uBiome results

[alicec]

i'm going to order the 3-sample kit, with 50% discount that should be only $99

I tried that but the promotion only applies to the single gut kit. I just ordered multiple single kits.

 

[hopeful2]

I sent in a Ubiome kit back in July that ended up failing for lack of DNA. They sent me a new one that I shipped back the end of October and the results are in already. I could use some help in interpreting and deciding what to do next.

Here are my results at the Phylum level:
Firmicutes: 1.10 X
Bacteroidetes: 0.90 X
Verrucomicrobia: 1.61 X
Actinobacteria: 0.44 X
Proteobacteria: 0.11 X

From the Insights page:

Firmicutes: 67.4%
Bacteroidetes: 27.73%

Akkermansia: 3.28% - Average is 1.98%

Bifidobacterium: .02%
Lactobacillus: .02%

My diversity score is 7.78 which puts me at 60%. However when I look through all 5 levels on the compare page, it becomes clear that I have very low levels of a lot of the bacteria.

I'm really confused by the bottom of the page where it lists Unique Bacteria. It says "These are the 10 bacteria in your sample that are found least frequently in our results." It also says "Number of Very Elusive Bacteria: 5 (Bacteria found in less than 5% of all samples.)"

The confusing part is that when I look at the list of 10 bacteria, including the 5 "very elusive bacteria", they have listed for me and then go to the compare pages to locate them, it appears to me that I actually don't have them in my sample at all.

Also, when I look under Lipid Metabolism, should I be concerned about not being able to break down alpha-linolenic acid?

Steroid biosynthesis: 3.64 X

Steroid hormone biosynthesis: 1.14 X

Biosynthesis of unsaturated fatty acids: 1.12 X

Linoleic acid metabolism: 1.03 X

Fatty acid biosynthesis: 1.02 X

Glycerolipid metabolism: 1.02 X

Glycerophospholipid metabolism: 1.00 X

Sphingolipid metabolism: 0.99 X

Ether lipid metabolism: 0.97 X

Synthesis and degradation of ketone bodies: 0.87 X

Arachidonic acid metabolism: 0.72 X

alpha-Linolenic acid metabolism: 0.16 X

 

[Jjnz]

Is there someone here who understand the datas related to metabolism and that kind of stuffs on Ubiome?

This is what I have:

Metabolism:
x0.14 for D arginine and D ornithine
x0.33 for Ether lipid
x0.1 for alpha-Linolenic acid

Biosynthesis:
x0.23 for Stilbenoid, diarylheptanoid and gingerol

Degradation:
x0.58 for Chlorocyclohexane and chlorobenzene
x0.51 for Dioxin
x0.5 for Xylene

What I am not sure about is what would be the difference between me taking for example Ornithini and someone who has a "x1" for his metabolism.

Also I can't find what probiotics I should take for very low proteobacteria...

Thxxx

Boy you must just about have the same gut as I do !
I've had 2 tests 6 months apart, largely the same readings.
I'd love to know how they calculate these and what bacteria are missing or in abundance.
Did you have any luck finding out why your arginine or gingerol metabolism is poor ?
I have similar deficiencies in those functionalities . I have good diversity ( 96%) which sounds great but half of my bacteria look like hangers-on, several times lower populations than the average.
Do you have any lactobacillus, I have none

F U N C T I O N S
LIPID METAB
Steroid biosynthesis:9.56 X
alpha-Linolenic acid metabolism:2.25 X

AMINO ACID METAB
D-Arginine and D-ornithine metabolism: 0.16 X
Flavone and flavonol biosynthesis:0.47 X

SECONDARY METABOLITE BIOSYNTHESIS
Caffeine metabolism:10.49 X
Flavonoid biosynthesis:2.09 X
Stilbenoid, diarylheptanoid and gingerol biosynthesis:0.15 X

C O M P A R I S O N S
Compared to Ubiome Selected Healthy
Phylum
Proteobacteria: 4.89 X
Verrucomicrobia: 3.98 X
Bacteroidetes: 1.11 X
Firmicutes: 0.71 X
Actinobacteria: 0.31 X
Lentisphaerae: 0.04 X

CLASS
Deltaproteobacteria: 11.46 X
Betaproteobacteria: 7.97 X
Verrucomicrobiae: 3.96 X
Bacteroidia: 1.12 X
Clostridia: 0.73 X
Gammaproteobacteria: 0.73 X
Bacilli: 0.72 X
Actinobacteria: 0.31 X
Negativicutes: 0.09 X
Alphaproteobacteria: 0.07 X
Erysipelotrichia: 0.07 X
Lentisphaeria: 0.04 X

