Interview: Ian Lipkin’s Million Dollar Appeal for Microbiome Study

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Simon McGrath recently secured an interview with the world famous Dr Ian Lipkin – a scientist who continues to believe that ME/CFS has a physical cause – to discover more about his plans for a major study of the gut microbiome and to find out why he's asking the patient community for its support…


Dr W. Ian Lipkin has demonstrated a clear commitment to ME/CFS research. First came his study looking at Borna virus in the 1990′s, and then the landmark study that ruled out XMRV as a cause, and most recently we have heard about the huge pathogen and immune study – a vast collaboration with many key clinicians and researchers, including Dr Dan Peterson and Professor Jose Montoya.

That research had already found clear signs of immune activation in patients and, when I spoke to him, Lipkin was clearly excited about the very latest results to emerge from the study - I wish I could reveal more, but a paper has just been submitted and details are embargoed until publication.

Lipkin believes that immune activation may be responsible for driving the symptoms associated with ME/CFS. And that the immune activation and could itself be triggered by bugs, not in the blood, but found in the vast ecosystem of bacteria, viruses and fungi, that constitute the gut microbiome.

However, he doesn’t have the funds to pursue this research and so he’s appealing to the patient community for the one million dollars he needs to get the work done. The payoff? A better understanding of the illness and the possibility of new treatments.

Dr Lipkin on ME/CFS

Lipkin made a splash in the world of ME/CFS when he led the XMRV study that both disproved its role in the illness and also managed to unite the patient community. At the press conference for that study he said his first brush with CFS was a large study in the 1990s that demonstrated no connection between the Borna virus (one of many viruses he’s discovered) and CFS. But he stressed that their findings in the same study of B-cell activation in CFS patients was a clear sign that this was not a psychosomatic disorder. The findings in his new study have only confirmed his views:

“There is no question in my mind that this is a physical disorder. The fact that we haven‘t been smart enough or invested enough in it to sort that, doesn’t mean that this is anything else.”

The smoking gun

The immune activation he’s found could explain fatigue – it’s almost a universal symptom of infections like flu, and is actually a consequence of immune activation rather than caused by pathogens themselves.

The same could be true of other ME/CFS symptoms including disturbed sleep and brain dysfunction which again are typical symptoms of immune activation.

Lipkin is eager to build on this work. He believes the immune activation is a smoking gun and now wants to track down who or what pulled the trigger.

“I am more keen than ever … to see if we can identify the trigger”
- all quotes are from Dr Lipkin

There are several credible places to look for the culprits triggering the activation. One is white blood cells: some viruses could be hiding out in cells and so wouldn’t have been found by the initial search in the blood plasma – and Lipkin already has a white blood cell study lined up.

However, his attention is particularly focused on the microbiome, the large ecosystem of bugs that live on our skin and within our ‘inner tube‘ that leads from mouth to bottom.

There are at least one trillion bugs in the gut microbiome – and there are more immune cells in the gut than anywhere else: it’s a great place to hunt for bugs that might be triggering immune activation.

Microbiome problems are increasingly being linked to serious illness. The most striking example is the superbug Clostridium Difficile (C. diff), which has become a major problem in hospitals. C. diff lives in most of our guts harmlessly at low levels, but it can take over (particularly if ‘good’ bacteria are killed off) – causing diarrhoea and even death. Happily, doctors have discovered that severe C. diff cases can be treated relatively easily by restoring the microbiome; unhappily, this involves a faecal transplant.

The potential to treat disease by restoring the microbiome is one reason this area of research is attracting so much attention. This recent article explains more about the microbiome, how it might link to ME/CFS and looks at other research being performed.

“If the answer were simple, it would be done by now”

Irritable Bowel Disease is another example – here inflammation is believed to result from changes in the microbiome. Lipkin’s team have just been studying women in sub-saharan Africa and found that certain bacteria in the vaginal microbiome increase the risk of HIV infection. Lipkin thinks the gut microbiome could be playing a similarly important role in ME/CFS:

“By analogy with animals and human situations, we see that different populations of fungi, bacteria and viruses in the colon can have an impact on the immune system and give rise to cytokine activation which could cause the symptom complexes we see in ME/CFS”

in other words:

changes in microbiome > immune activation > symptoms of ME/CFS

I asked Lipkin if this meant particular bugs causing inflammation and he said that is certainly possible. But, he added, another route to illness is that an overgrowth of ‘’bad’’ bacteria could form a film, preventing ‘’good’’ bacteria from interacting positively with the immune system (see this article for more) – an indirect way of causing immune dysfunction.

