uBiome results

[alicec]

there is a issue with the probiotic Vivomixx or with the prebiotics.

I am just thinking out loud, maybe taking one single strain at a time would be better...
Or, have you already tried Short Chain FOS? I don't think most of FOS are SC...

No I don't think there is any particular problem with the probiotic or prebiotics.

I have tried many other probiotics, single strains and a wide variety of prebiotics, albeit in very small doses. I am one of those who reacts adversely to even moderate doses of concentrated prebiotics.

I think there are two issues. The most important one is the gut. For reasons that are not clear, our gut flora has become unbalanced and is resistant to change. It is very difficult to perturb the system. Maybe some key species that cross-feed or otherwise facilitate others are absent.

Secondly, all available probiotics are very poor substitutes for what we really need. After all they almost invariably consist of Lactobacilli and Bifidobacteria. The latter are significant, but still only minor constituents of the gut. The former are very minor.

Apart from B. longum, the keystone species in our guts are simply not available as supplements.

It does seem that there is a beneficial effect from existing probiotic species just transiting through the gut and that is why I continue to take them. I certainly don't expect them to transform my gut - and they clearly don't.

I think the claims by Elixa that transformation will occur in 6 days are ridiculous - just hype.

 

[alicec]

@Theodore, you are in a perfect position to put Elixa's claims to the test. You already have a baseline uBiome test.

Take the probiotic for the recommended 6 days, wait a few weeks, then do another test.

If you find your gut is transformed I will happily eat my hat.

 

[Biarritz13]

No I don't think there is any particular problem with the probiotic or prebiotics.

I have tried many other probiotics, single strains and a wide variety of prebiotics, albeit in very small doses. I am one of those who reacts adversely to even moderate doses of concentrated prebiotics.

I think there are two issues. The most important one is the gut. For reasons that are not clear, our gut flora has become unbalanced and is resistant to change. It is very difficult to perturb the system. Maybe some key species that cross-feed or otherwise facilitate others are absent.

Secondly, all available probiotics are very poor substitutes for what we really need. After all they almost invariably consist of Lactobacilli and Bifidobacteria. The latter are significant, but still only minor constituents of the gut. The former are very minor.

Apart from B. longum, the keystone species in our guts are simply not available as supplements.

It does seem that there is a beneficial effect from existing probiotic species just transiting through the gut and that is why I continue to take them. I certainly don't expect them to transform my gut - and they clearly don't.

I think the claims by Elixa that transformation will occur in 6 days are ridiculous - just hype.

I didn't know that you tried all those things so you may be right. Have you tried ScFOS as well?

@Theodore, you are in a perfect position to put Elixa's claims to the test. You already have a baseline uBiome test.

Take the probiotic for the recommended 6 days, wait a few weeks, then do another test.

If you find your gut is transformed I will happily eat my hat.

I think I am gonna do that or maybe take the prebiotic ScFOS first then run a test...We will see.

Regarding Bifidos :
"Bizarrely, the Hadza have no Bifidobacteria—a group of bacteria that makes up to 10 percent of a Western gut population and is generally viewed as ‘healthy’. They’re the main microbes in infants and they seem to feed on special sugars in breast milk. As we get older, they lose their dominance but they still stick around, possibly because we continue to eat dairy foods. It makes sense that the Hadza, which don’t eat dairy and don’t keep livestock, would be missing these otherwise omnipresent bugs."

Maybe Bifido is not the way to go...

 

[jepps]

I know they say 6 days is enough but I don't believe that. In my experience, stopping the probiotics leads to gut deterioration.

Maybe "6 days is enough" may be right for healthy people - but not for people with autoimmune disease with chronic dysbiosis, chronic candida and maybe chronic viruses in the gut.

 

[alicec]

@jepps and I had a side conversation on another thread which was really a diversion - it should have happened here, so I thought I'd post an interesting review I found when thinking about some of the issues raised.

In our conversation, she noted that uBiome reported a low level of Eukaryota in her last analysis, then soon after I found a low level of Euryarchaeota reported in my most recent test.

So it seems that uBiome is expanding its analysis.

The phylogenetic tree on the website still shows only bacterial phyla and their constituents and we were speculating about identifying the constituents of these new phyla/super kingdom.

The archaea were easy to track down since there are very few of them. In my case I could work out that the entire count came from Methanobrevibacter smithii.

Eukaryota is much more complex and could take a bit of chasing. However I just found a wonderful review of the human gastrointestinal microbiota, which includes a run down of what is known about the entirely of the microbiota, including eukaryotes.

