uBiome results

[Thinktank]

What's the norm. based on?

I've done the ubiome test a long time ago but lost the data and my loginstuff. I'm going to do the monthly ubiome kit from now on.

My REDlab results are as follows. October 2013 / June 2015
Which of 18 months on antibiotics for lyme disease. The abx has clearly affected my gut but i'm sure the numbers will bounce back with proper nutrition and supplements.

Actino 5 % / 23,23%
Firmicutes 75,55 % / 6,92 %
Bacteroidetes 16,14 % / 46,76 %
Proteobacteria 0,05 % / 0,54 %
Other 0,26 % / 22,55 %

The high actinobacteria consists mainly of bifidobacterium (22,77 % in June 2015, 0,05% in October 2013), not sure if 22,77% is considered overgrowth or not.
Firmicutes have suffered a heavy blow, bacteroidetes have taken over, the little nazis are going for total gut domination.
Other bacteria consists mainly of clostridium XIVa (19,02 %)
Streptococcus is close to overgrowth.

 

[jepps]

What's the norm. based on?.

Ubiome defines the percentages as norm.

The high actinobacteria consists mainly of bifidobacterium (22,77 % in June 2015, 0,05% in October 2013), not sure if 22,77% is considered overgrowth or not.

Bifido can be to high or to low (or not detectable as in my gut) in UC or DC.

Could you receive a new login from Ubiome to determine the older Ubiome result?

Firmicutes have suffered a heavy blow, bacteroidetes have taken over, the little nazis are going for total gut domination.
Other bacteria consists mainly of clostridium XIVa (19,02 %)

Clostridium XIVa are firmicutes, the healthy one, that lower inflammation. @Vegas wrote a post, where high proteobacteria (also lyme, increase inflammation because of to much LPS) and to low firmicutes inflammation decreasing bacteria (clostridial cluster IV like faecalibacterium prausnitzii, and clostridial cluster XIVa, above all Roseburia intestinalis and Eubacterium rectale - are listed here) are a puzzle of chronic inflammation.

It looks like treating the gut with diet, prebiotics and probiotics over the long run changes the composition of the microbiome in the direction of lowering inflammation. This fits well to my better condition.

 

[Thinktank]

I don't think i can collect the old data, i've lost access to the email account i signed up with. Anyway, that old data doesn't reflect my current situation so i'm not going to bother. I'm going to sign up tomorrow for the monthly auto-ship kit.

If clostridium XIVa belongs to the firmicutes then my numbers in % don't make much sense i guess.
Roseburia has been wiped out by the antibiotics, also akkermansia now shows 0.

Have you noticed any health benefits since changing your diet and supplements?
What are your main goals now microbiome-wise?

For me, according to my LLMD, besides diet i also need to lower PGE2, elevated levels obstruct oxygen to the intestines and that causes anaerobic bacteria to flourish.
But then, PGE2 is also stimulated by LPS.
Leaky gut -> LPS from gram negative bacteria -> increased level of PGE2 -> anaerobic bacteria flourish -> vicious cycle?

 

[jepps]

Have you noticed any health benefits since changing your diet and supplements?
What are your main goals now microbiome-wise?

Yes, after 1 year of changing diet and treating the gut chronic inflammation reduced a lot, above all in the last 3 months, and the test reflects this. I take a variety of prebiotics and resistent starches and probiotics, eat PHD, treat fungi and methylation, for me this was the right direction. The next step are fermented foods, and I am curious, how they influence the microbiome.

For me, according to my LLMD, besides diet i also need to lower PGE2, elevated levels obstruct oxygen to the intestines and that causes anaerobic bacteria to flourish.
But then, PGE2 is also stimulated by LPS.
Leaky gut -> LPS from gram negative bacteria -> increased level of PGE2 -> anaerobic bacteria flourish -> vicious cycle?

Some things are a cycle, and looking forward is the best step. Treating the gut is always a good decision.

 

[snowathlete]

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

Interesting. I have practically nil Ruminococcus bromi, three tests so far; while other genera/species have come back after I was treated with abx, this key player has not. I wish I knew how to increase Ruminococcus but no one really seems to know how.

 

[alicec]

Thanks for sharing @jepps.

