented food theoretically the diversity should increase. I did the first Ubiome test after 9 months of RS+probiotics+prebiotics, the second now before taking ferments, and after a few months with ferments (I take pickl-it, they have low histamines) I will see, if ferments change the microbiome.

 

[Avengers26]

@jepps What changes did you make in your diet in between the 2 tests? Were there any significant differences between the 2 test results?

 

[alicec]

It will be interesting to see what difference, if any, fermented foods make in the subsequent test results.

I've finally got around to downloading my raw taxonomy data from uBiome and analysing in Excel. I had looked previously using the %data on the uBiome website and didn't see any obvious effects from introduction of fermented foods.

After looking at direct counts from the raw data I still can't see much effect. After 4 months of virtually daily sauerkraut (something I'd not eaten previously) lactobacillus went from 0 to 6, certainly nothing to get excited about. Leuconostoc stayed at 2. Diversity remained the same (about 480 different genera, more than half of these at extremely low level) and total counts increased somewhat (332,000 to 448,000) but as @snowathlete has noted above, this is probably just due to differences in sample size.

I did see some big changes but these are undoubtedly due to other dietary changes.

@jepps how did you do that neat double sorting shown in your PDF where you were able to arrange genera within their phyla?

 

[jepps]

@jepps What changes did you make in your diet in between the 2 tests? Were there any significant differences between the 2 test results?

@Avengers26 there were absolutely no changes in diet, I eat PHD, RS and prebiotics and probiotics since almost one year. I want to see, if there is a tendency with this kind of diet, and if this is a good tendency.

 

[jepps]

@jepps how did you do that neat double sorting shown in your PDF where you were able to arrange genera within their phyla?

Double sorting was manually sorting with wikipedia and other sites, much work, but I was interested to see the number of the several phylums. According to this sorting I have (compared to the test of my husband) a low diversity of actinobacteria, a great diversity of proteobacteria, bacteroidetes and firmicutes.

 

[alicec]

Double sorting was manually sorting with wikipedia and other sites, much work, but I was interested to see the number of the several phylums. According to this sorting I have (compared to the test of my husband) a low diversity of actinobacteria, a great diversity of proteobacteria, bacteroidetes and firmicutes.

Thanks. I've done that laborious route - just thought you might have found something better.

 

[snowathlete]

I've finally got around to downloading my raw taxonomy data from uBiome and analysing in Excel. I had looked previously using the %data on the uBiome website and didn't see any obvious effects from introduction of fermented foods.

After looking at direct counts from the raw data I still can't see much effect. After 4 months of virtually daily sauerkraut (something I'd not eaten previously) lactobacillus went from 0 to 6, certainly nothing to get excited about. Leuconostoc stayed at 2. Diversity remained the same (about 480 different genera, more than half of these at extremely low level) and total counts increased somewhat (332,000 to 448,000) but as @snowathlete has noted above, this is probably just due to differences in sample size.

I did see some big changes but these are undoubtedly due to other dietary changes.

@jepps how did you do that neat double sorting shown in your PDF where you were able to arrange genera within their phyla?

Here's an article about the bacteria you get in sauerkraut. It seems to differ depending on how long it is fermented.
https://autodidactauthor.wordpress.com/2014/11/06/the-science-of-sauerkraut/

If you are saying your lactobacillus went from 0 up to 6% then that sounds like a huge increase to me. Not sure of the top of my head what kind of normal range is for Lactobaccilus but I doubt it's higher than that. 480 different genera also sounds like really good diversity to me - I'd be really happy with that. Have you taken a look at your species diversity?

 

[alicec]

If you are saying your lactobacillus went from 0 up to 6%

Thanks for the article. 0 to 6 counts - percentagewise that's reported as 0.0. Still it's the first time I've even registered for Lactobacillus.

480 different genera also sounds like really good diversity to me - I'd be really happy with that. Have you taken a look at your species diversity?

I was indeed happy with the diversity - and I have a similar number of different species. However my gut flora is still very imbalanced with very low Actinobacteria (10.9 x depleted with 0 Bifidobacteria) and negligible amounts of all the minor phyla. Many genera are significantly depleted, the most notable being Faecalibacterium, 1,590 x depletion ( others are more like 5-30 x depletion).

Still I've seen quite a bit of improvement - am waiting for new results now to see if there are any significant changes coinciding with a period where there has been little dietary change but a worsening of my condition.

 

[Gondwanaland]

I did see some big changes but these are undoubtedly due to other dietary changes.

