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

Discussion in 'Phoenix Rising Articles' started by Phoenix Rising Team, Feb 10, 2014.

  1. Phoenix Rising Team

    Phoenix Rising Team

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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…

    [​IMG]

    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
    [​IMG]

    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


    [​IMG]
    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.

    [​IMG]

    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.

    [​IMG]

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    Last edited by a moderator: Feb 10, 2014
  2. aimossy

    aimossy Senior Member

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    I AM IN!!! Enough said. Except for thankyou!
    Izola, rosie26, Firestormm and 3 others like this.
  3. Christopher

    Christopher Senior Member

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    So the CFI will not donate anything?
    justinreilly likes this.
  4. Simon

    Simon

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    Here's the appeal page from Ian Lipkin's The Center for Infection and Immunity
    Izola, aimossy and vli like this.
  5. Simon

    Simon

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    Thanks, Aimossy, that's fantastic.
    As I understand it, the CFI have contributed a great deal to the pathogen/immune study - millions of dollars I think - but are not going to fund more at this stage - they have funded a lot of other work, including a large epidemiological study, a biobanks and a 'mechanism of illness fellowship'.
  6. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    I think that this research has enormous promise, and crowdfunding is a great idea.

    I have one main reservation:

    Lipkin is quoted as saying:

    Yet later the article states, sensibly:

    There is likely to be a great deal of interpersonal variability, and we may need very personalised approaches. Presumably the initial part of the research will reveal much of what we need to know about the variability of gut microbiomes.

    I cannot see how an animal model will help, if there is so much variability between human patients with regard to genotype, epigenotype (is that a word?), age, environmental factors (e.g. diet and geographic factors), body mass and co-morbidities.

    Add to that the substantial differences between humans and other animals: genetics (including different effects of the same genes in different species), natural habits (e.g. diet but also including things such as hygiene with regard to faeces), lifespan, bowel structure and much more, and the very poor record of translatability from animal studies to human patients...

    If Dr Lipkin were to state categorically that he would not use animal studies, I would seriously consider donating, as would some other people I know.
    Last edited: Feb 10, 2014
    irwinsturtle likes this.
  7. acer2000

    acer2000 Senior Member

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    Wow thanks for setting this up. I am in and I will tell my friends and family!
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  8. vli

    vli

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    Thank you so very much @acer2000 .

    I would be very grateful too if anyone interested in this study and with fundraising/crowdsourcing experience could step forward and join the crowdfunding group here so that ideas for a campaign can be thrown around!
    Izola and Firestormm like this.
  9. Christopher

    Christopher Senior Member

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    I don't see anything in the cost breakdown in the article referencing animal studies, @MeSci
  10. Christopher

    Christopher Senior Member

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    @Wally Maybe we can try to put some pressure on the NIH to cough up some funding by shaming them for the lack of funding in the past, present, and the CDC misappropriation incident.

    $1 mil is nothing relative to our collective disability.
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  11. MeSci

    MeSci ME/CFS since 1995; activity level 6

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    No, but the reference to animal studies suggests that this might follow the initial research. Here is the quote with the preceding paragraph (red font indicates the connection):

    The initial research all looks great, but if that is what would follow, I'm out. It's a huge shame. If this 'animal model' were the next step it would likely produce misleading results, thus delaying progress or leading to harmful human trials. This has happened time and time again.

    Others are of course free to make their own decisions. Just pointing this out.
    irwinsturtle and vli like this.
  12. PDXhausted

    PDXhausted Senior Member

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    Anyone know if they will give an update as to how much they've collected so far and how much there is to go? I feel like that can be helpful in reaching a critical mass.
  13. Marco

    Marco Old blackguard

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    Thanks Simon

    I've just donated.

    I feel that we are enormously fortunate to have someone of Ian Lipkin's calibre working on our 'little syndrome' and for as long as he's here we should use him to the max.

    If we can't pull together and treat this as a priority then why expect anyone else to. Short of cash? Think of what you may have spent in the past or might spend in the future on all sorts or 'treatments. Have they worked?

    PS - Thanks also for sorting out my evening viewing.

    I've just dug the Contagion DVD out again : )
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  14. SkagitWabbit

    SkagitWabbit

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    It looks like Dr Lipkin has read neither http://www.cortjohnson.org/blog/2013/09/05/changing-gut-flora-feeding-good-bacteria-chronic-fatigue-syndrome/ nor http://cfsremission.wordpress.com/ where links to pub med studies showing the results that he seems to be seeking. While duplication of prior results is good, it also delays the time to a cure.