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.

I have practically nil Ruminococcus bromi

Me three, though I do have moderate amounts of other Ruminococci - no Bifido either.

I'm looking for ways to increase firmicutes and decrease bacteroids.

I managed to achieve that by adding moderate amounts of resistant starch (as food, not raw potato starch) at each meal to a fairly low carbohydrate paleo diet - ie changing to PHD. I posted the analysis above but here it is again.

I was expecting another analysis but have been notified that it was pulled out by quality control because of low DNA in the sample. They say they are doing further analysis so I have to wait a few more weeks. I don't know how this will affect the reliability of the results.

 

[jepps]

Interesting. I have practically nil Ruminococcus bromi, three tests so far; while other genera/species have come back after I was treated with abx, this key player has not. I wish I knew how to increase Ruminococcus but no one really seems to know how.

Tim Steele writes, that everybody has Ruminicoccus bromi, and R.bromi loves starches and various fibres, so patience and holding on might be the key. Could you have candida because of abx, and as the bifidos are needed for candida, ruminococcus bromi also are needed for candida infection?

I did stool tests the last 5 years (not Ubiome) every 3 months. Sometimes the bifidos (the test measures only bifidos, lactos and bacteroides species) are present, then they are depleted. During and after detoxification processes they were depleted. Methylation also depleted bifidos (methylation depleted bifidos+lactos+bacteroides species), but as the therapy holds on, detoxification processes and challenged immunity need all bifidos.

 

[snowathlete]

Tim Steele writes, that everybody has Ruminicoccus bromi, and R.bromi loves starches and various fibres, so patience and holding on might be the key. Could you have candida because of abx, and as the bifidos are needed for candida, ruminococcus bromi also are needed for candida infection?

I did stool tests the last 5 years (not Ubiome) every 3 months. Sometimes the bifidos (the test measures only bifidos, lactos and bacteroides species) are present, then they are depleted. During and after detoxification processes they were depleted. Methylation also depleted bifidos (methylation depleted bifidos+lactos+bacteroides species), but as the therapy holds on, detoxification processes and challenged immunity need all bifidos.

I don't know really. It's possible but it's not something on my radar a great deal. I don't suspect that I have a candida problem. Its been 18 months since abx stopped now, and I've had three uBiome tests in that time. The most consistant thing is that Ruminococcus is barely present. As it seems to be universally present in the healthy it does seem worth trying to improve. I only had one test prior to abx, with Redlabs, whose test isn't as good as uBiome's, but it reported Rumminococcus genus as zero. So it is possible that it is an ME thing I guess. At least there is going to be some research from Lipkin and his team now so that we won't be left guessing forever more on that front.

 

[Oci]

I'm wondering what value anyone has found in the Ubiome test? They have a 5 for 1 sale on ending tonight. Is it good value for my money?

 

[searcher]

I'm wondering what value anyone has found in the Ubiome test? They have a 5 for 1 sale on ending tonight. Is it good value for my money?

Did you end up doing the 5 for 1 deal? I ordered the kit last week and am sending in my samples today. I haven't ever tested anything outside the gut, so don't know how useful the results were be. The gut microbiome test is a good value I think, although I can't say that my original results told me anything I didn't know already. It's nice to have an interactive interface to look at your results vs the usual static printout from standard tests.

uBiome just sent me a special code that can be used for the rest of the month-- it is GLOBAL50. I don't get any rewards from people using the code, but wanted to share since using the code would make a one-time gut test <$45 and a three-time test $104.50.

 

[alicec]

I've received new test results recently that were a bit alarming but the more I looked at them the more I became convinced that there was a problem. There was difficulty with the analysis in that it had to be repeated because of too little DNA in the first sample. The things that made me suspicious were about 10X fewer bacterial counts compared with previous samples (I haven't taken any antibiotics or really made any other significant changes) and greatly different proportions of the phyla.

I emailed them and they agreed there was some problem with the whole test and are sending me a complimentary kit for another test.

The reason I am making this post however is that I noticed other differences on the website. Just as an example, in my test from 1 May they are now reporting the top three genera as Roseburia, 19.8%, Bacteroides 12.94 % and Blautia 9.36% whereas previously these genera were shown as 3.93, 5.89 and 26.4% respectively (the top three had been Blautia, Bacteroides and Anaerostipes).

