Nature Article Uses ME/CFS to Examine The Microgenderome

[A.B.]

If the same holds true for humans, it's easy to see why each generation is becoming more obese and sicker. The derangement in the gut microbiome would be more intractable if you are born to a sick mother.

Another likely reason is the herbicide glyphosate in foods. It kills plants by interfering with the shikimic acid pathway. Since humans don't have a shikimic acid pathway, glyphosate was believed to be safe for them. It turns out that about 70% of bacterial species in our gut uses the shikimic acid pathway.

 

[Sidereal]

Another likely reason is the herbicide glyphosate in foods. It kills plants by interfering with the shikimic acid pathway. Since humans don't have a shikimic acid pathway, glyphosate was believed to be safe for them. It turns out that about 70% of bacterial species in our gut uses the shikimic acid pathway.

Yes, by introducing various industrial toxins and antibiotics whose effects we did not understand at the time we've created mass extinctions in our guts and now we're paying the price. We're now only beginning to understand the roles that all these bacteria play in our metabolic processes. In the meantime we're all taking part in a mass uncontrolled experiment inflicted on the population by the arrogant medical profession and governments and now our healthcare systems are going to bankrupt us and the diseases of civilisation might kill us all before we figure out how to reverse this catastrophe.

 

[MeSci]

Another likely reason is the herbicide glyphosate in foods. It kills plants by interfering with the shikimic acid pathway. Since humans don't have a shikimic acid pathway, glyphosate was believed to be safe for them. It turns out that about 70% of bacterial species in our gut uses the shikimic acid pathway.

That's interesting. Do you have any links, for example that show when it was discovered that human gut bacteria use the shikimic acid pathway?

 

[MeSci]

Yes, by introducing various industrial toxins and antibiotics whose effects we did not understand at the time we've created mass extinctions in our guts and now we're paying the price. We're now only beginning to understand the roles that all these bacteria play in our metabolic processes. In the meantime we're all taking part in a mass uncontrolled experiment inflicted on the population by the arrogant medical profession and governments and now our healthcare systems are going to bankrupt us and the diseases of civilisation might kill us all before we figure out how to reverse this catastrophe.

I wonder whether this type of overlooked pathway could explain chemical sensitivity?

 

[Gemini]

Does anyone know how to get these microbiome or gut tests in the U.S.?.... Does it require a doctor to order and interpret the tests? .

Anyone can order ubiome tests online at www.ubiome.com & receive self-test kits mailed to their homes.

They're currently offering a 5-site testing kit--gut, mouth, nose, skin & genital microbiomes -- for US$89 valid through 1/17/2016 at midnight. Use discount code "5FOR1JAN" at checkout. You access your test results online.

Like @alicec I think ubiome results are interesting. Their website is easy to use I find.

Their science team posts blogs about microbiome discoveries like "Does Your Microbiome Sleep?"

www.ubiomeblog.com

 

[alicec]

Are you finding that the ubiome test gives you actionable information or just information that is interesting?

I answered this in a hurry previously - was getting tired.

It is mainly interesting info but it can be broadly actionable. Mainly this comes from looking at changes in pattern that result from dietary or other changes - ie retrospectively. Because so little is known this is not an exact assessment - and it is only with time and accumulating a number of tests that I think I am beginning to see things.

I decided I needed to do monthly tests for quite some time in order to understand these patterns. This is not such an expensive exercise since uBiome often offers specials.

I ignore the 5 different sites specials - I don't have the energy to try to work out what data from all the sites means - though the microbiome from the other sites is much less complicated than the gut.

There are often 3 for 1 gut test specials also.

Are these the tests offered by Red Labs in Belgium or somewhere different?

The Red Labs test is like the uBiome and American Gut tests but I don't know any more than that.

 

[alicec]

It seems to be giving further support to my belief that it is better to use diet/prebiotics to bring the gut microbiome into balance, rather than probiotics

Probably we need them all but most of the available probiotics just don't contain species and strains that colonise the gut.

Still there might be other reasons to take probiotics - like flooding the gut with benign organisms to prevent something nasty from taking up residence. With this in mind, I started taking VSL3 (now called Vivomixx; a very high dose mixture containing some 450 billion organisms per dose) daily some years ago when I undertook a very nasty antibiotic treatment to eliminate Blastocystis.

Several years later I took another nasty antibiotic combination for more than 12 months (for Borellia and Bartonella infection). Regular gut tests (culture-based) showed no real nasties appearing in the gut so I just continued to take the VSL3.

More recently I found another reason to continue taking VSL3, viz, it helps deal with oxalate problems.

Early last year I got completely fed up with taking expensive VSL3 which was apparently doing nothing to change my gut imbalances, as seen in uBiome tests, so stopped taking VSL3 and started experimenting. To cut a long story short, the period of several months without VSL3 and with only relatively small amounts of various other probiotics caused a lot of deterioration (overall and in the gut).

