uBiome results

[Thinktank]

@alicec,
From the taxonomy tree:
Chlamydiae/Verrucomicrobia group -> Verrucomicrobia -> Verrucomicrobiae -> Verrucomicrobialis -> Verrucomicroiacaea -> Akkermansia

Genus akkermansia countnorm. = 154776

Have you been able to analyze your full taxonomy? It looks like it needs to be compiled somehow.

I'm interested to hear how you have managed to bring the bacteroidetes down without antibiotics.

What i find strange is that ubiome lists the bacteroidetes group average as 36.65%.

Edit:
It looks like Akkermansia indeed degrades mucin, would this lead to erosion / IBD?
http://www.pnas.org/content/110/22/9066.full

We recently isolated Akkermansia muciniphila, which is a mucin-degrading bacterium that resides in the mucus layer.

 

[alicec]

Have you been able to analyze your full taxonomy? It looks like it needs to be compiled somehow.

Well I've just converted it into Excel and used the sorting function to show as species, genus etc, as described by Richard Sprague here. The main things you can get out of this which is additional to the % info offered by uBiome on the website is the actual bacterial count and a list of some of the species detected. The latter is not exhaustive so they don't show it on the website.

I haven't yet looked at the various github tools to compare different analysis as noted here. I just put my various analyses into an excel spreadsheet, eyeball them and make some simple calculations about % change.

I'm interested to hear how you have managed to bring the bacteroidetes down without antibiotics.

Just by providing more food that firmicutes like. I made a post about the initial changes here. Essentially I went from a VLC Paleo diet to the PHD, keeping a wide range of fibrous vegetables but adding resistant starch to every meal.

With time it seems that the gut flora try to return to a previous balance and I noticed that bacteroides did tend to increase and firmicutes decrease somewhat, though not to pre-dietary change level. Then I added steel-cut oats and again saw firmicutes increase considerably and bateroidetes decrease. I suspect this will reverse a bit with time but am waiting on a new analysis to confirm this.

What i find strange is that ubiome lists the bacteroidetes group average as 36.65%.

This is indeed much higher than in many other studies. I think it just reflects the poor diet of the test population.

I'll just quote a section of a previous post I made here to illustrate this point

the increase in Firmicutes (1.5 X previous) and decrease in Bacteroidetes (0.43 X) could be interpreted differently depending on what is taken as average. According to uBiome, Firmicutes is now elevated (1.3 X) and Bacteroidetes is depleted (1.92 X). However the average values, which one presumes largely represent a North American population, are very different from much of the literature, not just for hunter gatherer populations but also Europeans.

The changes seen in my gut - Firmicutes 51.5 to 77.5 % and Bacteroidetes 27 to 11.7 % - are similar to those seen by Jeff Leach (in reverse)
http://humanfoodproject.com/going-f...cquire-healthiest-gut-microbiome-world-heard/

who like me didn't change protein and fat but went from high vegetable/fibre to very low vegetable/fibre (not that I was ever very low vegetable, more low resistant starch) .

A study of the French and Dutch found Firmicutes 79.4% and Bacteroidetes 16.9%. The famous Hadza study compared with an Italian population and found Hadza Firmicutes 72%, Italians a bit higher (couldn't find an exact figure in my quick trawl of the paper just because of the way things were reported), Hazda Bacteroidetes 17.1%, Italian 10.1%.

In other words I don't think my results now are abnormal, but rather reflect a relatively high fibre diet.

It looks like Akkermansia indeed degrades mucin, would this lead to erosion / IBD?

Yes that is what I am wondering. All the studies I have seen are describing the beneficial effects on gut integrity associated with increase in Akkermansia, which is very often extremely low. I haven't come across anything looking at overgrowth - not that I have looked for it specifically.

 

[knackers323]

Well I've just converted it into Excel and used the sorting function to show as species, genus etc, as described by Richard Sprague here. The main things you can get out of this which is additional to the % info offered by uBiome on the website is the actual bacterial count and a list of some of the species detected. The latter is not exhaustive so they don't show it on the website.

I haven't yet looked at the various github tools to compare different analysis as noted here. I just put my various analyses into an excel spreadsheet, eyeball them and make some simple calculations about % change.



Just by providing more food that firmicutes like. I made a post about the initial changes here. Essentially I went from a VLC Paleo diet to the PHD, keeping a wide range of fibrous vegetables but adding resistant starch to every meal.

