OAT, PLEASE INTERPET

[alicec]

There are thousands of species residing in the gut. How would one know who the key players are and how would you reseed them? What do you think of fecal transplants?

There are many species but there is a hierarchy when it comes to tackling food sources. A very few are keystones, ie necessary for making resources available to a wider group of organisms.

Here is a post I made about it.

There also seems to be some sort of ancestral core of organisms. Outside of these relatively few, there is huge diversity and the redundancy I mentioned previously.

Missing some of the keystones or important core is going to be be much more problematic than missing the others.

I seem to be missing Ruminococcus. So far nothing I have done has influenced this. Way back I considered FMT but given my sensitivity to influencing the gut flora through prebiotics, I thought this could be a disaster.

18 months down the track and knowing a lot more about what is going on in my gut ( including that it is not too bad given past antibiotics, but seems to be stuck in a holding pattern), I decided to make one more concerted effort to try to significantly influence flora balance but a vigorous prebiotic program. This time around I am tolerating them well and results are moving in the right direction. It took a while to get up to decent doses so the really telling gut analyses are still to come.

Maybe by the end of the year I'll be in a position to decide if I should reconsider FMT in order to replace the missing flora, or if indeed they are there at low levels but needed the right stimulation.

FMT is a very crude tool. What we really need is targeted probiotics, the kind that don't yet exist. I did read a paper a few months ago which gives me hope that this could be coming in the not too distant future. Researchers have found ways to culture many of the "unculturable" anaerobes and have found also that many form spores. The latter could be a way of preserving the organisms and formulating them into probiotics.

 

[Jimbo39]

organisms.

Here is a post I made about it.

Since I seem to be low in the primary degraders (bacteroids, firmicutes), would this be a possible cause of inflammation i.e. Undigested food particles? Hence your suggestion for BetaineHCL?

I can see what you mean by the hierarchy of digestion. If the primary and similar-primary degraders are not capable of doing their jobs then the vast majority of microbes cannot be supported. Would this cause them to starve?

 

[Jimbo39]

Researchers have found ways to culture many of the "unculturable" anaerobes and have found also that many form spores. The latter could be a way of preserving the organisms and formulating them into probiotics.

Maybe that's why soil based bacteroids, like those in PrescriptAssist, are becoming popular because many of them are in spore form?

 

[Jimbo39]

similar-primary degraders

I hate autocorrect. i meant simi primary degraders.

 

[Jimbo39]

My gut seems to be happy, well, happier. Would one notice a response so quickly? Maybe it's psychosomatic.

 

[Jimbo39]

I'm looking at gut/digestive issues from an ancestral viewpoint. My mom is Japanese, dad of European decent. Japanese being Budist for at least a thousand years, eschewed animal meat with the exception of fish. Probably their main source of protein came from soy (tofu, miso soup, etc). Of course, they ate a lot of rice and as a result have developed a larger pancreas than Europeans. Other grains were probably nonexistent. They eat a lot of fermented foods the most popular being Nukazuki, pickled vegetables fermented with rice bran powder and Koji (red rice yeast). Koji is also used to make miso, soy sauce and sake. Miso is a common breakfast meal. They also eat a lot of seaweed products the most popular being Gyokuroen Ume Konbucha (made from kelp) and Nori (dried seaweed).

I'm wondering how much genetic traits I've picked up from mom. For instance, I was allergic to eggs and dairy when I was young. As I got older, I have issues with dairy so perhaps my gut had always been allergic but I chose to ignore the symptoms. I've always craved carbs more than protein. I was just eating the wrong kind of carbs. I'm not sure what to make of this or how changing my diet would help. Perhaps an elimination diet would give me more insight.

 

[Jimbo39]

@alicec I read the first page of dannybex's thread on the benefits of folinic acid and there seems to be two viewpoints on whether to supplement with this or not. Freddd doesn't advocate it because of a possibility of causing a paradoxical folate deficiency. On the other hand, I read that folic acid along with l-methyfolate, and SAMe is needed to convert BH2 to BH4. I personally would rather on err on the side of caution. Does metafolin convert to folic acid?

 

[alicec]

Freddd doesn't advocate it because of a possibility of causing a paradoxical folate deficiency.