The exact role that microorganisms in the gut play in health and in the development of disease is complex and still being determined. There are many plausible hypotheses, says Lipkin, and only research can show which (if any) are right.

If the microbiome is the cause, is it treatable?

If the microbiome is the cause (or a cause, or even a contributor) of ME/CFS, it might be relatively easy to treat, perhaps with probiotics, restriction diets, drugs, or even faecal transplants.

Cause or effect?
Of course, the first step in this process is demonstrating a strong link between the microbiome and ME/CFS. If one is found then the next step is to look for evidence it plays a causal role: i.e. do microbiome changes cause immune dysfunction, as opposed to being a consequence of or simply associated with immune dysfunction?

Lipkin says one option is to use an animal model: the idea would be to introduce the microbes suspected of triggering ME/CFS into the gut microbiome of animals, to see if this leads to similar symptoms and immune activation as seen in humans. Something that has been used to study Metabolic syndrome.

Personalised medicine
If there is evidence of a causal role, Lipkin says they would look to establish clinical trials of treatments that could include probiotics, antibiotics followed by prebiotics, restriction diets and possibly even faecal transplants. He believes that there would not be a single microbiome cause of the illness, but different types – potentially fungal, bacterial and viral problems causing three separate types of immune dysfunction.

Lipkin calls these different types ‘endophenotypes’ and it could lead to personalised medicine, where the particular treatment depends on the specific form of the illness. There will be endophenotypes beyond those in the gut, such as genetics endophenotypes, and it is highly unlikely that the microbiome would account for all forms of ME/CFS – but this approach could tackle a very substantial proportion of cases.

The study breakdown

Lipkin’s proposed study will look at all three trees of life: bacteria, fungi and viruses in the microbiome of 100 patients and 100 controls recruited for a previous NIH study. It will cost a cool million dollars:

1. Sample collection: $150,000
Collection of faecal (and blood) samples from patients, including checking the initial ME/CFS diagnosis remains valid and shipping chilled samples back to the labs at Columbia.

2. Faecal Microbiome sequencing and Analysis: $317,000
- Separate, purify and perform high-throughput sequencing of viruses, fungi and bacteria
- Complete sequencing of viruses; partial sequencing to identify bacteria (using 16S rRNA) and fungi (using ITS, the ‘fungal barcode’)
- Generate microbiome profile for each patient, one each for bacteria, fungi and viruses​

Comparison of patient and control microbiomes: bacteria, fungi and viruses that differ in prevalence between CFS subjects and controls will be considered candidates for contributing to either health or disease.

3. Development of highly-accurate real-time PCR assays to confirm findings and levels of microbes: $328,000
This will quantify how much there is of each bug of interest (the main high throughput sequencing approach gives an indication of quantity but is less accurate than real-time PCR).

It’s possible, that the most important thing isn’t the presence or absence of a microbe, but the amount of it – as with C.Difficile. These assays will also be used to check that key microbes haven’t been missed in any patient or controls who were negative for them in initial sequencing, as PCR assays are far more sensitive than high-throughput sequencing.

4. Cytokine analysis: $86,000
The study will again measure cytokines in blood and undertake data analysis to see if there is an association between cytokine profiles and immune profiles. It would then provide strong evidence of an important relationship between the microbiome and immune dysfunction – the hypothesis driving this study. Sophisticated analysis will be required on the vast amount of data generated by microbiome and cytokine profiling; happily, Lipkin’s Center for Infection and Immunity have a team of biostatisticians dedicated to such work.

5. Development of antibody tests for important bugs identified by the microbiome work: $249,000
It could be a few individual species or particular groups of microbes, but antibody tests will be developed by Lipkin’s lab to allow much easier testing to see if the same problems in this sample are found in the wider patient population.

As well as guiding treatments, the PCR assays and antibody tests developed here could both provide a diagnostic test for ME/CFS.

Lipkin’s record



Featured in the New York Times, described by Discovery magazine as the world’s foremost virus hunter, and consultant to a successful Hollywood movie, Dr W. Ian Lipkin has a higher profile than most researchers. But this profile is built on a stellar scientific reputation.

He’s discovered more viruses than anyone else. He’s part of the World Health Organization (WHO) diagnostic discovery and surveillance programme designed to catch pandemics as they arise. And the Chinese recruited him play a leading role in their fight against SARS.

Amongst other things he is John Snow Professor of Epidemiology and Director, Center for Infection and Immunity at Columbia University. Full biography.