ORDER
Desulfovibrionales: 11.46 X
Burkholderiales: 7.96 X
Verrucomicrobiales: 3.96 X
Bacteroidales: 1.12 X
Lactobacillales: 0.78 X
Clostridiales: 0.73 X
Enterobacteriales: 0.67 X
Bifidobacteriales: 0.43 X
Coriobacteriales: 0.26 X
Selenomonadales: 0.09 X
Rhodospirillales: 0.07 X
Erysipelotrichales: 0.07 X
Actinomycetales: < 0.01 X

FAMILY
Desulfovibrionaceae: 11.46 X
Sutterellaceae: 7.82 X
Verrucomicrobiaceae: 3.96 X
Clostridiaceae: 3.12 X
Oxalobacteraceae: 1.95 X
Bacteroidaceae: 1.10 X
Oscillospiraceae: 0.94 X
Peptostreptococcaceae: 0.93 X
Prevotellaceae: 0.88 X
Enterobacteriaceae: 0.67 X
Porphyromonadaceae: 0.58 X
Ruminococcaceae: 0.55 X
Lachnospiraceae: 0.53 X
Rikenellaceae: 0.45 X
Bifidobacteriaceae: 0.43 X
Coriobacteriaceae: 0.26 X
Lactobacillaceae: 0.21 X
Acidaminococcaceae: 0.15 X
Rhodospirillaceae: 0.07 X
Streptococcaceae: 0.07 X
Erysipelotrichaceae: 0.07 X
Clostridiales Family XIII. Incertae Sedis: 0.07 X
Peptococcaceae: 0.04 X
Victivallaceae: 0.04 X
Actinomycetaceae: 0.01 X

GENUS
Desulfovibrio: 9.04 X
Sutterella: 7.69 X
Sarcina: 4.37 X
Akkermansia: 3.94 X
Paraprevotella: 2.88 X
Bilophila: 2.57 X
Terrisporobacter: 2.54 X
Herbaspirillum: 2.01 X
Intestinimonas: 1.37 X
Enterobacter: 1.15 X
Bacteroides: 1.11 X
Howardella: 1.10 X
Flavonifractor: 1.00 X
Blautia: 0.86 X
Parabacteroides: 0.81 X
Parasutterella: 0.69 X
Clostridium: 0.60 X
Dorea: 0.57 X
Butyricimonas: 0.56 X
Hespellia: 0.51 X
Alistipes: 0.47 X
Bifidobacterium: 0.42 X
Roseburia: 0.41 X
Faecalibacterium: 0.38 X
Anaerotruncus: 0.36 X
Adlercreutzia: 0.29 X
Anaerostipes: 0.29 X
Subdoligranulum: 0.28 X
Collinsella: 0.26 X
Shuttleworthia: 0.23 X
Intestinibacter: 0.18 X
Phascolarctobacterium: 0.16 X
Pseudobutyrivibrio: 0.14 X
Klebsiella: 0.13 X
Oscillospira: 0.12 X
Erysipelatoclostridium: 0.08 X
Thalassospira: 0.07 X
Lachnospira: 0.07 X
Slackia: 0.07 X
Dielma: 0.05 X
Actinomyces: 0.04 X
Victivallis: 0.04 X
Streptococcus: 0.01 X
Lactobacillus: < 0.01 X
Prevotella: < 0.01 X

 

[Thinktank]

Is anyone still using Ubiome?

I sent a sample 2 months ago and it's still processing... That really is a long time.

 

[RL_sparky]

Is anyone still using Ubiome?

I sent a sample 2 months ago and it's still processing... That really is a long time.

I also sent in a sample a little over two months ago. After six weeks they confirmed they received my sample and told me they were behind in their processing. I was told six more weeks before I would receive my results and that was about two weeks ago I received that email. They are behind at the lab since they launched their new SmartGut kit from what I understand.

 

[Thinktank]

Hmmm ok.. Then i'll wait sending in any additional samples until they have caught up, a gap of 3 months i just too long, big shifts can happen during that time making the data basicly useless.

 

[alicec]

Yes it's frustrating. Processing time has more than doubled. It used to be about 3 weeks.

I've been getting monthly tests for a while trying to understand what is happening in my gut. Just when some problems have arisen which could be gut related and it would be really helpful to get results relatively quickly, processing time has increased.

I believe American Gut is even longer though.

 

[Patrick*]

I just received my uBiome results.

