Nature Article Uses ME/CFS to Examine The Microgenderome

[Gingergrrl]

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.

@alicec I truly lack the science on this to even give an intelligent response so please forgive me in advance! I was trying to sort out in my brain if these microbiome tests (I think they are the same as the gut dysbiosis tests but correct me if I am wrong) are something available to the lay person without a doctor to order, like 23andMe, or if they require a doctor to order, interpret, and recommend treatment?

I am now getting the sense that this is truly still in the research stage and is cutting edge with maybe only a few doctors worldwide who can interpret the results (let alone order the tests.) I've tried many probiotics and the one I took the longest was S. Boulaardi (but not sure where this one fits in the scheme of things.) I briefly tried Align/Bifido Infantis and prior to becoming really ill, I tried all kinds of random probiotics.

Can you explain what is the difference between these tests and the culture based tests that more traditional doctors order? I saw an "Integrative GI doc" about two years ago when I was still well enough to walk without wheelchair and he did a stool test for things like H Pylori, Candida, etc, plus a SIBO test and I was told all were normal. Do any of these relate to the microbiome test or are they in a totally different league?

No info is too basic for me, I am a complete novice here!

 

[Richard7]

@Gingergrrl

The things you can do as a lay person is go to either American gut https://fundrazr.com/campaigns/4Tqx5 http://humanfoodproject.com/americangut/ or ubiome http://ubiome.com/

Ubiome is commercial, American Gut is not, its lab is at UCSD. American gut is a little more expensive.

One of the articles I found reading about on the American Gut site explains:

16S rRNA is a sort of telescope through which we see species that would otherwise be invisible. Let me explain. Historically, microbiologists studied bacteria and other microscopic species by figuring out what they ate and growing them, on petri dishes, in labs, in huge piles and stacks. On the basis of this approach — which required great skill and patience — thousands, perhaps hundreds of thousands, of studies were done. But then ... in the 1960s, biologists including the wonderful radical Carl Woese, began to wonder if the RNA and DNA of microbes could be used to study features of their biology. The work of Woese and others led to the study of the evolutionary biology of microbes but it also eventually led to the realization that most of the microbes around us were not culturable — we didn’t know what they ate or what conditions they needed. This situation persists.

No one knows how to grow the vast majority of kinds of organisms living on your body and so the only way to even know they are there is to look at their RNA. There are many bits of RNA and DNA that one might look at, but a bit called 16S has proven particularly useful

http://humanfoodproject.com/wp-cont...-gut-from-Evolutionary-Biologist-Rob-Dunn.pdf

The difficulty with these tests is that you are a research subject in a crowd funded project. They are trying to work out what is going on not trying to give you advice about how to become well.

Well the last is not entirely true, they have blogs, TED talks etc explaining their findings.
http://www.ted.com/talks/rob_knight_how_our_microbes_make_us_who_we_are
http://ideas.ted.com/how-microbes-define-shape-and-might-even-heal-us/

The problem we and our doctors face is that they know a lot about the old cultured tests, they were the standard faecal tests until very recently. As alicec explained they missed most of what was going on in the gut so the science based on them is suspect.

This nature article is an example science based of this older sort of test (the tests were done between 2011 and 2013. Ubiome only started in October 2012 and I think the American Gut project started about the same time.

 

[Gingergrrl]

Ubiome is commercial, American Gut is not, its lab is at UCSD. American gut is a little more expensive.

@Richard7 Thank you and will read through all of this info tomorrow and really appreciate it. Do you know if UCSD has doctors/clinicians who see patients in person re: these tests or if it is purely research? I have not read the links yet in case it explains this.

 

[Richard7]

@Gingergrrl

I think it is just purely research.

I should also note that these tests are just bacteria. The American Gut project has much more expensive tests that look at viruses and fungi but the basic ubiome of american gut project is just bacteria.

The cultured tests also test for bacteria, parasites and fungi, but miss most of them for the reasons mentioned by Rob Dunn (in my previous post) though I am not sure if this applies to parasites. The cultured tests I have looked at also test for other things such as short chain faty acids and biochemical markers to see if your pancrease is working properly.

 

[MeSci]

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

I'm glad you said that. I thought that prebiotics were essentially food substances, but people have been citing supplemental sources of them and I was starting to doubt my memory.

This page gives what looks like a good definition of prebiotics:

Prebiotics are defined scientifically as "selectively fermented ingredients that result in specific changes in the composition and/or activity of the gastrointestinal microbiota, thus conferring benefit(s) upon host health." They are non-digestible carbohydrates (mainly oligosaccharides and non-starch polysaccharides) which act by promoting the growth and/or activity of probiotic bacteria in the gut. The most common are fructo-oligosaccharides (FOS), inulin and galacto-oligosaccharides. They are found in various vegetables and fruit such as tomatoes, onions, garlic, leeks, asparagus and bananas. Prebiotics are relatively stable and, unlike probiotics, can be relied on to arrive relatively unchanged in the gut despite the presence of digestive enzymes.