I emailed them about this and they tell me they have just updated their algorithm and database, allowing them to identify bacteria and eliminating some of the bacteria that were unnamed. This has changed the percentages.

As you can see the changes can be dramatic and it means that all the tables I drew up comparing samples mean nothing. I'll have to do it all again.

Those of you who have done tests previously might like to look again at their new interpretation of your results.

 

[jepps]

Today I looked at my ubiome test results again, and found new interesting markers, that result from my microbiome (or not):

Ubiome offers a lot of new markers at his homepage: pathways for

- carbohydrate metabolism (gluconeogenesis and glycolysis, citrate cycle, starch metabolism, pentose interconversions), - several markers for lipid metabolism,
- markers for amino acid metabolism (selenocompound metabolism, tryptophan metabolism, glutamate metabolism, histidine metabolism, tyrosine metabolism, glutathione metabolism)
- vitamin metabolism for folate and ubiquinone biosynthesis and all other b-vitamins, lipoic acid metabolism
- secondary metabolite degradation: degradation for bisphenol, styrenes, aminobenzoates, fluorobenzoate, xenobiotics by cytochrome P450
- secondary metabolite biosynthesis: flavone biosynthesis (how to detox ROS), penicillin biosynthesis
- bacterial abilities: cell division, sporulation, cell motility and secretion

 

[Avengers26]

@jepps Does this info any functional relevance that can be utilized? For eg. my Arachidonic acid metabolism is 0.48x & alpha-Linolenic acid metabolism is 0.47x. My [URL='https://app.ubiome.com/KEGG/357/5']Fluorobenzoate degradation is 0.04x. What should I make of it[/URL]?

 

[alicec]

@jepps Does this info any functional relevance that can be utilized? For eg. my Arachidonic acid metabolism is 0.48x & alpha-Linolenic acid metabolism is 0.47x. My [URL='https://app.ubiome.com/KEGG/357/5']Fluorobenzoate degradation is 0.04x. What should I make of it? [/URL]

https://app.ubiome.com/KEGG/359/5


Yes getting your head around what all this new data means in a practical sense is the problem. I'm still thinking about it all.

I see that they have changed the alogarithim yet again. Most of my data is totally different from what was originally reported. Raw taxonomy data is different too.

I've started doing tests more frequently to try to understand how changeable my gut flora is with time. Very changeable it would appear even though there has been little dietary change.

It is too early to say if this variability in flora has any correlation with symptoms.

 

[consuegra]

I've received new test results recently that were a bit alarming but the more I looked at them the more I became convinced that there was a problem. There was difficulty with the analysis in that it had to be repeated because of too little DNA in the first sample. The things that made me suspicious were about 10X fewer bacterial counts compared with previous samples (I haven't taken any antibiotics or really made any other significant changes) and greatly different proportions of the phyla.

I emailed them and they agreed there was some problem with the whole test and are sending me a complimentary kit for another test.

The reason I am making this post however is that I noticed other differences on the website. Just as an example, in my test from 1 May they are now reporting the top three genera as Roseburia, 19.8%, Bacteroides 12.94 % and Blautia 9.36% whereas previously these genera were shown as 3.93, 5.89 and 26.4% respectively (the top three had been Blautia, Bacteroides and Anaerostipes).

I emailed them about this and they tell me they have just updated their algorithm and database, allowing them to identify bacteria and eliminating some of the bacteria that were unnamed. This has changed the percentages.

As you can see the changes can be dramatic and it means that all the tables I drew up comparing samples mean nothing. I'll have to do it all again.

Those of you who have done tests previously might like to look again at their new interpretation of your results.

@alicec

Do they update old test results with these new algorithms?

Thanks,
Chris

 

[alicec]

Do they update old test results with these new algorithms?

Yes - twice now that I have observed.

 

[jepps]

@jepps Does this info any functional relevance that can be utilized? For eg. my Arachidonic acid metabolism is 0.48x & alpha-Linolenic acid metabolism is 0.47x. My Fluorobenzoate degradation is 0.04x. What should I make of it?