He is passionate about communicating science to a wider audience but is insistent the science is right.

Lipkin only agreed to consult on Contagion, a movie about the terrifying potential of epidemics, because of director Steven Soderbergh’s desire to make a film that was true to the science – having turned down offers to advise on several movies with somewhat wilder plots.

When Lipkin was shown a near-final version of the film he threw up his hands at the scene near the climax where a scientist injects herself in the leg with the new vaccine, through her tights – a poor practice that could easily introduce an infection.

This might seem a small detail given everything else the film had right, but Lipkin was adamant it had to go: cue a $100,000 reshoot.

This near-obsession with getting things right is a Lipkin hallmark. The very first point he made to me about this study, before discussing any details, was the need for real, robust findings – because there have been too many false dawns in this field.

At the end of the interview he emphasised the need of crisp, rigorous data. Whatever the findings from this new study – positive or even negative, we should be able to rely on them.​


Scientist in a hurry for answers

Dr Lipkin is a scientist in a hurry for answers. That’s true both in his work trying to stop a new pandemic in its tracks, and in his work on ME/CFS.

He wants to follow up as many promising leads as possible, as soon as possible – rather than waiting for the results of a single study before planning a new one if the first draws a blank.

That’s why he set up a huge study looking for specific pathogens such as EBV, but also used deep sequencing alongside that to search for any other pathogen, known or unknown.

He’s looked in blood plasma for pathogens but is also about to look for them in white blood cells too.

He set the study up to look at immune markers including cytokines as well as for pathogens – and the significant findings of immune activation show the value of backing more than one horse.

On top of all this, Lipkin has invested in a gene expression study using samples from the same study, with results expected shortly that could throw up new leads in epigenetics and genomics.

Dr Lipkin has committed a huge amount of his 60-strong institution’s time to pursuing numerous studies, all aiming to uncover what’s really going on in ME/CFS

Too much, too soon?
However, it may be that the NIH is not in such a hurry as it has declined to fund the study at this time.

But then the NIH has only ever committed relatively small amounts of funding to ME/CFS – around $5 million a year, compared with around $115 annually for MS and $284m for Asthma.

Its funding record firmly suggests the NIH’s priorities lie elsewhere.

So, as Lipkin says, “we are stuck”. It’s possible that the NIH will fund this work in the future, and possible they won’t.

The question is, do we want to wait?

“We are already well behind where we should be”

Dr Lipkin has now appealed to patients to fund his latest study that aims to hunt in the gut microbiome for the ‘trigger’ of the immune activation his study found in ME/CFS. And he needs a cool million dollars to pay for the study outlined above.

Actually, the study comes to a bit over a million dollars (see above) - $1.13 million, to which another $140,000 of costs for maintaining the high-tech equipment used and general lab costs making $1.27 million in total. However, the initial target has been set at $1 million.

In his CDC telecast to patients last September, Lipkin explained the microbiome project was being held up by this lack of funds, and urged patients to contact their representatives in Congress.

He also appealed directly to patients who could afford to do so, to invest in research:

“it may not be appropriate to pass the hat, but that is exactly what I am doing”

How long will it take for the results? “Within a year”, said Lipkin

The man is in a hurry, and the study is all set up and ready to go – once funding is available.

“As long as I can do it, I will do it. I‘m eager to start, I‘m optimistic it will bear fruit, it‘s not just an academic exercise, it could lead to treatment”
When I mentioned to Dr Mady Hornig, the Principal Investigator on this study, that I was interviewing Dr Lipkin she added: “Terrific – we need the resources to get this done”.

Crowdsourcing: Together we can make it happen

I do think we are very lucky to have Dr Lipkin on our case and believe that we should back his new study, which will be performed at his Center for Infection and Immunity, Columbia University – the world’s largest and most advanced academic center in microbe discovery, identification and diagnosis.

“Why don‘t we crowdsource this, we are all losing valuable time in our lives?”
Vanessa Li, Phoenix Rising member and fundraiser

ME/CFS patient, Vanessa Li, responded to Lipkin’’s call last year, by contacting his office and suggesting crowdsourcing in a similar way to MEandYou, which through the efforts of Dr Maria Gjerpe had raised an astonishing $0.5 million towards the Norwegian Rituximab trial in 90 days.

Lipkin was a physician in San Francisco at the start of the AIDS epidemic and commented how, when the government was reluctant to pay, much of the important early work was funded by private donors so he’s very open to this possibility. He continued to seek funds for his work from institutions, but as that hasn’t worked he is now asking patients if they can make the study happen - and has given this interview to launch the million dollar appeal.

