uBiome results

[alicec]

Bacteroides species are significant clinical pathogens.

Many gut bacteria are opportunistic pathogens but are normal gut constituents which rarely cause problems. They become troublesome when other problems arise in the host.

Bacteroides are the single most dominant genus in the gut of most people. They are able to breakdown complex glycans making them available for a wide range of other organisms. Without abundant Bacteroides, most other gut constituents would starve.

 

[Ravn]

Can any of you wonderfully clever people here explain the Ubiome bacterial functions in plain English?

Puzzling especially about the significance, if any, of the following 3 because of a massive upwards trend in my ubiome results.

Test 1: already diagnosed IBS-C, but pre-ME
Test 2: early, mild ME (gradual onset)
Test 3: full-blown ME plus likely MCAS

Phagosome: went from 0.2x of (ubiome-tested) populationin test 1 to 13x in test 2 to 16x in test 3.
Indole alkaloid biosynthesis: 18x - 28x - 49x
Betalain biosynthesis: 15x - 23x - 40x

What do these multi-syllables signify (did try Google but didn't understand any of the search results)?

And any possible link with ME, or IBS or MCAS or anything else for that matter?

 

[alicec]

Phagosome: went from 0.2x of (ubiome-tested) populationin test 1 to 13x in test 2 to 16x in test 3.
Indole alkaloid biosynthesis: 18x - 28x - 49x
Betalain biosynthesis: 15x - 23x - 40x

I am puzzled about the phagosome reference, it is not a listed function in my tests and I am not sure what it is referring to.

Phagosomes are vesicles formed around particles, including microbes, engulfed by immune cells such as phagocytes. This is part of the process whereby the host (us) gets rid of invading pathogens - ie not a bacterial function. There are a couple of bacteria that can evade this process and become intracellular pathogens.

Here is the wikipedia entry.

Indole alkaloids are a broad group of substances, many of which have significant physiological activity. Here is the Wikipedia entry.

Among the best known of these are psychoactive substances from plants and fungi, but there are many others, some beneficial, some toxic.

In general the substances act on the central and peripheral nervous system, including neurotransmitter-like action. Some have anti-cancer properties.

The substances produced by bacteria have been less well studied and just from the general category of increased indole alkaloid biosynthesis, it is impossible to predict consequences. More specific investigation would be needed.

All we can say is that the substances can have potent effects so could be making some differences to you.

Also, the starting point for biosynthesis is the amino acid tryptophan. So increased use of these pathways by your gut bacteria could be depleting your supplies of this essential amino acid.

Betalains are red and yellowish pigments most commonly known in plants (the name is derived from beetroot). Here is the Wikipedia entry.

They appear to have antioxidant-like properties.

Again it is hard to make general predictions about effects on you but it could be beneficial.

Also they are derived from the amino acid tyrosine, so increased use by your gut bacteria could be depleting this amino acid. It is not considered to be essential because it can be made from phenylalanine, but it is an important neurotransmitter precursor so excess consumption could perhaps be problematic if you are unable to produce enough by this route.

 

[Ravn]

Thanks alicec. Weird that we seem to be getting different ubiome reports. Below is a screen grab of mine, with the Phagosome.

I had already tried to get through those Wikipedia articles but they're a bit over my head.

I sort of understand the concept of phagosome, but not what it has to do in my "Bacterial Abilities".

As for the alkaloids and betalains, I understand they are plant components and have a variety of effects on the body when consumed as food or medicine. Thanks to ubiome I now also know that gut bacteria can produce them, too. But just why would my gut bugs feel the need to make so much of them? And how does that relate to my health (or lack thereof)?

You said "more specific investigation would be needed" to understand those health consequences. Do you, or anybody else, know where/how/with whom to start such an investigation?

 

[alicec]

I sort of understand the concept of phagosome, but not what it has to do in my "Bacterial Abilities".

I don't really understand this either.

You could always email uBiome and ask them to explain this bacterial function.

I assume it is not shown in my results because my particular mix of bacteria doesn't have the capability.

I have never been able to understand the companies decision to show only comparisons that relate to an individual's results rather than showing the totality of average.

But just why would my gut bugs feel the need to make so much of them? And how does that relate to my health (or lack thereof)?

Not all bacteria have this capability, so it's not that yours are producing at an increased rate but that, with the particular collection you have, more have the capacity compared with average.