The excellent Fig 2 gives a graphic overview of the phylogenetic relationships of the entire microbiota, with all the detail given throughout the review.

The review is very comprehensive (52 pages), starting from the very first culture-based studies and proceeding to today where new generation DNA sequencing has revealed an enormously more complicated picture and new generation culturing techniques are enabling detailed study of many of these new species.

There is extensive phylogenetic analysis which clearly shows all the family relationships and helps to sort out the very confusing and often wrongly allocated Firmicutes (including all those clostridial clusters).

There are concise summaries of the characteristics of the various families, genera and species which are very helpful, if like @jepps and I, you are trying to complete a comprehensive picture of your gut microbes.

 

[jepps]

Thank you @alicec for the review the human microbiome. I will read this, and hope to get a clearer picture about the structure of the microbes, and how the structure my personal Excel-comparision of the several Ubiometests.

If anybody is interested: a comparasion of the 4 Ubiometests until now is here:
https://www.dropbox.com/s/pqnxgjbim09hyyf/Ubiome Test.xlsx?dl=0

It´s very interesting to try, to have a look on the functions of the individual microbes. They produce enzymes, that we know from the methylation cycle. F.ex. Pseudomonadales produce Aldehydeoxidase (ALDH), and we also have the gene ALDH, that can be partially mutated according to 23andme. If I understand it right, we are genetically able to detoxify aldehydes, and certain bacteria produce the enzymes to detoxify aldehydes, too, so we have more capacity to detoxify them.
Same with bacteria, that are involved in methylation of folic acid and so on.

F. ex. Ruminococcaceae consumes hydrogene, and produces Acetate. The Acetate is consumed by Roseburia. So they nourish each other, and this should happen in the whole body. If we have no Roseburia, Acetate builds up in the body, and gets toxic. If we are successfully in creating a healthy flora in the gut, we are less toxic, and have less inflammation. Similar like that I could imagine homoestasis.

If important strains are missing, or less, other bacterial strains (or even pathogens, but they have side effects) are able to undertake the function of the missing, and here probiotics could be important. And the more microbes we have in the gut, the are the microbes able to undertake the important functions of metabolis and detoxifying.

This interesting research about the microbioe and the brain writes

And it’s not simple to deliver microbes to the gut and persuade them to stay.

but working on this task is worth it.

 

[jepps]

It does seem that there is a beneficial effect from existing probiotic species just transiting through the gut and that is why I continue to take them. I certainly don't expect them to transform my gut - and they clearly don't.

Maybe probiotics and fermented foods do not settle down in the intestine, but they at least partially inherit tasks that lost oder underrepresented microbes should do.

PS: I have Eukaryota in my Ubiome test result, but no M. sithii. The next Ubiome results maybe show more according the Eukaryota

 

[Biarritz13]

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

 

[TigerLilea]

I was reading a few days ago that the test results from uBiome and American Gut Project can have totally opposite results even though the person sent in samples from the same piece of toilet paper used to collect the sample. It now makes me wonder how accurate these tests are as I have been thinking of having one done myself. Has anyone else who's had testing done by both companies had the same experience?

 

[alicec]

can have totally opposite results

Well I think that is a bit of an exaggeration. There can be discrepancies, but they can match up remarkably closely also.

There are technical differences between the companies with sample treatment which can account for much of the difference and these can be corrected for. When this is done, there is usually good agreement.

Here is just one article which canvases some of the issues.

None of this is reason to think that the test is not "accurate" and so not worth doing.

First of all you shouldn't think of the test as showing a right or wrong pattern. The gut is much more complex than that.and there is no correct pattern that we should all aspire to.

The value of the test is in identifying your own pattern, does it show gross distortions from average, unusual species, absence of known keystones etc. Following your own pattern over time can be very valuable in showing response to dietary and other interventions.

 

[alicec]

datas related to metabolism

They are summarising the metabolic functions present in your microbiome compared with average.

So for the ornithine example you give, they are saying your gut flora have less capacity to metabolise this amino acid than average.

What does this mean for you? Impossible to say since this is just one part of a complex whole. It might mean that ornithine supplementation would be more effective for you since it is less likely to be degraded.

On the other hand it might be a metabolite of ornithine that is important. One such is putrescine, a biogenic amine - maybe having less of this is a good thing.

Alternatively some bacteria use ornithine in more complex reactions to obtain energy, and the by-products are various SCFAs.Having less of these might not be a good thing.