My oxalate problems flared up and I saw a huge change in my uBiome test. Proteobacteria (mainly in the form of Kluyvera) skyrocketed and Firmicutes were greatly depleted. Once I added back the VSL3, the pattern gradually normalised, though it took till the end of the year and several more tests to really see this.

I might add that of course I don't really know that the changes to VSL3 were responsible for the gut changes but the timing seems very suspicious so I'll continue to think that it is likely until something else happens to change my mind.

So for now at least I'll keep taking VSL3 and do any experimenting with probiotics in addition!

 

[Gingergrrl]

The Red Labs test is like the uBiome and American Gut tests but I don't know any more than that.

How does someone in the U.S. do the UBiome or the American Gut test? I mentioned Red Labs b/c it is the only one I have ever heard of. For the ones in the U.S., do you know if they need to be ordered by a doctor who interprets them and prescribes treatment?

Thanks to anyone who knows the answer!

 

[alicec]

I'm not overly optimistic about our prospects of being able to fully restore a healthy microbial community with diet & prebiotics only

I agree, we need better, more targeted probiotics, a next generation FMT, in addition to diet and prebiotics.

Still my experience over the past year or so combined with tracking by uBiome gives me some hope. I think my gut started out reasonably (vaginal birth, breast feeding), no childhood antibiotics, although my mother did have a mysterious waxing and waning illness which I strongly suspect might have been ME/CFS - so maybe not!

Certainly I never had any gut problems and was a healthy child. I took a lot of antibiotics in my 20s and 30s (for what I now believe was a chronic Chlamydia pneumonii infection and likely the beginning of my ME/CFS) and again in my 40s and 50s (as in the post above).

From my first uBiome test it was clear that lack of diversity was a big problem. I simply didn't have many of the known important genera, or had them in tiny amounts, and the minor phyla were absent.

I tried various concentrated prebiotics but proved to be very sensitive to them, as well as to many probiotics (apart from VSL3) so I have mainly concentrated on diet and incorporating as many MACS as possible that way. (I do intend to revisit concentrated prebiotics at some point but have too many other things to deal with now - so it will be later).

With time the diversity has improved a bit (though still don't have any of the minor phyla) but the distribution of genera is normalising. Some genera which were absent have started to appear consistently and increase in number - eg Bifidobacterium. Some changes have been quite astonishing - eg in Faecalibacterium , the 2nd most numerous gut constituent on average and the most numerous Firmicutes (av 9.9%). From undetectable, it first appeared at fluctuating low levels but at the last test was 14.2% (things seem now to have gotten out of hand but I imagine with time will settle).

So change is possible. I still seem to be missing some major genera - eg Ruminococcus, but maybe it will just take longer for them to come back. If this doesn't ever come back then that would seem to be a good candidate for some future tailored probiotic treatment (which of course doesn't currently exist - but who knows what may result from the explosion of studies on our microbiome).

I have come to realise it will take a long time to get perspective on gut changes but I think it is worth the effort and so will continue with the uBiome tests (now monthly).

 

[Sushi]

Does anyone know how to get these microbiome or gut tests in the U.S.?

Genova has some of these tests, though maybe not as comprehensive.

Does it require a doctor to order and interpret the tests? Are there doctors who know which kinds or probiotics someone might benefit from or is it all still guesswork?

The ones I have had require a doctor's order. A comprehensive microbiome test that is competently read, should show what type of probiotics a person would benefit from.

Are these the tests offered by Red Labs in Belgium or somewhere different?

RedLabs is also in the US now and should be offering the same tests. I don't know if they are up and running yet though: http://www.redlabs.com/

 

[alicec]

How does someone in the U.S. do the UBiome or the American Gut test?

As @Gemini said, just go to the website and order a collection kit, take sample as instructed and send back to the lab. You don't need a doctor to order it.

Knowing what the results mean is the difficult part. There is no interpretation and no-one will tell you what to do with them, though there is some useful info on the website. You have to work at understanding the results, do your own research unfortunately.

 

[alicec]

Genova has some of these tests, though maybe not as comprehensive.

I think the Genova test is pretty useless as discussed here.

A comprehensive microbiome test that is competently read, should show what type of probiotics a person would benefit from.

I've never found such a beast. What tests are you referring to and?

 

[Gingergrrl]

As @Gemini said, just go to the website and order a collection kit, take sample as instructed and send back to the lab. You don't need a doctor to order it.

Knowing what the results mean is the difficult part. There is no interpretation and no-one will tell you what to do with them, though there is some useful info on the website. You have to work at understanding the results, do your own research unfortunately.

Thank you and I totally missed that post from @Gemini b/c I started reading later in the thread so am glad you pointed it out to me. Thank you @Sushi for the info as well.

It's a bummer that you have to interpret the results yourself if you don't have a doctor to do it b/c I would have no clue what to do. If left up to myself to interpret, I probably would not bother just b/c I lack the skills.

 

[Gingergrrl]

I think the Genova test is pretty useless as discussed here.
I've never found such a beast. What tests are you referring to and?