Donate to the the ME/CFS microbiome study
I have just donated and hope many other patients will do too. Just click on the button below and follow the instructions. The option is to donate to CFS research, but in the next page you can add ‘special instructions’ such as ‘for the microbiome study’.

We need only for every US patient to donate $1. Or one in ten patients to donate $10.


If people want to do more to help – and this is a big target – they can help to promote this crowdsourcing initiative at this new group, or email Vanessa Li. I will give her the last word:

The CDC says there are more than one million ME/CFS patients today in the US alone. There is no reason why, if every patient were made aware of Dr. Lipkin’s appeal and donated $1, that we should fail to raise the $1 million. An esteemed researcher doing high-caliber work is taking a serious interest in finding out the cause of our desperately under-researched illness. Now is the time to act!​

Simon McGrath tweets on ME/CFS research:


Phoenix Rising is a registered 501 c.(3) non profit. We support ME/CFS and NEID patients through rigorous reporting, reliable information, effective advocacy and the provision of online services which empower patients and help them to cope with their isolation.

There are many ways you can help Phoenix Rising to continue its work. If you feel able to offer your time and talent, we could really use some more authors, proof-readers, fundraisers, technicians etc. and we’d love to expand our Board of Directors. So, if you think you can help then please contact Mark through the Forum.

And don’t forget: you can always support our efforts at no cost to yourself as you shop online! To find out more, visit Phoenix Rising’s Donate page by clicking the button below.


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Comments

Million Dollar Bug Hunt is cute, but I'm not sure cute is what we should be shooting for if we want high money donors. Perhaps we should aim for something more professional or serious-minded and save the fun, cute name for using among ourselves.
 
Is this too long.

"Give your heart out to ME - Lipkin's 1 Million Microbiome Study 2014"
 
Hello @Jarod

Like I said to @Jon_Tradicionali and @Daffodil, members are free to donate or not to donate to Columbia whether it be for financial reasons (like @Bob said) or because they have doubts and queries about the study. I am compiling an email to Columbia that contains all these questions and as much as anyone would like them resolved as fast and as unequivocally as possible.

When I was helping (in a very small way) Simon put the article together I asked around for people's opinions on researching the microbiome for ME and heard from many De Meirleir patients and others who complained that funds should be given to their researchers, not Lipkin. My immediate gut reaction was (if you'll excuse the pun): well if you feel this strognly about it, why don't you try to organise a campaign for him? As should be obvious, even the person with the least experience or knowledge of these things (me) can initiate such a campaign--it's just that I need tons of help.

I am also a little confused as to why you think any results that Lipkin sees researching the microbiome would not be "tangible and usable" even if other points that you made are valid; but perhaps I'll let others jump in here.
I am also a little confused as to why you think any results that Lipkin sees researching the microbiome would not be "tangible and usable" even if other points that you made are valid; but perhaps I'll let others jump in here.

Hiya,

Let me just respond to this last to the group "as a whole" since it gets right to the heart of the problem.

CFS community has been doing all this academic stuff for decades and NONE of it has produced anything that is useful for the community.

I'm in favor of academic research and everything, but it never seems to end up leading to anything tangible.

If I am going to fund something, at the end I want it to produce something tangible that will help me and other ill people dying without one peep out of anybody except the psychiatrists making it look like I'm crazy, lazy, mentally ill, or whatever other nonsense.

Crowd funding is a a unique opportunity to hold somebody accountable for a change. Set up requirements and milestones to clearly define want to deliverables are going to be. Demonstrate they can deliver something, and have deliverables each time a check is released from escrow. That is how stuff works in the business world outside academia. It's called project management.

Run the dang thing like a venture capital firm.

The most urgent need to is fund education and testing so people don't die or commit suicide like "hubcap halo" did when social security cut him off because the paper pushers in govenment have no clue what our illness is due to the misinformation in the media, hollywood, and government. I've been through those reviews and it is a joke.

Number two is to provide treatment. Test the best medications and glutathione building techniques and get those working now.


What a blown opportunity.

Doing the same thing over and over again isn't going to move the ball.

Lipkin has plenty of starpower and can raise money from many other places the way I see it.
 
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I'll simplify it a bit more.

Government, universities, and big pharma have NOT been able to make progress for decades.

Crowd funding can make it possible to change this. The way to do that is to fund an outsider. People are too divided and the potential leaders on the outside can't get the traction it seems.
 