Would you mind sharing them, Alice? I have eaten sauerkraut, I took water kefir, I made my own yogurt, I bought organic locally produced yogurt, and the only change I had was unbearable high HIT...

 

[alicec]

Would you mind sharing them, Alice?

Sure. I have posted my analysis at the phylum level I think on the Resistant Starch thread but will post again. Since then I have gone through and done a similar analysis at the genus level so will add that also. Happy to answer questions but unfortunately I think it is only possible to draw very general conclusions.

 

[Gondwanaland]

Thanks, @alicec but I meant about diet changes... What do you feel that made a difference? I gave up on fermented foods at least for a while... I must stay away from anything containing potato starch... I was eating this gluten free bread which contains only safe flours incl PS, but apparently my body had enough from it. Everything builds up

 

[alicec]

but I meant about diet changes

These are listed in the first document. The biggest single change was including a source of resistant starch at each meal (cooked and cooled rice or potatoes or mung bean noodles or other legumes). The other new things I added were small amounts of seaweed several times a week, a prebiotic-rich muffin virtually daily (I've posted my recipes for these somewhere - can't remember) and sauerkraut virtually daily. I've always eaten a lot of vegetables but I was particularly careful to eat a wide variety daily including mushrooms like shitaki often.

 

[Avengers26]

Hi @alicec Those documents that you posted, Did you create them using your raw data from the ubiome site or these were already available for download?

Also, what seaweed are you taking?

 

[alicec]

Hi @alicec Those documents that you posted, Did you create them using your raw data from the ubiome site or these were already available for download?

Also, what seaweed are you taking?

I created them by laboriously going through my data on the uBiome website - not the raw data though I have looked at that subsequently. The raw data provides additional information about DNA counts and some species info, plus has the advantage that it can be fed into other programs to do comparisons - eg as noted here http://forums.phoenixrising.me/index.php?threads/ubiome-results.28867/page-2#post-621463

I haven't done that type of analysis yet but presume it might make comparing two samples a bit quicker - I doubt it can extract more info than I got by individual comparison and calculation.

On the website data is reported as % of total DNA. Originally average values were also provided (at least for the genera found in one's own samples) and this is where my average column came from. This is no longer available, instead it can be inferred from the % depleted or enriched values which are now used. There is no facility to compare two samples on the website, instead a very general graphic based on % phylum changes is shown.

Also although a taxonomy tree is provided on the website I found it much easier to do internet searches for individual genera in order to work out their taxonomy.

Regarding seaweed, I think any red or brown alga would be fine - I just happened to buy the red alga Dulse (dried). The packet is almost empty so next time I'll try something different.

 

[jepps]

These are my latest Ubiome results, compared with the result of May 2015. The firmicutes increased from 48,7 % to 55,9 % (markable increase of Roseburia, F.prausnitzii and Ruminococcaceae), Proteobacteria reduced from 12,73 % to 10,5 %) after one year of taking probiotics, RS and prebiotics.

Still not detectable are Bifidobacterias. As RS needs Ruminococcus bromi (also not detectable) as cofactor to feed Bifidos, maybe first R.bromi must be present.

https://www.dropbox.com/s/j2jv8qtl5g9lt05/Ubiome.xlsx?dl=0

This is a kindle e-book that explains how to analyze the Ubiome test, and how to interprete it.

https://books.google.at/books?id=FqwwCgAAQBAJ&pg=PT83&lpg=PT83&dq=analysis ubiome root&source=bl&ots=guzWmKX16k&sig=JBNz_4zGCmLyReq6L2Hc_4AWpk4&hl=de&sa=X&ved=0CEIQ6AEwBGoVChMIrKad4rG6xwIVCuwUCh0mPwzO#v=onepage&q=analysis ubiome root&f=false

https://play.google.com/store/books...urce=gbs_atb&pcampaignid=books_booksearch_atb

 

[Thinktank]

Thanks for sharing @jepps, what's your percentage of bacteroids?
I'm looking for ways to increase firmicutes and decrease bacteroids.

 

[jepps]

Thanks for sharing @jepps, what's your percentage of bacteroids?
I'm looking for ways to increase firmicutes and decrease bacteroids.

@Thinktank, these are the results of May 2015, August 2015, Norm

Actino 0,02 % / 0,02 % (Norm 2,48 %)
Firmicutes 48,73 % / 55,93 % (Norm 59,3 %)
Bacteroidetes 13,23 % / 8,28 % (Norm 22,54 %)
Proteobacteria 12,73 % / 10,5 % (Norm 3,25 %)
Other 25,29 % / 25,27 % (Norm 12,43 %)