With time it seems that the gut flora try to return to a previous balance and I noticed that bacteroides did tend to increase and firmicutes decrease somewhat, though not to pre-dietary change level. Then I added steel-cut oats and again saw firmicutes increase considerably and bateroidetes decrease. I suspect this will reverse a bit with time but am waiting on a new analysis to confirm this.



This is indeed much higher than in many other studies. I think it just reflects the poor diet of the test population.

I'll just quote a section of a previous post I made here to illustrate this point



Yes that is what I am wondering. All the studies I have seen are describing the beneficial effects on gut integrity associated with increase in Akkermansia, which is very often extremely low. I haven't come across anything looking at overgrowth - not that I have looked for it specifically.

have you noticed any changes in symptoms along with the change in biodome?

anyone seen what a symptom free persons biodome looks like?

 

[alicec]

have you noticed any changes in symptoms along with the change in biodome?

One obvious improvement that I feel confident about attributing to changes in microbiota is marked improvement in BMs. I have gone from Bristol 6-7 to Bristol 3-4, occasional 5. Nothing else I have ever tried has achieved this.

As for other symptom changes, well it is difficult to know what might be due to what. I see it more as trying to improve what we are now coming to understand as a foundation stone to good health in the hope that this might help my overall condition. I did think this was happening in the beginning, then I had a set-back. This coincided with a big spike in Proteobacteria, though I can't say that there was a causal link.

I think it requires quite a bit of time to build up a picture of pattern changes and how this might relate to symptoms and I have not been following my gut for long enough yet.

anyone seen what a symptom free persons biodome looks like?

There are a many studies of the microbiome of "healthy" people, from a variety of different environments. There is no one "right" pattern that we should all be aspiring to achieve.

 

[Interactome]

@alicec

Hi

Do you know what the "Secondary metabolite degradation" part means? Am I being poisoned by dioxin or is it insignificant?

This is compared to all samples:

• Dioxin degradation 1.31X
• Xylene degradation 1.31X
• Drug metabolism - other enzymes 1.07X
• Polycyclic aromatic hydrocarbon degradation 1.06X
• Chloroalkane and chloroalkene degradation 1.04X
• Nitrotoluene degradation 1.04X
• Benzoate degradation 1.01X
• Atrazine degradation 0.96X
• Naphthalene degradation 0.95X
• Aminobenzoate degradation 0.9X
• Bisphenol degradation 0.88X
• Styrene degradation 0.88X
• Ethylbenzene degradation 0.84X
• Chlorocyclohexane and chlorobenzene degradation 0.84X
• Toluene degradation 0.81X
• Drug metabolism - cytochrome P450 0.6X
• Metabolism of xenobiotics by cytochrome P450 0.59X
• Caprolactam degradation 0.43X
• Fluorobenzoate degradation 0.06X

Also, is this something that is important:

• Arachidonic acid metabolism 1.47X

 

[alicec]

Do you know what the "Secondary metabolite degradation" part means? Am I being poisoned by dioxin or is it insignificant?

Secondary metabolites are organic molecules which are not involved in major metabolic pathways such as growth.

So as well as identifying the various bacteria present in a gut sample, uBiome is now identifying bacterial genes which are known to be involved in degradation of the various secondary metabolites listed (along with the various other metabolic pathways now listed under bacterial function).

In the case of dioxin, you have a higher than average number of such genes - ie your gut bacteria have more capacity to degrade dioxin, so this is a good thing.

It is the other end of the list that is of more concern. Genes for fluorobenzoate degradation are very low, so you will be getting little help from your gut microbiota in dealing with this compound.

These results are just dealing with capacity of gut bacteria - they say nothing about the human capacity for degradation of these same molecules.

 

[satori]

Well I've just converted it into Excel and used the sorting function to show as species, genus etc, as described by Richard Sprague here. The main things you can get out of this which is additional to the % info offered by uBiome on the website is the actual bacterial count and a list of some of the species detected. The latter is not exhaustive so they don't show it on the website.

I haven't yet looked at the various github tools to compare different analysis as noted here. I just put my various analyses into an excel spreadsheet, eyeball them and make some simple calculations about % change.



Just by providing more food that firmicutes like. I made a post about the initial changes here. Essentially I went from a VLC Paleo diet to the PHD, keeping a wide range of fibrous vegetables but adding resistant starch to every meal.