Bacteroidetes: 66.13%
Firmicutes: 26.25%
Verrucomicrobia: 6.91%
Proteobacteria: 0.61%
Actinobacteria: 0.10%

On the genus level, I have no measurable bifidobacterium or lactobaccilus -- although I understand from alicec that the latter isn't too important.

I can't figure out why I'm so heavily shifted toward Bacteroidestes, or what that means to my health. @alicec would you mind giving me your thoughts?

 

[Thinktank]

@patrick, thanks for sharing your results. Did you take any antibiotics? Did you collect your stool sample the same way as you did the first time?

 

[alicec]

I can't figure out why I'm so heavily shifted toward Bacteroidestes

Diet can have a big influence on Bacteroidetes proportions. In general these genera thrive on complex carbohydrate and tend to be much higher in populations eating unrefined, high fibre carbohydrate sources.

The typical Western diet of relatively high fat, high refined carbohydrates and simple sugars favours Firmicutes, with Bacteroidetes being proportionately low.

Also there do seem to be a few basic types, termed enterotypes, which tend to be dominated by different bacterial clusters. There has been some disputation about the concept and changes to the original ideas about this, but it does seem that individuals do fall in to three or four basic categories. One is these is dominated by Bacteroidetes genera.

Still your results are unusual, very heavily skewed to Bacteroidetes.

As for health implications it's a bit hard to say. More information about dominant genera might give some clues.

 

[Patrick*]

@patrick, thanks for sharing your results. Did you take any antibiotics? Did you collect your stool sample the same way as you did the first time?

Thinktank, I did take antibiotics - at least once per year since first getting ME/CFS in 2011. The longest stretch was for about 3 months in 2014.

I have only collected one sample, once.

 

[Patrick*]

Diet can have a big influence on Bacteroidetes proportions. In general these genera thrive on complex carbohydrate and tend to be much higher in populations eating unrefined, high fibre carbohydrate sources.

The typical Western diet of relatively high fat, high refined carbohydrates and simple sugars favours Firmicutes, with Bacteroidetes being proportionately low.

Also there do seem to be a few basic types, termed enterotypes, which tend to be dominated by different bacterial clusters. There has been some disputation about the concept and changes to the original ideas about this, but it does seem that individuals do fall in to three or four basic categories. One is these is dominated by Bacteroidetes genera.

Still your results are unusual, very heavily skewed to Bacteroidetes.

As for health implications it's a bit hard to say. More information about dominant genera might give some clues.

Alicec, thank you very much for that information. I am on a paleo-ish diet with a lot of vegetables and meat and, at the time the sample was collected, also a lot of nuts. (I have since eliminated nuts).

Here are my top 8 genera (the only 8 genera that are over 1%):

Bacteroides: 54.60%
Faecalibacterium: 13.71%
Parabacteroides: 6.98%
Akkermansia: 6.91%
Alistipes: 4.27%
Blautia: 4.18%
Roseburia: 2.16%
Anaerotruncus: 1.85%

32 total genera found. uBiome says I'm in the bottom 13% in terms of diversity.

 

[alicec]

They are behind at the lab since they launched their new SmartGut kit from what I understand.

They do seem to have caught up. My last results came in about the usual time.

 

[alicec]

Here are my top 8 genera (the only 8 genera that are over 1%):

Bacteroides: 54.60%
Faecalibacterium: 13.71%
Parabacteroides: 6.98%
Akkermansia: 6.91%
Alistipes: 4.27%
Blautia: 4.18%
Roseburia: 2.16%
Anaerotruncus: 1.85%

None of those are problematic, most are really valuable, especially the star butyrate producers Faecalibacterium and Roseburia.

Bacteroides are pioneering species, among the few that can tackle really complex carbohydrate. They start to break this down to simpler forms which a much wider variety of species can then feed on.

Blautia is one of the few genera that consumes gas (hydrogen and carbon dioxide). Removal of hydrogen is in itself important since accumulation would interfere with reoxidation of NADH and hence ATP and SCFA formation. In addition it uses the hydrogen to produce acetate which in turn cross-feeds an important group of butyrate producers, such as Roseburia.

Blautia is a relatively recent classification which covers a groups of species formerly classified as Ruminococcus. Genetic analysis showed that there were two distinct groups within this genera. True Ruminococcus are part of clostridium cluster IV, of the family Ruminococcaceae. R. bromii typifies this group.

Blautia are part of cluster XIVa, of the family Lachnospiraceae. Formerly R. gnavus typifies this group.

