uBiome results

jepps

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snowathlete

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Wondering how my results compare to others; specifically, in terms of species divesity.
My number of species have doubled in the last year. My first test was soon after a long course of antibiotics. I had around 50 species at that time, and now have around 100. How about you?
 

jepps

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Hi folks,

I got my Ubiome results today, and not sure exactly what to do with this data. It bothers me that the report doesn't tell me much in terms of what these bacterial percentages means to my health, or what actions should I take. Here's the percentage numbers:
  • Bacteroidetes 35.54% (Avg: 11.96%) High
  • Firmicutes 13.78% (Avg: 35.98%) Low
  • Proteobacteria 3.86% (Avg: 3.25%) Normal
  • Actinobacteria 0.10% (Avg: 3.43%) Low
  • Spirochaetes 0.09% (Avg: 0.02%) High
I also downloaded the raw data file from uBiome, and was wondering if you guys know of any analysis services online that could import my data and analyze to provide more info that I could really use. Thank you.
 
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Your firmicutes are low, which usually means you need to eat more plant fibers, and less meat.
Thanks, Adreno. Any reason for my gut spirochaetes to be higher than normal? I tested Lyme positive, so i wonder if other folks that tested the same have a higher spirochaete count. Just a thought, since that very word gives me a jolt the moment I see it in any of my medical reports.
 

snowathlete

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Hi folks,

I got my Ubiome results today, and not sure exactly what to do with this data. It bothers me that teh report doesn't tell me much in terms of what these bacterial percentages means to my health, or what actions should I take. Here's the percentage numbers:
  • Bacteroidetes 35.54% (Avg: 11.96%) High
  • Firmicutes 13.78% (Avg: 35.98%) Low
  • Proteobacteria 3.86% (Avg: 3.25%) Normal
  • Actinobacteria 0.10% (Avg: 3.43%) Low
  • Spirochaetes 0.09% (Avg: 11.96%) High
I also downloaded the raw data file from uBiome, and was wondering if you guys know of any analysis services online that could import my data and analyze to provide more info that I could really use. Thank you.
I'll do some analysis for you if you want. Just send me your raw taxonomy in a file.
 

globalpilot

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A question for those who have downloaded the taxonomy data - does anyone know what the line labeled 'root' represents ? The number (in my case) is slightly higher than the total bacterial number.
 

jepps

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Does this anybody know:
The Ubiome test result shows the quantity of bacteria (count): can we relate this number to the full number of bacteria (100 trillions), that we should have in the gut?
 

alicec

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Does this anybody know:
The Ubiome test result shows the quantity of bacteria (count): can we relate this number to the full number of bacteria (100 trillions), that we should have in the gut?
Results for individual phyla, genera etc are shown as % of total DNA sequenced - ie it is not a bacterial count but simply the amount of DNA relative to the total.
 

jepps

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Results for individual phyla, genera etc are shown as % of total DNA sequenced - ie it is not a bacterial count but simply the amount of DNA relative to the total.
Thank you alicec! So the count number has nothing to do with 100 trio? But I thought: 1 bacteria has 1 DNA?

Primarily I thought: much to do: I have 1,365 bio count nr., and I need 100 trio. count nr.
My husband has 365000 count (normal western diet, healthy). Do you know, if this number is good for anything? Should it increase with better gut immunity?

This is my test result:
48,73 % Firmicutes, 13,23 % Bacteroidetes, 12,73 % Proteobacteria, 6,6 % Cyanobacteria, 0,02 % Actinobacteria

After one year of high dosage RS and prebiotics I have a diversity of 300 microbes in my gut, along with Christensella, several clostridia cluster strains (a few pathogenic strains of Clostridium, but low), Eubacterium, Faecalibacterium prausnitzi, Holdemania, Lactobacillales, Roseburia), but no Bifidobacteria, and also high Proteobacteria.

Ubiome test kits only cost USD 44,-- for the next 72 hours with the code: CELEBRATEWITHUS74
 

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searcher

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For anyone who wants to share their ubiome Results, ubiome just announced a repository where you can put your ubiome results; more info is at http://www.ubiomeblog.com/invitation-to-join-the-ubiome-github-repository/

It will also have tools to allow you to do comparisons and other analyses.