I'm sorry, @Jarod, but you haven't quite addressed my reply to your reply.

I can put those points in bold if you like.
Like I said to @Jon_Tradicionali and @Daffodil, members are free to donate or not to donate to Columbia whether it be for financial reasons (like @Bob said) or because they have doubts and queries about the study.
When I was helping (in a very small way) Simon put the article together I asked around for people's opinions on researching the microbiome for ME and heard from many De Meirleir patients and others who complained that funds should be given to their researchers, not Lipkin. My immediate gut reaction was (if you'll excuse the pun): well if you feel this strongly about it, why don't you try to organise a campaign for him? ...
CFS community has been doing all this academic stuff for decades and NONE of it has produced anything that is useful for the community.

I'm in favor of academic research and everything, but it never seems to end up leading to anything tangible.
It appears you have just contradicted yourself in two consecutive paragraphs.

In addition, I'd like to ask:

What qualifies as "academic stuff"? Does De Meirleir's work on HERVs, Chia's work on enteroviruses or Dr Peterson's work on HHV-6 qualify? If so, I think you can find MANY patients on PR alone who will testify to such "academic stuff" producing a tangible effect on their treatment options; perhaps a forum search on "KDM (De Meirleir)", "John Chia" or "Daniel Peterson" will help?

If I am going to fund something, at the end I want it to produce something tangible that will help me and other ill people dying without one peep out of anybody except the psychiatrists making it look like I'm crazy, lazy, mentally ill, or whatever other nonsense.
Perhaps you did not read Dr Lipkin's quote here and I will let him speak for himself:
But he stressed that their findings in the same study of B-cell activation in CFS patients was a clear sign that this was not a psychosomatic disorder. The findings in his new study have only confirmed his views:

“There is no question in my mind that this is a physical disorder. The fact that we haven‘t been smart enough or invested enough in it to sort that, doesn’t mean that this is anything else.”
That is how stuff works in the business world outside academia. It's called project management.

Run the dang thing like a venture capital firm.
If you have experience in this arena, frankly our project IS indeed in dire need of someone with that expertise, and we would be more grateful than anything for such help because in the end we're just a bunch of sick folk trying to help each other. We'd love for such expertise to come in.
The most urgent need to is fund education and testing so people don't die or commit suicide like "hubcap halo" did when social security cut him off because the paper pushers in govenment have no clue what our illness is due to the misinformation in the media, hollywood, and government.
Can you please specify to educate WHAT and to test WHAT?
Number two is to provide treatment. Test the best medications and glutathione building techniques and get those working now.
Again, please specify WHAT of the best medications you are talking about. If you mean drugs like Rituximab or Ampligen, well I'm sure you already know about the UK and Norwegian campaigns for the former, and advocates like Mary Schweitzer and others have been bravely pushing for approval of the latter (which I've also tried, by the way... and Valcyte/Vistide? Oh yeah tried those, too. Still sick.)
What a blown opportunity.
I'm not sure exactly what opportunity of yours I've blown here because, like I said, neither Lipkin nor anyone else here is preventing other things from being tested/funded. Please specify.
Again:
Like I said to @Jon_Tradicionali and @Daffodil, members are free to donate or not to donate to Columbia
.
 
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@Jarod - I believe that some of the items on your list are already on the research project list that the OMNI-MERIT Group has developed. I believe they have also tried out crowd source funding for one of their projects. If I remember correctly, they are also trying to address some of their research projects toward nutritional treatments and other medications/supplements that while not a cure for this illness may provide much needed symptom relief for patients, while they also hunt for answers to solve this illness.

There may not be answers to all the concerns you have, but it seems that some of your concerns may already be in the pipeline to be addressed. Perhaps because organizations like the Open Medicine Institute and others are fairly new, there has not been a lot of information available about how they are going about tackling research projects, including raising funds. Maybe this Forum or other forums, bloggers etc... could interview the Open Medicine Foundation and its founder, Dr. Kogelnik, as was done by Simon McGrath in his interview with Dr. Lipkin. This might help patients understand the different type of research projects that have been proposed by researchers, as well as to highlight those projects that are currently looking for funding. Maybe what is needed is a series of interviews with different researchers, as well as those who are handling the donation side of the project. I do realize this takes some time and effort for such articles to be generated, but it may be the most efficient use of time and energy to flush out all of the questions that are bubbling up around this fundraising topic

It is my understanding that some of the fundraising questions about Dr. Lipkin's microbiome project could be reviewed in light of how Rituxan/Ritiuximab funding raising project was handled in England and how the Open Medicine Institute handles donations that come in to fund either the Institute, the Clinic, the Foundation and/or individual research projects.