You can't know for sure if it relates to your health but it could raise suspicions. Mostly suspicions could only be confirmed in retrospect by correlation of symptoms and any changes in bacterial pathways resulting from changed bacterial composition.

Given the known effects of indole alkaloids on the nervous system, neurological symptoms and things like neurotransmitter balance might be worth considering.

You said "more specific investigation would be needed" to understand those health consequences. Do you, or anybody else, know where/how/with whom to start such an investigation?

I was thinking of detailed metabolomic analysis that might help to pinpoint more precisely which substances are being over-produced.

One PR member @Cheesus has had some experience in pursuing individual metabolomic analysis. Perhaps he might respond about his experiences.

 

[Cheesus]

One PR member @Cheesus has had some experience in pursuing individual metabolomic analysis. Perhaps he might respond about his experiences.

It was an enormous waste of money. I was given a list of hundreds of metabolites and their values relative to each other, but not the actual quantity of each metabolite. I had no information about what should be considered a normal value. I couldn't do anything with the information.

It might be more effective if undertaken in a format different to mine. There is a doctor that does metabolomics analysis, so I would guess they have the capacity to interpret such things: https://www.metabolomicmedicine.com/english/index.html

 

[MaximilianKohler]

Guys, these tests are mostly a waste of money right now. See the "testing" section here: https://www.reddit.com/r/HumanMicrobiome/wiki/index

 

[alicec]

Guys, these tests are mostly a waste of money right now. See the "testing" section here: https://www.reddit.com/r/HumanMicrobiome/wiki/index

I agree the tests have limitations, including providing information that we don't yet know how to interpret, but I most definitely disagree that they are a waste of money.

They can be very helpful in giving an overall picture of what is going on in the gut to counter the extremely distorted picture presented by culture based tests (CDSAs) which try to convince people they have overgrowths of minor aerobic species.

They can show if there are serious imbalances in potentially harmful genera that may warrant treatment.

They can show the extent (or lack thereof) of diversity, something that has been shown consistently to be associated with adverse health outcomes, flagging that serious efforts need to be made to adequately feed the gut microbiota.

For those of us who like to have as much information as possible, following the gut over time can help us to see if our efforts at gut improvement are bearing fruit.

I was not particularly impressed with the selective use of information in the link you provided. I strongly take issue with your microbiological "expert", who seems to be using classic smear techniques to make a case for a predetermined conclusion, rather than attempting to lay out the facts.

16S sequencing of stool samples is the mainstay of all microbiome research, used and validated in many thousands of research papers, it is not some clever way that a few companies have devised to fleece us of our money by performing useless tests.

Yes this technique does have limitations but it also has many pluses, including the capacity for extensive sampling of any microbial environment quickly and cheaply. This is why it is the workhorse of microbiome research.

Shotgun metagenomic sequencing does give much finer detail but it is much more time-consuming and expensive. It is essentially a research tool which might be used to answer questions raised by earlier 16S studies.

Yes stool samples are studied because they are easy to obtain but results have been compared with those obtained from biopsies throughout the gut and we do know quite a lot about the differences and similarites. Those many thousands of research studies have concluded that stool sampling is a valid way to sample the gut.

To answer particular questions that require detailed knowledge of the gut mucosal surface at a particular location, yes biopsy would be required, but this invasive procedure is not necessary for routine sampling.

 

[sb4]

How many people here also have low probiotic bacteria (Bifido and lactobacilius)?

My levels are pretty low:

Bifidobacterium compared to Selected Samples:
0.16x
Lactobacillus compared to Selected Samples:
0.3x

 

[joeblow604]

How many people here also have low probiotic bacteria (Bifido and lactobacilius)?

My levels are pretty low:

Bifidobacterium compared to Selected Samples:
0.16x
Lactobacillus compared to Selected Samples:
0.3x

Mine were at zero

Bifidobacterium compared to Selected Samples:
0x
Lactobacillus compared to Selected Samples:
0x

But everything else was out of the ordinary also

Firmicutes: 96.60%
Actinobacteria: 2.23%
Proteobacteria: 0.93%
Bacteroidetes: 0.23%

With all those Firmicutes you'd think i'd be a heavy guy but actually lost almost half my body weight in the first 1-2 years and only in the 90-100lb range.

Not entirely sure what to think of my results

 

[pamojja]

Some month ago there were free ubiome kits available (except the shipping, $20,-). Though not that reliable yet, thought if worth for that low price.