    I would strongly recommend people do http://americangut.org/ first, before donating. This allows you to put your gut bacteria available to more researchers -- especially those skilled in handling BIG DATA, which is not one of Dr.Lipkin's qualifications. It is likely a faster path to a cure for all.
  15. Ritto

    Ritto

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    I agree, I think updates could help.
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  16. vli

    vli

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    @PDXhausted and @Ritto , as of December 2013 they've received $1500 or so. I will keep asking the Dept. of Gifts at Columbia how much they are receiving, but I think this highlights the need for a crowdfunding campaign, because people like to see how much of the goal they have achieved. Please show your interest by joining the group here.
    Ritto, Izola, Firestormm and 4 others like this.
  17. Dreambirdie

    Dreambirdie work in progress

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    I donated and would like to see updates too.
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  18. Sasha

    Sasha Fine, thank you

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    Great article, Simon, and many thanks to Vanessa for getting the fundraising underway. I've just donated.

    I think we could get this funded very quickly. Maria Gjerpe's campaign raised $500,000 in three months and shamed her government into fully supporting the Norwegian Rituximab study. Norway's population is 5 million; the US's population is 314 million, which is over 60 times as large. Look how quickly Jen Brea's Canary in a Coalmine fund raised $200,000 - less than a month. There's serious money spread across our enormous community and our supporters, if we see a project that we want to support.

    In the last year we've seen several highly successful projects that very rapidly reached their funding goals - Norwegian Rituximab, UK Rituximab (all there bar the shouting, given the large MEA pledge), Ryan Prior's Blue Ribbon, Jen Brea's Canary and most recently the OMI's B12 study (almost there with $125,000 out of the $150,000 raised in just a few weeks) - and they've one big thing in common: they've been for specific projects, not just calls to pour cash into some charity's bottomless general research fund. And all of a sudden, sums of money that we previously wouldn't have thought possible have been donated, and the many small donations of patients and supporters have often stimulated big donations from other sources.

    We can do this, and we can do it fast. We've already been doing it with these other projects.

    Please donate, and do it now!
    Last edited: Feb 10, 2014
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  19. Sasha

    Sasha Fine, thank you

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    Hi @MeSci - I'm no expert on the applicability of animal models to human health but this issue doesn't put me off, for several reasons:

    • the current study is aimed at trying to determine cause indirectly (correlationally) and that's the study that we're being asked to support. Depending on the results, presumably, it might or might not end up with animal studies but we can't know that now - animal studies are being described as one 'option'. The first thing to do is establish whether having ME is correlated with having certain bugs. We need to know this, regardless of what happens next. We can't afford to stay in ignorance. This is the first step in any bug-hunt and has been the same for looking for viruses in the blood, enteroviruses in gut biopsies and so on. First we need knowledge; once we've got it, I can see lots of research teams and clinicians coming on board to tackle the problem.
    • there seem to be plenty of options available that wouldn't involve animal models. Researchers could go straight to therapeutic trials, if they had a sound rationale. I can imagine patients doing their own n=1 studies, once they know what they're targetting, and our specialist clinicians giving it a go. There may be antibiotics already suitable that we could use.
    • I trust Dr Lipkin not to be stupid in his use (or choice not to use) of animal models. He's clearly an excellent scientist and I'm sure he'd be aware of the limitations. Maybe people might think I'm being naive about that but if so, you've got my first two arguments to fall back on. :cool:
    taniaaust1, aimossy, vli and 3 others like this.
  20. Sasha

    Sasha Fine, thank you

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    Hi SW - I remember reading that a while back - it seems to be just one guy's experience.

    I've just had a quick look at that and it seems to be another one guy's experience and with shedloads of references about all sorts of things.

    I don't know if you had a particular study in mind but what we need is a large study, with a well-defined population of PWME and suitable controls, and then we need the modern techniques that Lipkin's lab can offer to do a proper job of things. I don't think he'll be duplicating what's gone before.

    I'm all for people taking part in the American Gut Project and it could be a good starting point but strict diagnostic guidelines are a big deal for ME and I can imagine a lot of people with undiagnosed primary depression or idiopathic chronic fatigue who've been given a binbag 'CFS' diagnosis by an incompetent primary care physician messing up any attempt by us to piggyback on such a project.

    I think we need to support Lipkin's study. Let's get that money flowing in! :)
    justy, taniaaust1, Izola and 8 others like this.

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