Some people seem to react adversely to folinic acid. The reason is not understood but presumably it has something to do with the two enzymes which act on it - MTHFS and SHMT. If it not being processed and so accumulates it can inhibit SHMT (maybe other enzymes also, not sure) and this in turn can affect the folate pathway adversely.

As I recall Freddd reacted badly to folinic. At least as a starting point, until your reactions to the active B12 protocol is clear, avoiding folinic is a precautionary step.

Folinic acid is a storage form of folate and can feed into folate pathways other than the methionine synthase path that converts methylfolate to THF. People have suggested that it could be a useful addition to folate supplementation, particularly if there is difficulty at methionine synthase. This may well be so, PROVIDED THAT it can be processed and there is no way of knowing this in advance. It has to be tested empirically.

I read that folic acid along with l-methyfolate, and SAMe is needed to convert BH2 to BH4. I personally would rather on err on the side of caution. Does metafolin convert to folic acid?

That's not quite right. SAMe has nothing to do with converting BH2 to BH4. It is involved when BH4 is used to make neurotransmitters - maybe there is some conflation of ideas here.

Folic acid is a laboratory creation, it plays no role in our metabolism. We can convert it into a usable form (dihydrofolate, DHF) with the enzyme dihydrofolate reductase (DHFR) albeit slowly and for some people very poorly.

DHFR doesn't exist to convert folic acid to DHF, despite what manufacturers of folic acid would have us believe. Because of structural similarities it can make the conversion, though not well.

The normal role of DHFR is to convert DHF to tetrahydrofolate (THF), which then feeds into various aspects of the folate cycle. DHF is the product of thymidylate synthase - ie it is formed as part of the nucleotide synthesis function of the folate cycle.

As part of the reaction in which DHF is converted to THF, BH2 is converted to BH4.

Methylfolate is not involved directly in this reaction. It is used by methionine synthase, in the process being converted to THF, which then enters the folate cycle and among other things, can end up as DHF.

The other indirect link is that methylfolate is a peroxynitrile scavenger and so can have a BH4 sparing effect. Studies have shown this property to be very important in protecting the activity of BH4 with the NOS enzyme.

You will find claims that methylfolate directly regenerates BH4 when the MTHFR enzyme runs backwards. These largely originate from Yasko's misreading of research studies. MTHFR does not run backwards.

 

[Jimbo39]

That's not quite right. SAMe has nothing to do with converting BH2 to BH4. It is involved when BH4 is used to make neurotransmitters - maybe there is some conflation of ideas here.

Folic acid is a laboratory creation, it plays no role in our metabolism. We can convert it into a usable form (dihydrofolate, DHF) with the enzyme dihydrofolate reductase (DHFR) albeit slowly and for some people very poorly.

Whoever made this chart must be trying to sell folic acid ans SAMe.

 

[Jimbo39]

The other indirect link is that methylfolate is a peroxynitrile scavenger and so can have a BH4 sparing effect. Studies have shown this property to be very important in protecting the activity of BH4 with the NOS enzyme.

So methylfolate not only reduces oxidative stress but also "spares" BH4 to be used in the production of NTs?

Could you provide a link that would help me understand the folate cycle i.e. the interaction of amino acids, enzymes, minerals, vitamins?

BTW, Medical Insider helped tremendously in understanding my gut issues.

 

[Jimbo39]

I've been reading Medical Insider's post on the mitochondria. I'm starting to question my low sugar paleo diet. ATP needs a steady supply of glucose to function. While it may be true our ancestor's diet consisted mainly of animal fat, my reference to the Japanese developing a larger pancreas due to a heavy carb intake, seems to suggest that genetic changes can occur within a thousand years if not sooner.

I wonder if the epidemic of diabetes may stem from other factors, refined flour, processed foods, additives? Probably a compromised HTP may play a role as well. This will be study in itself.

It's true that too much sugar, especially simple, processed sugar, will tax the pancreas, maybe glucose obtained from fruit and sugar bearing vegetables may not have this effect?

 

[alicec]

Whoever made this chart must be trying to sell folic acid ans SAMe.

And/or has a poor grasp of biochemistry and can't read a metabolic diagram. Yasko has a lot to answer for in this respect. She seems to have kicked off a lot of the myths about BH4 and its links to the folate cycle. Her misreading of research and diagrams has been endlessly repeated.

 

[alicec]

Could you provide a link that would help me understand the folate cycle i.e. the interaction of amino acids, enzymes, minerals, vitamins?