Now got my funny results came in:

Body weight bacteria match: Low

Probiotics match: Low

Diversity percentile: 93rd

Wellness match: 96,4%

Basically my bacteria aren't those of a skinny person I've been my whole life; despite eating Sauerkraut, yogurt and raw chesses every day my sample contained zero probiotics; and despite having numerous serious health conditions my results greatly overlap with those from individuals who report no ailments and high levels of wellness.

Nevertheless, once this new testing technology get more accurate in a couple of years, it for sure will become very helpful. Thought would share my results, so others thinking about getting it too, can get an accurate idea of what one actually gets.

The results themselves are terribly scattered under numerous tabs in one's online ubiome account, and nothing comprehensive to print out to discuss with a health professional. For example the whole taxonomy tree is a mind-map, where one has to click each node to read further. Therefore I painfully copy and pasted each bit of info combined into a spreadsheet, which now could also easily be printed out.

Omitted are short pop-up descriptions of all prebiotic and some other bacteria, were I only added those for the 2 main - firmicutes and bacteroides - to the intro tab in my spreadsheet. And a in my case useless time-line function for multiple ubiome results.

Added last year results of a cultured stuhl test, short descriptions for my rare and too abundant bacteria, lists of possibly opportunistic or beneficial bacteria by Dr. Grace, and marked those bacteria and predicted metabolic functions most close to mine.
https://docs.google.com/spreadsheet...Vwu6k8sf9DQ1HCErTP3VBy-tWw/edit#gid=368328141
https://docs.google.com/spreadsheet...Vwu6k8sf9DQ1HCErTP3VBy-tWw/edit#gid=368328141

 

[juniemarie]

Well that doesn't sound encouraging about the kraut,yogurt etc ability to do much for us.

 

[pamojja]

Well that doesn't sound encouraging about the kraut,yogurt etc ability to do much for us.

Better don't take a not yet reliable test to make any premature conclusions about probiotic foods. In fact, with changing diet and comprehensive supplementation I could revert a 60% walking-disability from a severe PAD. That is totally encouraging.

 

[juniemarie]

I see so the test isn't too reliable? Why is everyone getting it? Oh well, good news for me cause I eat a lot of probiotic foods and would like to think they are helping repopulate my gut.

 

[pamojja]

I see so the test isn't too reliable? Why is everyone getting it?

Not everyone is getting it at all, that's an exaggeration. And which lab tests are that reliable, really? It did contain some interesting information for me, regular cultured stuhl tests couldn't. Then I got it for for free, just had to pay the shipping. - In my opinion this will become a very important test once it's more accurate.

 

[juniemarie]

Really what I meant is seems like this is the new darling of the unreliable test that are available these days. I am glad you got some good info from it . For me after so many years of taking unreliable tests I just called it quits. A few of them did give me some vague answers, a few gave me some possibilities to look into but most of them were a waste of time and money.
I did do the CSA from Genova or Metametrx a couple a yrs back. I need to do a search here on PR and see what the word is on the reliability of that test and recheck my test results.
In the meantime going to keep eating my probiotic foods........talk about a deep well. Probiotics! It's mind boggling all the different types and what health issue is helped by which probiotic or even made worse.
My brain fog is way to bad most days to tackle that one.

 

[MaximilianKohler]

Yeah I posted sources previously in this thread saying these tests are mostly useless at the moment. For example, I had one done recently that showed my Bifido WAY higher than average, and I'm having a TON of very severe, life threatening problems, and foods/supplements that increase Bifido make me worse.

Additionally, fermented foods are quite overhyped. Human-sourced strains of probiotics should be superior: Probiotic guide.

 

[pamojja]

For example, I had one done recently that showed my Bifido WAY higher than average, and I'm having a TON of very severe, life threatening problems, and foods/supplements that increase Bifido make me worse.

So your microbiome test basically confirmed your experience with raising Bifido. Don't understand whats useless about that confirmation? Exactly what to expect from such a test.

 

[MaximilianKohler]

Bifido is claimed to be one of the "only good" "probiotic bacteria". I say useless because the test gave me nothing actionable. Nothing new or useful was gained from doing the test. I did it because I got it for free, but if you pay for one of these tests I think it's a waste of money.

 

[alicec]

Though not that reliable yet

In what way do you think it is not reliable?