I think it also important to understand that a large project like what is envisioned by Dr. Lipkin will probably have a lot of difficulty being funded by just individual patient contributions. One million dollars it a lot of money to raise even if using crowd source funding. Could it be done? Perhaps, but it is more likely that the funds will need to come from several sources. Therefore, it is important to understand how your donation will be handled if it will be hanging out while other funds are being raised - how long will the donations have to sit while additional funds are being raised? Where will the funds go if the project cannot be fully funded? I believe V1i is working to get some of these answers and for some people it may be enough to want to make a donation right now without having all the details hammered out. But for others it may be better to wait until all their questions are answered and they are comfortable with where their donation will go and how it will be accounted for.

For those who want to take action now with Lipkin's micobiome study, Columbia has set up an account that is earmarked for CFS research. The Open Medicine Foundation has a list of projects. Dr. Enlander has a project out of Mt. Sinai in New York that is looking for donations, and there are projects in the pipeline in Australia and Europe. Perhaps you do not like any of them, then don't donate at this time. Making a donation is really a personal choice, but I think you have raised some really good points about fundraising for research projects in general.

Personally, I think it the responsibility of the researchers and their respective institutions to do a much better job at publicly addressing these questions/concerns upfront when asking for donations from a patient population that is quite ill and may be both cognitively and financially challenged.

@V1i - Thank you for getting the discussion started about fundraising. I know that you are not well yourself and it can be overwhelming taking on any project for our patient community. Just hope you don't feel like you are under attack with all the questions and ideas people have raised. Your idea is a good one and you are right that you will need help to figure this out. But I believe the help you may be seeking might first need to be come from those who are holding their hand out to the patient community.
 
Maybe this Forum or other forums, bloggers etc... could interview the Open Medicine Foundation and its founder, Dr. Kogelnik, as was done by Simon McGrath in his interview with Dr. Lipkin. This might help patients understand the different type of research projects that have been proposed by researchers, as well as to highlight those projects that are currently looking for funding.
Et voila:

http://forums.phoenixrising.me/inde...itute-big-plans-and-a-sense-of-urgency.24043/

I just got in my time machine and did that for you, Wally! :)
 
Thanks Sasha. I apparently missed this interview and now it makes me wonder what else I missed during the times my illness was really flaring up and my brain went on vacation. :(:sleep:
Ah, flares! Not much fun.

Here's our articles archive in case you find it easier than looking back over our front page and fancied doing some back-reading:

http://forums.phoenixrising.me/index.php?forums/phoenix-rising-articles.18/

though it's not in date order - just in the order of when someone last posted a comment on any of them.
 
You can use the search function, by category, on the Home/Blog Page as well should you want to check back-copies :)
 
If microbiomes are to blame, what sort of treatments would be indicated?
 
If microbiomes are to blame, what sort of treatments would be indicated?
IMO the first thing to try for gut dysbiosis is a change of diet. A lot of us discuss diet and supplements for healing leaky gut in this forum.

This paper, which I have only glanced through, discusses effects of diet on the microbiome.
 
If microbiomes are to blame, what sort of treatments would be indicated?
Hi Womble - it says in the article (which is substantial so I'm not surprised you overlooked it!):

If there is evidence of a causal role, Lipkin says they would look to establish clinical trials of treatments that could include probiotics, antibiotics followed by prebiotics, restriction diets and possibly even faecal transplants. He believes that there would not be a single microbiome cause of the illness, but different types – potentially fungal, bacterial and viral problems causing three separate types of immune dysfunction.​
 
IMO the first thing to try for gut dysbiosis is a change of diet. A lot of us discuss diet and supplements for healing leaky gut in this forum.

This paper, which I have only glanced through, discusses effects of diet on the microbiome.
I bet HIV would not get better from diet changes only, even if they too have gut dysbiosis.
The gut problems are in my opinion just another symptom of ME and results from a very dysfunctional immune system. While I do not oppose to funding a microbiome study, I believe that multi-system, computational biology research will be able to connect the dots and not just a study of fecal matter.
 
The gut problems are in my opinion just another symptom of ME and results from a very dysfunctional immune system.
But as Dr. Lipkin says, "There are at least one trillion bugs in the gut microbiome – and there are more immune cells in the gut than anywhere else: it’s a great place to hunt for bugs that might be triggering immune activation."