As I see it, the pathways which are dramatically different from average are worth further consideration and research. Knowing a bit more about what they do might tie in with some particular problems that we identify as a host, might explain some odd reactions to things or might suggest areas of metabolism that need reinforcement.

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

There aren't any, indeed virtually all available probiotics have little to do with the species in the gut.

Some people would be very pleased to have fewer proteobacteria.

 

[jepps]

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

Hi @Theodore,

The Prescript Assist contains these Proteobacteria: Pseudomonas calcis, Ps.dentrificans, Ps. fluorescens, Ps. glathei, Acinetobacter calcoaceticus, Azospirillum lipoferum, Azospirillum brasiliense, Azotobacter chroococcum, Azotobacter paspali

PA is interesting, as it contains microbes of all 4 phylums (Proteo, Actino, Firmicutes, Bact., it also contains fungi). It also containes bacteria, that settle down in the intestine.

My first Ubiome-test 1 year ago showed 12,7 % proteos, the next 10,4, next 1,4, next 2,6, the latest 5,4. When I compare the results with the diagnostic instrument (it´s only energetic), then viral mobilization (and also enhanced inflammation) from the cells means high proteos. There is also one interesting microbe "Candidatus Arthromitus" (Clostridium), which induces a strong Th17-answer. And my test shows this microbe, when proteos are high, and no presence of C.Arthromitus, when proteos are low.
Maybe higher proteos are needed for immune answer:
http://www.scientificamerican.com/a...lp-determine-our-immune-response-to-vaccines/

Many Proteobacteria propel themselves with the help of tail-like flagella. Those tails contain flagellin, a protein known to bolster immune cell activity. An abundance of such bacteria in the body could act as a natural immunity-booster

Best regards, jepps

 

[jepps]

German user can order a free kit: The university Tübingen makes a project "The Tübiom project", and searches 10000 participants for studying their microbiome. It´s the same test like Ubiome.

https://www.tuebiom.de/

Sadly it´s only for German people

 

[Biarritz13]

They are summarising the metabolic functions present in your microbiome compared with average.

So for the ornithine example you give, they are saying your gut flora have less capacity to metabolise this amino acid than average.

What does this mean for you? Impossible to say since this is just one part of a complex whole. It might mean that ornithine supplementation would be more effective for you since it is less likely to be degraded.

On the other hand it might be a metabolite of ornithine that is important. One such is putrescine, a biogenic amine - maybe having less of this is a good thing.

Alternatively some bacteria use ornithine in more complex reactions to obtain energy, and the by-products are various SCFAs.Having less of these might not be a good thing.

As I see it, the pathways which are dramatically different from average are worth further consideration and research. Knowing a bit more about what they do might tie in with some particular problems that we identify as a host, might explain some odd reactions to things or might suggest areas of metabolism that need reinforcement.



There aren't any, indeed virtually all available probiotics have little to do with the species in the gut.

Some people would be very pleased to have fewer proteobacteria.

Hi Alice

Thank you for your reply.

So if I understand you well, when you are a slow metaboliser you absorbe more and degrade less because you have less of these bacteria? Is that what you're saying?

Why some people would be very pleased to have fewer proteo?

Hi @Theodore,

The Prescript Assist contains these Proteobacteria: Pseudomonas calcis, Ps.dentrificans, Ps. fluorescens, Ps. glathei, Acinetobacter calcoaceticus, Azospirillum lipoferum, Azospirillum brasiliense, Azotobacter chroococcum, Azotobacter paspali

PA is interesting, as it contains microbes of all 4 phylums (Proteo, Actino, Firmicutes, Bact., it also contains fungi). It also containes bacteria, that settle down in the intestine.

My first Ubiome-test 1 year ago showed 12,7 % proteos, the next 10,4, next 1,4, next 2,6, the latest 5,4. When I compare the results with the diagnostic instrument (it´s only energetic), then viral mobilization (and also enhanced inflammation) from the cells means high proteos. There is also one interesting microbe "Candidatus Arthromitus" (Clostridium), which induces a strong Th17-answer. And my test shows this microbe, when proteos are high, and no presence of C.Arthromitus, when proteos are low.
Maybe higher proteos are needed for immune answer:
http://www.scientificamerican.com/a...lp-determine-our-immune-response-to-vaccines/


Best regards, jepps

Hi jepps, thank you, I will take a look at PA and your link

 

[alicec]

when you are a slow metaboliser you absorbe more and degrade less because you have less of these bacteria? Is that what you're saying?