What I find interesting:

- the differences in metabolism of fats, carbohydrates and proteins to adapt the diet
- to avoid certain medicaments (f.ex. penicilline), where we do not have the bacteria for detoxing.
- supplement f.ex. with ALA (or glutathione), if lipoic acid metabolism is low

 

[Thinktank]

I've just received my results from Ubiome.
How are you guys doing gutwise?

My results after 2 years of intravenous and oral antibiotics for lyme disease:

Ubiome 8/1/2016:
Bacteroidetes me: 42.77%
Bacteroidetes group average: 36.65%

Firmicutes me: 41.04%
Firmicutes group average: 56.48%

Verrucomicrobia me: 15.49%
Verrucomicrobia group average: 2.07%

Proteobacteria me: 0.48%
Proteobacteria group average: 3.31%

Actinobacteria me: 0.23%
Actinobacteria group average: 2.48%

 

[alicec]

Verrucomicrobia me: 15.49%

What is the predominant genus of this phylum? Is it Akkermansia? If you've downloaded raw taxonomy, does it list the species?

A. muciniphila, abundant in the mucus layer of our gut, seems to account for almost all of this phylum in our gut and is important for maintaining the integrity of the mucosal barrier.

I wonder what an overgrowth would do - ie would it erode the mucosal layer?

How are you guys doing gutwise?

I had my first uBiome test about 6 months after stopping long term antibiotics for Lyme and Bartonella. Like you my Bacteroidetes were high (43%), Firmicutes low (50%), Actinobacteria low (0.25%). Unlike you my Proteobacteria were highish (6%) and Verrucomicrobia, along with other minor phyla, virtually non-existent.

More than 12 months later, I am seeing big changes. Minor phyla are still virtually non-existent and the abundance of the various genera that are present drop off much more quickly than the average, so I still have a problem with diversity. However Firmicutes have increased dramatically (perhaps a bit too much at 77.97%), including many of the important butyrate-producing genera such Roseburia and Faecalibacterium, Actinobacteria are now 3.5% (a lot of this increase is Coriobacteriaceae rather than Bifidobacteriaceae, though the latter has still improved considerably) and Bacteroidetes has declinded (perhaps a bit too much, now at 13.3%).

Proteobacteria were declining, then I had a big spike in the middle of the year (mainly in the form of the genus Kluyvera). This started resolving itself fairly quickly though I am waiting for test results due any day now to show how well things have returned to the norm.

 

[jepps]

I had my first uBiome test about 6 months after stopping long term antibiotics for Lyme and Bartonella. Like you my Bacteroidetes were high (43%), Firmicutes low (50%), Actinobacteria low (0.25%). Unlike you my Proteobacteria were highish (6%) and Verrucomicrobia, along with other minor phyla, virtually non-existent.

More than 12 months later, I am seeing big changes. Minor phyla are still virtually non-existent and the abundance of the various genera that are present drop off much more quickly than the average, so I still have a problem with diversity. However Firmicutes have increased dramatically (perhaps a bit too much at 77.97%), including many of the important butyrate-producing genera such Roseburia and Faecalibacterium, Actinobacteria are now 3.5% (a lot of this increase is Coriobacteriaceae rather than Bifidobacteriaceae, though the latter has still improved considerably) and Bacteroidetes has declinded (perhaps a bit too much, now at 13.3%).

Proteobacteria were declining, then I had a big spike in the middle of the year (mainly in the form of the genus Kluyvera). This started resolving itself fairly quickly though I am waiting for test results due any day now to show how well things have returned to the norm.

I make the same observations as you, @alicec. 1 year ago I had low Firmicutes, low Actinos, high Proteos and high Bacteroidetes, no bifidos. Repeated Ubiome-tests showed increasing Firmicutes, above all Faecalibacterium and Roseburia, decreasing Proteos, increasing Actinos, the last test also showed Bifidos.

Regarding diversity: This research shows a picture of healthy microbiome for comparing:

Athletes also had a far higher diversity of gut bugs -- 22 phyla, 68 families, and 113 genera compared with just 11 phyla, 33 families and 65 genera for controls with a low body mass index (BMI), and 9 phyla, 33 families and 61 genera for controls with a high BMI.