Here are two diagrams which may help.

The folate cycle energy path was posted by a PR member @Kimsie. She was trying to emphasise a little known aspect of the cycle, namely that it can be used for energy production (production of ATP and NADPH ), though this is usually in adverse circumstances and at some cost to other pathways. She has made detailed posts on various aspects of metabolism if you want to search PR, though it may be more info than you really want to know about.

This diagram shows vitamin cofactors for the various reactions (no minerals) and amino acid involvement, namely the homocysteine to methionine conversion done by the MTR enzyme, serine to glycine conversion done by SHMT, and the less well known glycine cleavage reaction in which glycine is converted to ammonia.

The folate cycle is very complex and diagrams often omit or abbreviate some part of it. This diagram is pretty comprehensive, but doesn't show where folinic acid fits in.

The second diagram, the folate cycle, does show this, plus the mineral cofactors. The other name for folinic is 5 formyl THF and you will see the folinic interconversion shown as a side branch from 5,10 methenyl THF.

Please note that the diagram implies that vegetable folates are similar to DHF. This is not quite right. Some may be, but analysis I have seen of various leafy greens shows that more are in the form of methylfolate and to a lesser extent, folinic. It does vary between vegetables and I haven't looked at this in great detail, nor is it important for understanding the folate cycle. It is just something I considered briefly since there is so much contradictory information about vegetable folates.

 

[alicec]

I wonder if the epidemic of diabetes may stem from other factors, refined flour, processed foods, additives

There is a lot of evidence to support this idea. Carbs as such are not the problem so much as concentrated carbs minus their natural fibre-rich matrix.

I found the Jaminet's book on the Perfect Health Diet very helpful. Here is the website. They are still talking about a lowish carb diet but one that includes things like starchy and sugary vegetables and some fruit. Refined sugars and grains are most definitely out.

They do enter the controversial topic of legumes and nuts and seeds and in general come out against. Most of their concern is for soybeans. In the end I decided that these are such valuable foods that small amounts were worth including (provided legumes are properly prepared, and not soybeans, though fermented versions like tofu might be acceptable).

In the end we have to find a diet that suits us as individuals. The principle should be, however, that it is based on real food, stuff that our grandparents and great grandparents would recognise as food, and is very rich in a wide variety of vegetables and moderate amounts of fruits.

 

[Jimbo39]

Thank you for this and thank you @Kimsie.

The folate cycle is very complex and diagrams often omit or abbreviate some part of it. This diagram is pretty comprehensive, but doesn't show where folinic acid fits in.

Yes, I can see that. It's going to take me many days to understand this. I don't even know what the abbreviations mean much less those unpronounceable words.

 

[Jimbo39]

In the end we have to find a diet that suits us as individuals. The principle should be, however, that it is based on real food, stuff that our grandparents and great grandparents would recognise as food, and is very rich in a wide variety of vegetables and moderate a

I agree. We've moved away from organic, fresh vegetables since the advent of mechanistic, mass production of food. Of course this relies heavily on pesticides and additives. On that note did you know the American Association of Homeopathy is much older than the American Medical Association? Well, you probably wouldn't since you're from down under. But it's probably true in your country as well. Anyway, the AAH got pushed to the fringes (even discredited) by "modern" medicine. I'm not saying one is better that the other. I think both have a useful place.

 

[Jimbo39]

Correction: I meant the American Institute of Homeopathy.

 

[Jimbo39]

fermented versions like tofu might be

I don't know if you eat tofu, but it is not a fermented product. It is soy "juice" with a thickening agent. I say away from soy products as well with the exception of miso (fermented). I don't use soy sauce because of its propensity to cause glutamate excitability.

 

[alicec]

I don't even know what the abbreviations mean much less those unpronounceable words.

The abbreviations are the names of enzymes. You don't need to know the full name though it is easy enough to look up if you want to. You can see from the diagrams what the enzymes do and where they fit into the overall scheme of things.

You don't need to be able to pronounce the names either!

 

[alicec]

I don't know if you eat tofu, but it is not a fermented product. It is soy "juice" with a thickening agent

I don't eat tofu but thought that traditional tofu was fermented. I can well imagine that industrial tofu is artificially thickened, but it seems that it all is. Thanks for letting me know.