Akkermansia feeds off mucous (produced by us) and is important in maintaining gut integrity. At high levels (which you have - average is 1.2%) it might erode the mucous barrier.

Alistipes thrives on fat. Anaerotruncus produces hydrogen sulfide. You have highish levels of the latter (average is 0.41%) so possibly this could be an issue for you. Both can be opportunistic pathogens (so can Bacteroides and many other normally harmless genera) but are run of the mill gut constituents. Not a problem but nothing special either.

Your biggest problem seems to be the low diversity. This is allowing a few species to dominate.

Even if you do manage to increase diversity, you will probably find that Bacteroides and Blautia will remain dominant in your gut. This has been the case with me. It is an example of a particular enterotype I think.

You might consider supplementing a variety of concentrated fibre sources. Smaller amounts of a variety of types rather than large amounts of a few is a good strategy. As usual, start low and build up slowly to gauge your response.

Change to the gut flora will take time but I have had great success with this approach.

Here, here and here are relevant posts.

 

[ChrisD]

I have attached two Ubiome tests of mine:- The first in January 2016 when I first started to have Fibromyalgia/Arthritis symptoms (Streptococcus and Dialister overgrowths).

Then the second is in January 2017 when I just had my onset of Moderate M.E. - The results of this one are quite different yet completely relate to the Gut biomarkers that were currently identified by Columbia University (Alistipes, Faecalbacterium, Roseburia, Dorea).

I've also noticed that I have quite large overgrowths of Parasuterella and Odoribacter, anyone know anything about these?

It has been suggested that I might benefit from Rifaximin... Any thoughts? DO anyone elses results correlate with Columbia study?

 

[gabriella17]

@searcher I haven't even taken the test yet, my kit is still sitting on my counter. I'm not familiar with any of the terms in your results, though, so I don't think I'd even know how to interpret it!

 

[adreno]

It has been suggested that I might benefit from Rifaximin... Any thoughts?

You have too few of those bacteria you mentioned - why would you want to take an antibiotic? I would go for a fecal transplant, if possible.

 

[ChrisD]

@adreno What makes you think that? Do these ratios not show significant overgrowths or imbalances?
Bacteroides: 1.63 X
Faecalibacterium: 1.24 X
Alistipes: 1.96 X
Roseburia: 0.47 X
Parasutterella: 2.46 X
Dorea: 0.92 X
Dialister: 1.19 X
Odoribacter: 3.41 X
Hespellia: 3.28 X
Adlercreutzia: 2.58 X

I would love to have FMT but it seems far too risky at the moment....

 

[ljimbo423]

Summary: Bacteroides species are significant clinical pathogens and are found in most anaerobic infections, with an associated mortality of more than 19%. The bacteria maintain a complex and generally beneficial relationship with the host when retained in the gut, but when they escape this environment they can cause significant pathology, including bacteremia and abscess formation in multiple body sites.

LINK

@ChrisD - I think high bacteroides levels are very common in cfs, if I remember right. If I understand your tests, your levels dropped from 2016 to 2017. It seems like your doing something right!

 

[alicec]

DO anyone elses results correlate with Columbia study?

No - here and here are two relevant posts.

Your results don't correlate either. For example, using topographical data analysis, they conclude

At the genus level, the abundances of Dorea, Faecalibacterium, Coprococcus, Roseburia, and Odoribacter were lower in the ME/CFS compared to the controls, whereas abundances of Clostridium and Coprobacillus were higher.

Yes your Roseburia is definitely lower but the rest of the pattern doesn't follow.

In any case, as I say in one of those posts

I don't think it is particularly helpful to focus on the list of organisms. Yes it is necessary to accumulate this info to understand if there are differences in overall composition but that is as far as it goes.

The significance doesn't lie in the actual organisms present. There is no single ideal pattern, there are many possible combinations, all of which work because of the considerable redundancy in the microbiome. Many different organisms can fulfill the same function.

So all of the studies showing differences in composition in various disease states are just the first step. Working out the meaning of the difference will be far more important and will be much harder to do.

You are making the mistake of thinking that there is one gut pattern that we should all aspire to. In reality, because of the redundancy of the gut microbiota (many organisms can fulfill the same role), many patterns are possible and perfectly functional.

Your results are quite normal and none of those genera are problematic. You don't show the full range of results so it is hard to say more but possibly you have low diversity which is allowing some genera to over-expand and fill the gaps.

You should be thinking about encouraging diversity with prebiotics, not killing off normal constituents with antibiotics.