With time it seems that the gut flora try to return to a previous balance and I noticed that bacteroides did tend to increase and firmicutes decrease somewhat, though not to pre-dietary change level. Then I added steel-cut oats and again saw firmicutes increase considerably and bateroidetes decrease. I suspect this will reverse a bit with time but am waiting on a new analysis to confirm this.

Thanks for your posts. What are you using for resistant starch? I've found that cooking and cooling various things is a nuisance and not appealing to me. I know there are some RS3 commercial product out there, but have yet to research them.

I've read that the akkermanisa is high in athletes. I think the mucin layer is supposed to be replenished constantly as long as your body has the right substrates. I know my leaky gut tests did not improve until I added proline.

This is indeed much higher than in many other studies. I think it just reflects the poor diet of the test population.

I'll just quote a section of a previous post I made here to illustrate this point





Yes that is what I am wondering. All the studies I have seen are describing the beneficial effects on gut integrity associated with increase in Akkermansia, which is very often extremely low. I haven't come across anything looking at overgrowth - not that I have looked for it specifically.

 

[alicec]

What are you using for resistant starch? I've found that cooking and cooling various things is a nuisance and not appealing to me. I know there are some RS3 commercial product out there, but have yet to research them.

I use food not supplements. Cooking and cooling seems easier to me than cooking everything freshly. I cook a cup of rice or a pack of mung bean noodles and so have several days worth ready to eat in the fridge. I make potato and bean salad and again have several days worth in the fridge.

 

[Interactome]

Secondary metabolites are organic molecules which are not involved in major metabolic pathways such as growth.

So as well as identifying the various bacteria present in a gut sample, uBiome is now identifying bacterial genes which are known to be involved in degradation of the various secondary metabolites listed (along with the various other metabolic pathways now listed under bacterial function).

In the case of dioxin, you have a higher than average number of such genes - ie your gut bacteria have more capacity to degrade dioxin, so this is a good thing.

It is the other end of the list that is of more concern. Genes for fluorobenzoate degradation are very low, so you will be getting little help from your gut microbiota in dealing with this compound.

These results are just dealing with capacity of gut bacteria - they say nothing about the human capacity for degradation of these same molecules.

Ok. Thank you. What if the extra dioxin genes represent an adaptation of the microbiome to cope with an increased dioxin load?
I don't know much about the microbiome, but wouldn't most compounds be absorbed in the stomach/ upper small intestine where there aren't any bacteria, so perhaps they do not do that much to protect one from those compounds?

 

[alicec]

What if the extra dioxin genes represent an adaptation of the microbiome to cope with an increased dioxin load?

Well I suppose that's possible but then presumably there would be increased exposure. Do you have reason to think that dioxin exposure is a problem for you?

but wouldn't most compounds be absorbed in the stomach/ upper small intestine where there aren't any bacteria, so perhaps they do not do that much to protect one from those compounds

Nutrients from food are absorbed primarily from the small intestine but various other substances are absorbed throughout the length of the GIT.

Bacteria are naturally present in the stomach and small intestine, though at much lower levels than in the colon. It is still very early days in understanding the role in the upper GIT and even though more is known about the role of the colonic bacteria there is much still to be understood there also.

Still there are many examples where colonic bacterial products have a systemic effect in the host - eg SCFAs, vitamins, neurotransmitters (in the latter case travelling from the ENS to the CNS via the vagus nerve).

At this point I have no idea of the relative contributions to host metabolism of the various bacterial pathways which uBiome is now identifying. It is something which I have promised myself I will research, but haven't done it yet.

 

[Interactome]

Well I suppose that's possible but then presumably there would be increased exposure. Do you have reason to think that dioxin exposure is a problem for you?

I don't know. I'm just questioning everything and trying to understand what's going on with me. It would be helpful to have a histogram showing the distribution of the data, and what are the min and max. 1.31X doesn't tell me that much. I asked and they said that they'll provide more info in time.

I'll have to look into this more also.

Thanks for your help

 

[alicec]

It would be helpful to have a histogram showing the distribution of the data, and what are the min and max.

The abundance of the genes reflects the abundance of the bacteria expressing them. Since there is no "right" pattern of bacterial abundance and a great deal of redundancy, I suspect the range would be very broad. I doubt that 1.31X would be very different from 1.

I'd be thinking about the absence of genes and what that might mean.