Your bacteria are making less of a contribution to your overall metabolism of, for example, ornithine. So yes there would be less degradation, which would likely mean more absorption, and fewer breakdown products. The latter could have various effects, depending on the different bi-products.

Why some people would be very pleased to have fewer proteo?

The Proteobacteria contain some of the worst pathogens. Mostly these are in the gamma Proteobacteria class, but not entirely. The gammas include E.coli, Shigella, Yersinia, Salmonella, Enterobacter, Haemophilus, Helicobacter, Pasturella, Proteus, Pseudomonas - the list goes on and on.

Other classes contribute pathogens - eg Sutterella (beta), Desulfovibrio and Bilophila (delta).

As well as being involved in infection, metabolism of some of the bacteria cause other problems - eg Proteus produces so much ammonia that it stimulates formation of kidney stones. Both of the deltas produce hydrogen sulphide which can be toxic.

On a more general level, high levels are associated with many adverse health outcomes - obesity, IBD, colon cancer, dyslipidaemia - to name just a few.

Many of the adverse outcomes may be linked directly or indirectly to the potent LPS produced by these gram -ve bacteria. Yes other phyla, most notably, Bacteroidetes, are gram -ve but the latter have special lipids in their cell walls which counter the inflammatory effects of LPS. Not so with Proteobacteria.

Having said all that the phylum is clearly a part of the normal gut flora and plays a necessary role. It's members tend to be bullies, however, and readily get out of hand. This often leads to trouble.

 

[jepps]

The Proteobacteria contain some of the worst pathogens. Mostly these are in the gamma Proteobacteria class, but not entirely. The gammas include E.coli, Shigella, Yersinia, Salmonella, Enterobacter, Haemophilus, Helicobacter, Pasturella, Proteus, Pseudomonas - the list goes on and on.

Other classes contribute pathogens - eg Sutterella (beta), Desulfovibrio and Bilophila (delta).

As well as being involved in infection, metabolism of some of the bacteria cause other problems - eg Proteus produces so much ammonia that it stimulates formation of kidney stones. Both of the deltas produce hydrogen sulphide which can be toxic.

This is the pathogenic side of proteos. What is, when proteos are high because of an underlying cause?
This example describes viral etiology increases Proteobacteria. Viral infections cause changes in gene expression, therefore they are able to change carb metabolism. An essential part of carb metabolism are the methanotrophic bacteria, (they oxidize methane) mainly related to proteobacteria. Actinobacillus, another proteo bacteria, produces igG, that works against viruses.

Maybe proteobacteria are high, because they work against damage from viral infections (producing igG, assimilating to high methane because of disrupted carb metabolism).

Nevertheless high proteo cause harm by itself because of toxic LPS, as you and Vegas posted. @Vegas wrote a post, where high proteobacteria increase inflammation because of to much LPS and to low firmicutes (inflammation decreasing bacteria like clostridial cluster IV like faecalibacterium prausnitzii, and clostridial cluster XIVa, above all Roseburia intestinalis and Eubacterium rectale) are a puzzle of chronic inflammation.

Regarding ammonia: not all proteos produce ammonia: Bilophila and Chromatiales produce ammonia, but Rhodospirillaceae assimilates ammonia.

I know very less about the microbes. But it´s my thought, that an underlying cause contributes to a shift in the microbiome causing inflammation. For me chronic viral infections as underlying cause make sense.

 

[Biarritz13]

Thank you both of you!

 

[Interactome]

The Proteobacteria contain some of the worst pathogens. Mostly these are in the gamma Proteobacteria class, but not entirely. The gammas include E.coli, Shigella, Yersinia, Salmonella, Enterobacter, Haemophilus, Helicobacter, Pasturella, Proteus, Pseudomonas - the list goes on and on.

I just did another uBiome and seem to have Proteobacteria in excess.

I've uploaded a tree classification diagram from uBiome that shows some of the major ones.

Your Bacteria at the Phylum rank compared to All Samples
Proteobacteria: 3.31 X
Tenericutes: 1.73 X
Firmicutes: 1.10 X
Actinobacteria: 0.73 X
Bacteroidetes: 0.52 X
Verrucomicrobia: 0.01 X


And more in depth it shows a lot of Haemophilus and also Streptococcus (Firmicute according to Wiki). Do you think this could be a potential problem that I should try to address? And speaking about viruses, I know that I have (at least) EBV and CMV in me.