 

[Richard7]

Hi MeSci

when I was trying to get my head around this I found this page useful.

http://www.vegetablepharm.blogspot.com.au/p/dietary-fiber-info.html

Personally I get about 50-75g of fibre from food most days and also have recently been taking some mucilage (marshmallow root "tea" and slippery elm bark), at the moment I am really liking the mucilages, but its only been 2 or 3 weeks.

 

[adreno]

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

Maybe. But the collective experience of PWME here on PR using prebiotics have not impressed me. There are very few who have significantly improved, and lots more who don't seem to tolerate them.

I am personally beginning to suspect that fungi is playing a part in my disease; there are just so many patterns pointing to this, and I believe Lipkin has hinted at fungal involvement also. But this is perhaps for another thread.

I am somewhat skeptical of stool tests at present, as they don't seem to be reliable (consistent). Also, if fungi or bacteria are engulfed in a goo of biofilm, they might not show much on a stool test at all.

Regarding FMT, transfusions might be too much of a good thing, but I am less worried about trying poo pills from openbiome, as they can be more lightly dosed. I find it not much more dangerous than trying mutaflor, SBOs or whatever people are trialling.

 

[MeSci]

Hi MeSci

when I was trying to get my head around this I found this page useful.

http://www.vegetablepharm.blogspot.com.au/p/dietary-fiber-info.html

Personally I get about 50-75g of fibre from food most days and also have recently been taking some mucilage (marshmallow root "tea" and slippery elm bark), at the moment I am really liking the mucilages, but its only been 2 or 3 weeks.

From a quick look my diet should be a good source of prebiotics (vegan, lowish-grain, gluten-free, low-sugar, as much as possible organic and/or cooked from fresh).

But a month or so ago I was assailed with an antiviral and an antibiotic while in hospital which, from the state of my bowels when I got home, may have pretty-well cleared out my microscopic friends.

Hence eating some yoghurt at present, in addition to consuming my usual healthy diet again (the hospital 'food' available for vegans was atrocious on this occasion).

 

[alicec]

Can you explain what is the difference between these tests and the culture based tests that more traditional doctors order? I saw an "Integrative GI doc" about two years ago when I was still well enough to walk without wheelchair and he did a stool test for things like H Pylori, Candida, etc, plus a SIBO test and I was told all were normal. Do any of these relate to the microbiome test or are they in a totally different league?

There are three places that do the microbiome testing, American Gut and uBiome in the USA, as @Richard7 has referenced, and RedLabs in Belgium, as discussed by @Sushi. You can order yourself from the first two, you need a doctor's name on the order form for RedLabs.

All of them sequence all bacterial DNA in the sample and so try to identify all bacterial constituents in the gut. They are research based tests which won't lead to specific recommendations about your health problems, though some general conclusions about gut health might be drawn. As well, you need to work at understanding the results.

@Sushi's doctor works with the RedLab people to make such recommendations but I don't know of any other person who does. Someone will eventually set themselves up as a guru but I would be sceptical of such a person. It could just be a repeat of all the nonsense propagated about 23 and me results - ie you would need a good understanding already to know if what the guru is saying is plausible.

Given your poor state of health and lack of scientific knowledge, there may not be much advantage to you in ordering such a test - too much effort for too little direct gain.

All other tests, such as the ones that you have done, are in a totally different league. Some aspects of them may be useful. In this thread I have just been questioning the value of tests which try to identify the bacterial components of faecal samples by growing the organisms in an artificial laboratory situation (culture-based tests), thus increasing their numbers until they can be physically seen and identified. Most gut bacteria just wont grow under these conditions and so are missed. We have been given a completely distorted picture of what is in the gut from using these tests.

 

[alicec]

I am less worried about trying poo pills from openbiome, as they can be more lightly dosed.

Yes I'd be willing to try those also but I didn't think they shipped outside the US. The Centre for Digestive Diseases in Sydney Australia is one of the pioneers of FMT and I know has been trying to develop a poo pill for years, apparently without success. Maybe now that someone else has done it, they will follow and it might become an option for me.

 

[Gingergrrl]

Given your poor state of health and lack of scientific knowledge, there may not be much advantage to you in ordering such a test - too much effort for too little direct gain.

@alicec I totally agree with you and it is not something that I am going to pursue at this time. I just wanted to make sure that it was not something I was missing that could possibly help me but in learning more about it in this thread, it is not something that I have the skills to interpret on my own at this time. Thank you and @Richard7 for taking the time to explain it to me.

 

[Sidereal]

From a quick look my diet should be a good source of prebiotics (vegan, lowish-grain, gluten-free, low-sugar, as much as possible organic and/or cooked from fresh).

@MeSci, with no meat or dairy in your diet and lowish-grain intake, where do you get most of your caloric intake from?