If anyone is interested in putting their data up there and need help, please let me know and I can post details on using git to put your data in the repository.
 

snowathlete

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Does this anybody know:
The Ubiome test result shows the quantity of bacteria (count): can we relate this number to the full number of bacteria (100 trillions), that we should have in the gut?
in short, no. each count represents a sequence read.

Thank you alicec! So the count number has nothing to do with 100 trio? But I thought: 1 bacteria has 1 DNA?

Primarily I thought: much to do: I have 1,365 bio count nr., and I need 100 trio. count nr.
My husband has 365000 count (normal western diet, healthy). Do you know, if this number is good for anything? Should it increase with better gut immunity?

This is my test result:
48,73 % Firmicutes, 13,23 % Bacteroidetes, 12,73 % Proteobacteria, 6,6 % Cyanobacteria, 0,02 % Actinobacteria

After one year of high dosage RS and prebiotics I have a diversity of 300 microbes in my gut, along with Christensella, several clostridia cluster strains (a few pathogenic strains of Clostridium, but low), Eubacterium, Faecalibacterium prausnitzi, Holdemania, Lactobacillales, Roseburia), but no Bifidobacteria, and also high Proteobacteria.

Ubiome test kits only cost USD 44,-- for the next 72 hours with the code: CELEBRATEWITHUS74
Personally, I am not convinced that taking lots of PS supplement is a good thing, and I think it may actually hinder the gut rather than help it. What probiotics have you been taking? You might find GOS works better to feed bifidobacteria. Do you have a raw tax text file of your results? That would be easier for me to view than the pdf version.
 

jepps

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in short, no. each count represents a sequence read.
Sorry, but I am a dummie: I thought a sequence read means a DNA of a bacteria, and one DNA of a bacteria means one bacteria. Isn´t that right? This is, what I learned from google, but google is sometimes hard to read.

Personally, I am not convinced that taking lots of PS supplement is a good thing, and I think it may actually hinder the gut rather than help it. What probiotics have you been taking? You might find GOS works better to feed bifidobacteria. Do you have a raw tax text file of your results? That would be easier for me to view than the pdf version.
The dosages are a mix of 1/4 PS, 3/4 several fibres, probiotics (Mercola Complete probiotics, prescript assist, Kyolo Dophilus-9, together 300 bio CFU). I am in the best condition I had the last years, I have ups and downs, but after an up I am better than before. I relate this to improvements in the gut. But GOS is on my to do-list, thank you.

Concercing bifidos: I have FUT2 homozygot, therefore I tend to a lack of bifidos. I do stool tests since 6 years in our laboratory. According to my stool test addressing viruses depleted bifidos. As I still address candida and viruses, it will be harder for the bifidos to establish. But I will do more Ubiome test to watch the gut flora and try several approaches with or without PS and more.

Thank you a lot, @snowathlete. Posting the raw datas in PR does not function, but could I send you an e-mail?
 
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jepps

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For anyone who wants to share their ubiome Results, ubiome just announced a repository where you can put your ubiome results; more info is at http://www.ubiomeblog.com/invitation-to-join-the-ubiome-github-repository/

It will also have tools to allow you to do comparisons and other analyses.

If anyone is interested in putting their data up there and need help, please let me know and I can post details on using git to put your data in the repository.
I am very interested, @searcher
 

snowathlete

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Sorry, but I am a dummie: I thought a sequence read means a DNA of a bacteria, and one DNA of a bacteria means one bacteria. Isn´t that right? This is, what I learned from google, but google is sometimes hard to read.
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.

The dosages are a mix of 1/4 PS, 3/4 several fibres, probiotics (Mercola Complete probiotics, prescript assist, Kyolo Dophilus-9, together 300 bio CFU). I am in the best condition I had the last years, I have ups and downs, but after an up I am better than before. I relate this to improvements in the gut. But GOS is on my to do-list, thank you.

Concercing bifidos: I have FUT2 homozygot, therefore I tend to a lack of bifidos. I do stool tests since 6 years in our laboratory. According to my stool test addressing viruses depleted bifidos. As I still address candida and viruses, it will be harder for the bifidos to establish. But I will do more Ubiome test to watch the gut flora and try several approaches with or without PS and more.

Thank you a lot, @snowathlete. Posting the raw datas in PR does not function, but could I send you an e-mail?
Sounds like you're doing great, that improvement sounds like a massive win, so I'd just keep on doing what you're doing!

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?