Thank you and I have found Genova tests fairly useless in the past myself even when ordered by my former naturopath b/c she did not know what to do with the results and tried to sell me her own supplements regardless. I no longer see her but at the time it wasn't helpful. If there was a doc who knew how to interpret the tests and prescribe or recommend probiotics (knowing I have MCAS and don't tolerate a lot of stuff), I would love to find that person!

 

[Sushi]

I've never found such a beast. What tests are you referring to and?

I'm referring to RedLabs MSA which tests the DNA of about 74 bacteria, the various types of balances between them and other things I can't remember without looking it up. It shows deficiencies and over-growths and a knowledgeable (that is the key word!) doctor should be able to see what type of probiotic a patient would benefit from. But, there are few such docs.

 

[Richard7]

The data that came back from bioscreen was pretty complete. Mine came back recommending which antibiotics to use, changes in diet, to supplement with betaine hcl and bile salts and recommendations for probiotics.

If you have a look at healthscope's tests (offered here in Oz) they say that they test overgrowths against antimicrobials
here is the sample report on their website www.healthscopepathology.com.au/index.php/download_file/view/168/204/
at the end they recommend a bunch of antimicrobials, 1 fibre, and 4 probiotics.

Their advice may well be wrong, for all I know, and for all they know given the bacteria they are not able to test as discussed above, but they do make recommendations.

And for me the recommendations I got (from bioscreen) about bile salts and betaine hcl were really useful. At the time (2004) I was unable to get them in Australia and eventually gave up and forgot about it, but when I realised that I could order them from the states and started taking them it made a huge difference.

 

[adreno]

I'm not overly optimistic about our prospects of being able to fully restore a healthy microbial community with diet & prebiotics only.

I agree; this isn't going to work. One problem is that prebiotics, while feeding the good guys, also feed bad guys like kleb and fungi. With not enough healthy microflora to keep it in check, it's a recipe for disaster. We need FMT.

Interesting that the study you posted suggested the use of FMT + prebiotics. Earlier research on FMT in humans have shown the effects to not last, this might be because the new microflora wasn't supported with diet (prebiotics).

 

[alicec]

I'm referring to RedLabs MSA

Yes I looked at RedLabs. Their test uses the same techniques as uBiome, offers less analysis and is far more expensive, even without the requirement to ship within 72 h (ie add cost of courier for most of us). The latter is really unnecessary since it is DNA that must be preserved in the sample, not organisms.

As Red Labs themselves say, they are a research laboratory and don't interpret the tests. You need a health-care professional for that.

It's a bummer that you have to interpret the results yourself if you don't have a doctor to do it b/c I would have no clue what to do. If left up to myself to interpret, I probably would not bother just b/c I lack the skills.

Much as I rail against the uselessness of the medical profession, in this case I think it would be quite unreasonable to expect any doctor to interpret these microbiome analyses. It is still cutting edge stuff and we don't know what a lot of the information really means. Even scientists in the thick of the research would talk only in fairly general terms. And unfortunately existing probiotics are almost exclusively variations on Lactobacillus and/or Bifidobacterium which are only very minor parts of the complex ecosystem, so not a fix for wider imbalances.

Of course you will get plenty of advice about what to do to fix the gut from practitioners using culture-based tests, whether it means much is another issue.

 

[Sushi]

You need a health-care professional for that.

True, my doctor works with the lab for interpretation.

 

[alicec]

One problem is that prebiotics, while feeding the good guys, also feed bad guys like kleb and fungi.

Or is this part of the mythology built upon the completely distorted view of the gut which the culture-based tests promoted?

While I don't doubt the fungal overgrowth can be an issue for some people, with all eukaryotes constituting about 0.5% of the gut microbiota, how much of an issue is it really in face of the 93% bacterial component?

As for Klebsiella, as I mentioned here, my moderate level on a culture test did not compute when the total gut bacterial content was analysed. I did not then and more than 12 months later, do not now have any detectable Klebsiella. Other organisms on the culture tests didn't compute either.

I've been trying to get as many prebiotics into me as possible (mainly in the form of food) over the past year or so and have been following what is going on in my gut. The only time that I have seen a distortion that I would consider adverse, ie overgrowth of Proteobacteria as discussed here (mainly increase in Kluyvera, a significant normal gut constituent at 3.2% on average) it didn't follow any change in prebiotics. Overall what I have seen is improvement.

We need FMT

FMT has been available for quite some time now. I considered it very seriously and eventually decided against it. I haven't been following it closely lately but there has been time enough to accumulate data on significant numbers of patients. Do you know of any studies which properly evaluate its usefulness?

In theory I like the idea of FMT, in practice I think I would rather wait until it can be done in a more considered and targeted way.

It is a bit like the people who deliberately infect themselves with hook worm in the hope they will induce changes in their immune system which will halt or reverse their out of control IBD. In the meantime back in the lab scientists are trying to unravel what those immune changes are so they can develop a better way of inducing them. If one were desperate, hook worm infection might seem like the only option. Likewise FMT.