 

[MeSci]

@MeSci, with no meat or dairy in your diet and lowish-grain intake, where do you get most of your caloric intake from?

I don't know. I don't analyse caloric intake, but as long as my weight stays healthy, I assume that it is adequate. I have plenty of coconut oil, which probably contributes a significant proportion of calories. Why do you ask?

EDIT

I assume that vegan milks and cheeses have a not-dissimilar calorific value to their non-vegan alternatives?

 

[Sidereal]

I don't know. I don't analyse caloric intake, but as long as my weight stays healthy, I assume that it is adequate. I have plenty of coconut oil, which probably contributes a significant proportion of calories. Why do you ask?

I ask because once you exclude meat, dairy, eggs and reduce grains there doesn't seem a whole lot left to eat. For what it's worth, although grains are inflammatory for me, if I exclude or reduce them, my energy goes down to zero.

 

[MeSci]

I ask because once you exclude meat, dairy, eggs and reduce grains there doesn't seem a whole lot left to eat.

I guess vegans should all be dead then!

Seriously, I just eat - food! (Vegans dread the all-too-common question "But what do you EAT?" as it is rather tiring and tedious to have to try to remember everything you eat.)

But there are plenty of non-animal, non-grain and minimally-sugary foods. Plenty of calorific veg, nuts, legumes, etc.

 

[Sidereal]

I guess vegans should all be dead then!

Seriously, I just eat - food! (Vegans dread the all-too-common question "But what do you EAT?" as it is rather tiring and tedious to have to try to remember everything you eat.)

But there are plenty of non-animal, non-grain and minimally-sugary foods. Plenty of calorific veg, nuts, legumes, etc.

No offence intended. I was just curious.

 

[Richard7]

@Sidereal that's interesting about the grains.

I know with people doing ketogenic diets there is meant to be a 2 - 4wk period where the body upregulates enzymes etc. So people who just jump in get what they call the low carb flu. And people who want to avoid that low energy state are advised to make gradual changes.

I wonder if there is something similar going on when you switch from readily available carbs to less available carbs and short chain fatty acids from fermented fibre.

And making those changes may be impossible for some dodgy gut microbiomes?

I know that I do sometimes find myself having cravings that I usually just give into. Will power takes energy, and is usually what gets me into trouble, so I have 4 kilos of carots over a weekend, or 500g of dates. And those cravings have sometimes been for bread. I had some in october or september or something but the results were not pretty.

Its not quite your low energy experience perhaps, though I guess I have had that too desiring steamed rice or some such thing. But to my mind it feels the same, this desire that goes on and on and will not go away.

I know that it is Art Ayres argument that if you fix up your gut, and produce enough Treg cells, the inflamation and allergies should go away. http://coolinginflammation.blogspot.com/2014/09/peanut-allergy-cause-and-cure.html
I rather hope he is right.

I also know that there are arguments that some of these cravings are generated by the gut microbiome or members of it.

 

[Sidereal]

@Richard7, you're right, there is a rough transition period (so-called Atkins flu) when you first go ketogenic. I'd been messing around with very low carb diets on and off for a decade prior to my severe ME crash (in which a strict ketogenic diet played an important role) so I'm well-acquainted with this phenomenon. I was talking about a different problem, however. My energy is much lower if I remove grains even if I keep my carb intake from other sources high. Grains contain important prebiotics like xylan and beta glucan which ferment in the distal colon and produce SCFA like butyrate. I've gone 180 on this issue, having previously believed in the paleo myth of grains + legumes = evil, I now think these foods are sine qua non of gut health.

 

[MeSci]

@Richard7, you're right, there is a rough transition period (so-called Atkins flu) when you first go ketogenic. I'd been messing around with very low carb diets on and off for a decade prior to my severe ME crash (in which a strict ketogenic diet played an important role) so I'm well-acquainted with this phenomenon. I was talking about a different problem, however. My energy is much lower if I remove grains even if I keep my carb intake from other sources high. Grains contain important prebiotics like xylan and beta glucan which ferment in the distal colon and produce SCFA like butyrate. I've gone 180 on this issue, having previously believed in the paleo myth of grains + legumes = evil, I now think these foods are sine qua non of gut health.

I think - if I may use a very non-vegan expression it is a bit of a chicken-and-egg question which I haven't quite figured out yet. I have come across the statement in a number of scientific papers that the composition of the gut microbiome is largely determined by the diet.

But then we have the question of whether our microbiome is well-suited to certain foods.

Then (a third issue) can we modify our microbiomes so that they are well able to cope with a particular diet? How long might it take? How much change can we cope with? How much is advisable?

Discuss.

 

[jimells]

Maybe. But the collective experience of PWME here on PR using prebiotics have not impressed me. There are very few who have significantly improved, and lots more who don't seem to tolerate them.

I keep expecting someone to invent "postbiotics" and turn that into a fad...