Your Bacteria at the Genus rank compared to All Samples
Haemophilus: 11.25 X
Streptococcus: 8.06 X
Faecalibacterium: 2.38 X
Erysipelatoclostridium: 1.94 X
Anaerostipes: 1.90 X
Bilophila: 1.29 X
Anaeroplasma: 1.18 X
Enterorhabdus: 1.14 X
Sutterella: 1.13 X
Blautia: 0.94 X
Terrisporobacter: 0.84 X
Barnesiella: 0.81 X
Phascolarctobacterium: 0.61 X
Roseburia: 0.61 X
Collinsella: 0.56 X
Bacteroides: 0.55 X
Subdoligranulum: 0.54 X
Actinomyces: 0.52 X
Sarcina: 0.46 X
Dorea: 0.45 X
Odoribacter: 0.43 X
Marvinbryantia: 0.42 X
Hespellia: 0.38 X
Bifidobacterium: 0.38 X
Pseudobutyrivibrio: 0.35 X
Corynebacterium: 0.33 X
Lachnospira: 0.33 X
Slackia: 0.31 X
Butyricimonas: 0.29 X
Paraprevotella: 0.29 X
Alistipes: 0.27 X
Veillonella: 0.27 X
Parabacteroides: 0.23 X
Turicibacter: 0.20 X
Gordonibacter: 0.20 X
Clostridium: 0.16 X
Intestinimonas: 0.13 X
Intestinibacter: 0.11 X
Flavobacterium: 0.10 X
Flavonifractor: 0.08 X
Howardella: 0.07 X
Aggregatibacter: 0.06 X
Dialister: 0.04 X
Candidatus Soleaferrea: 0.04 X
Anaerococcus: 0.02 X
Prevotella: 0.02 X
Peptostreptococcus: 0.02 X
Atopobium: 0.02 X
Peptoclostridium: 0.02 X
Peptoniphilus: 0.01 X
Finegoldia: 0.01 X
Granulicatella: 0.01 X
Rahnella: 0.01 X
Hafnia: 0.01 X
Aquabacterium: 0.01 X
Anaerosporobacter: 0.01 X
Akkermansia: < 0.01 X
Staphylococcus: < 0.01 X
Rothia: < 0.01 X
Enterococcus: < 0.01 X
Porphyromonas: < 0.01 X
Actinobacillus: < 0.01 X
Parasutterella: < 0.01 X
Methylobacterium: < 0.01 X
Lactobacillus: < 0.01 X
Gemella: < 0.01 X

 

[alicec]

it shows a lot of Haemophilus and also Streptococcus (Firmicute according to Wiki). Do you think this could be a potential problem that I should try to address?

I have seen a lot of variability in my gut tests, at times seeing Proteobacteria 3-4 X. Often this is from overgrowth of some of the apparently less harmful members, but once there was a big overgrowth of a member of the gamma proteobacteria (Kluyvera) which is a rare, serious, opportunistic pathogen.

I've not observed any obvious problems from these overgrowths and next test around things are usually back to more normal levels.

It is very hard to say what to make of a single result like this. Haemophilus is potentially a very serious opportunistic pathogen so having a lot of it in the gut is a bit worrying. Streptococcus is also potentially a pathogen, but both genera are also normal gut constituents present in reasonable amounts.

Personally I wouldn't be rushing into treating with something like antibiotics. This can often cause more problems than it solves.

I'd be looking to diet, pre and probiotics and having another test fairly soon. If these and/or other potential problem species seem to be persisting then you could rethink.

 

[Interactome]

I have seen a lot of variability in my gut tests, at times seeing Proteobacteria 3-4 X. Often this is from overgrowth of some of the apparently less harmful members, but once there was a big overgrowth of a member of the gamma proteobacteria (Kluyvera) which is a rare, serious, opportunistic pathogen.

I've not observed any obvious problems from these overgrowths and next test around things are usually back to more normal levels.

It is very hard to say what to make of a single result like this. Haemophilus is potentially a very serious opportunistic pathogen so having a lot of it in the gut is a bit worrying. Streptococcus is also potentially a pathogen, but both genera are also normal gut constituents present in reasonable amounts.

Personally I wouldn't be rushing into treating with something like antibiotics. This can often cause more problems than it solves.

I'd be looking to diet, pre and probiotics and having another test fairly soon. If these and/or other potential problem species seem to be persisting then you could rethink.

Hi. Was a bit away and missed the response. Thank you. I'll re-test it today. So in about 6 weeks I should have the results and will post it back here.