 

[Biarritz13]

Hi everyone!

I did a Ubiome test that I converted into an Excel file.

Unfortunately in the species this is what appears:

• Bacteroides vulgatus
• Bacteroides fragilis
• Bacteroides thetaiotaomicron
• Methanobrevibacter smithii
• Parabacteroides johnsonii
• Slackia sp. NATTS
• Dorea formicigenerans
• Adlercreutzia equolifaciens
• Faecalibacterium prausnitzii
• Odoribacter splanchnicus

This is my phylum:

• Firmicutes 74.3%
• Bacteroidetes 23.6%
• Verrucomicrobia 1.2%
• Actinobacteria 0.37%
• Proteobacteria 0.3%
• Euryarchaeota 0.24%
• Lentisphaerae 0.01%

Do you all see Bifidos in your species or?
If somebody has any insight...Thanks

 

[*GG*]

Oh, I have a good cartoon on this

 

[alicec]

Do you all see Bifidos in your species or?

The species identification is not complete because of technical limitations, that's why it's not reported on the website.

If you sort by genus you will get a more complete view.

What you do show for species all looks good as does the phylum breakdown, apart from low actinobacteria (the phylum which bifidobacteria belong to).

You may well be low on bifido, but join the club. I've been supplementing various bifido strains for years but still have only very low levels, despite assiduously trying to supply the things they like to eat!

 

[helen1]

@alicec Could you tell us what you've learned about what bifidos like to eat? I'm in the same boat...

 

[alicec]

Could you tell us what you've learned about what bifidos like to eat?

Starch - ie resistant starch - is the preferred substrate in the adult. Also starch hydrolysates such as maltodextrins, then FOS and GOS.

In infants, human milk oligos are the substrate sustaining their relatively high numbers.

EDIT to add. Some but not all strains can ferment longer chain inulins.

GOS is a very poor substitute for HMOs.

 

[Biarritz13]

The species identification is not complete because of technical limitations, that's why it's not reported on the website.

If you sort by genus you will get a more complete view.

What you do show for species all looks good as does the phylum breakdown, apart from low actinobacteria (the phylum which bifidobacteria belong to).

You may well be low on bifido, but join the club. I've been supplementing various bifido strains for years but still have only very low levels, despite assiduously trying to supply the things they like to eat!

Hi Alice,

Thank you for your reply

I wasn't aware bifido belongs to actino, I thought it was another phylum!

May I know what kind of probiotics have you used these past years?

Elixa sounds nice, I think I am gonna order it.

 

[alicec]

I wasn't aware bifido belongs to actino

If you look on the family tree on the website it will show you the relationship of all the genera in your gut.

Also it lists them all, grouped from phylum to genera, under all my bacteria as well as showing how you compare with others.

Note that they only make the comparisons and show the family tree for the genera you have. They don't show a total picture of the average gut. I think this is bizarre but that's how they choose to report.

May I know what kind of probiotics have you used

Mostly I use Vivomixx (formerly called VSL3). I've been taking it daily for years.

Like the Elixa (which I have not encountered before), it has a very high count (450 billion) and many of the same organisms, though the Elixa has a couple which have very good reputations (Lactobacillus reuteri and rhamnosis) which are not in Vivomixx.

I might be inclined to try the Elixa though am a bit put off by the price. I thought Vivomixx was expensive at AUD 120 for 30 sachets. Even if I buy in bulk and get the cheapest rate, the Elixa is AUD179 for 24 sachets.

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

Recently I put this to the test by following uBiome tests before and after a period without VSL3. During the without period I had a large overgrowth of Kluyvera, one of the potentially problematic gamma Proteobacteria family. Of course I don't know that there is a causal relationship, but I don't want to take the risk, so I keep taking the Vivomixx.

My impression is that the daily probiotic helps me to hold my own so to speak in the gut stakes. My gut is far from ideal (after a lot of antibiotics) but it doesn't get worse and there are some improvements if I maintain a diet rich in MACS (microbiota accessible carbohydrates).

 

[Biarritz13]

Elixa has also 2 more Bifido bacterias than Vivomixx.

I mean if you took it during years either 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...

In Vivo ScFOS is much more potent than other prebiotics
Actilight Scientific Evidence
Enhancement of gut Immune Functions by Short-Chain FOS

I did order a ScFOS prebiotic (Nutraflora) and I am still waiting for it...