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

View the Post on the Blog

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.

View the Post on the Blog
Last edited by a moderator:


I'm going to embarrass myself, but I'll throw out a few more:

help for …..

an inner space odyssey

the biome express

Microbiome magic

Microbiome mapping

Funding for friends and family

A bridge to health

Dial M for Microbes

Good Gut Hunting
' Good Gut Hunting'. I love it. Very original!
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.
Sorry - my link won't open for some unknown reason (at least for me). This may be the study in question but, if not, it is a good enough one!

Here's an alternative link in case the pdf one doesn't work.

Re the point about HIV, this is a different issue, as HIV is known to be caused by a specific virus. I don't think this is likely to be the case in ME, at least not most cases. Lipkin may have previously been looking for specific pathogens but I think he may have changed tack. This recent PR article may clarify:

Re other evidence for treating ME successfully by changing the gut microbiota through diet, supplements, antibiotics, etc., there is also the small Maes and Leunis study

@Simon, does the campaign still want name suggestions (post 179)?

If so... Cash for Cure // Fund Microbiomic Exploration // Cure Wanted // The Million Dollar Answer // No stone unturned. // Explore. Record. Cure. // Battle of the Bugs // Lipkin hates loves your guts! :D

Perhaps Lipkin could auction off the naming rights (of new bugs) to the highest bidder (with a guaranteed lowest bid of course)?
@Simon, does the campaign still want name suggestions (post 179)?

If so... Cash for Cure // Fund Microbiomic Exploration // Cure Wanted // The Million Dollar Answer // No stone unturned. // Explore. Record. Cure. // Battle of the Bugs // Lipkin hates loves your guts! :D

Perhaps Lipkin could auction off the naming rights (of new bugs) to the highest bidder (with a guaranteed lowest bid of course)?
Hi Ren - we're no longer in the market for names - currently drawing up a shortlist from the ones produced on the dedicated thread for that - sorry you missed it! Thanks anyway.

I love that idea of an auction of naming rights! I'll add it to the list of possibilities. :thumbsup:
I agree that the microbiome is unlikely to account for everyone's illness - indeed I doubt that any one thing could account for everyone's illness and I suspect even ME (let alone CFS) will turn out to be multiple diseases.

While there is certainly a degree of non-specificity in this approach - 'the immune system is activated, so who or what pulled the trigger?' is part of the rationale,I think it's worth pointing out that the gut microbiome is a much better candidate than, say. the skin. So it's not quite a case of 'could be this, could be anything'. here's a bit more info:
- there are more microbes in the gut than anywhere else in the body, by a trillion or so.
- there are way more immune cells in the gut than anywhere else in the body
- the gut has - has to have - a permeable lining to take food on board, making the contact between immune system and gut particularly itimate.
- there is an intimate and complex relationship between the microbiome and the gut immune system that is only beginning to be understood. For example, in gnobiotic mice (raised in sterile conditions, with no microbiome as a result), the immune system doesn't develop properly - in particular it doesn't regulate itself properly and is prone to inflammation. Interesting article on this from Science Daily
- and of course many people with ME/CFS have gut problems such as food sensitivity.

The gut microbiome is an exploding area of research and being linked to a number of diseases. This blog has more information Gut bugs misbehaving? The microbiome and ME/CFS

Yes, that's what Lipkin said - the antibiotics were as in 'antibiotics followed by probiotics', since antibiotics will wipe out much of the microbiome. He also mentioned faecal transplants were a possiblility - certainly they were used very successfully to treat drug-resistant C difficile infections. But exactly what treatment is appropriate (if any) will depend on the findings of this research.
I am surprised that Lipkin suggests this - although I take on board it all depends on the findings of the study - as I know quite a few people have tried this, especially KDM patients, with not significant benefits in many. I remember reading about one girl who went to see KDM after only being ill for a short while and did the abx probiotics rotation and did recover. I wonder if abx and probiotics work better at the start of the illness before the immune system gets very dysfunctional, all speculation of course

Anyway I still very much support this study and all the work Vli and team are doing in trying to get funds raised
Our contact for this at Columbia returned today and I am happy to report that as of today, we have raised $14,186 from 154 donors :balloons::thumbsup::balloons:
Not a bad start, but still a way to go. Thanks to all those who have already donated.
Thanks to the excellent new ME Global Chronicle newsletter for giving this appeal a mention:

Ian Lipkin study.
The initial target has been set at $1 million.
They also carry a brilliant editorial from Prof Leonard Jason:

“The future of the field is in connecting the many patient and
scientific groups into one larger body that is united for change.
Any events that bring people together across countries and
organizations should be promoted.

The message is simple, we have more impact with numbers, and when we flex
our collective muscles, then we become a movement like the civil rights,
women’s and disability revolutions of the 60s, 70s and 80s.

The HIV/AIDS groups changed policy throughout the world, but they did it by
keeping their focus on critical issues and demanding change, and although the
voices in that movement were also divided, for a few things like increased
funding and provision of services, they were all together.”
Ian Lipkin has mentioned more than once how impressed he was with the way HIV/AIDS campaigners pressured government to do more. He was a newly-qualified physician when he arrived in San Francisco in the early 1980s, just at the then-unamed AIDS epidemic was taking hold; at that time many doctors were reluctant to treat these patients and he told me about some of the problems he had persuading colleagues to let provide novel treatments to his AIDS patients. He also mentioned how some of the first HIV research was funded by private donors, work that persuaded a relucant government to fund more research.
Our disease is NOT caused by Lyme, mold, herpes viruses, gut bacteria, or anything these specialists are trying to look for and treat. These are infections our bodies should be able to control.

It is AUTOIMMUNE. see the new paper: Transcriptional de-repression of ERVWE1 following influenza A virus infection.

Again, the ONLY researcher I am aware of, who is looking at this factor, KDM/Lombardi/WPI.

Why do we continue to support the search for pathogens? I find this very frustrating.

Of COURSE we will have pathogens, gut inflammation, differences in gut flora. This is a given.

I urge you to support those who are narrowing in on the true cause.

some HIV drugs helps some people because they act on HERV. Ampligen helps some people because it makes us produce interferon, so our bodies can again control the infections.

I am so scared that these pathogen studies will be more of a waste of precious time some of us do not have.
Last edited:
Just donated.

Taking a cue from Wally's comments, I added an extra $25 on behalf of those patients who cannot afford anything at the moment.

(Excuse delay in donating, had to clear a couple of largish and unavoidable bills first.)
Is there any chance of getting an update on how the crowdfunding project is progressing? Are there updates on another thread that I'm not aware of? I wish I could help, but I can't do anything other than contribute funds, and I'm a bit anxious that we not lose momentum.
Is there any chance of getting an update on how the crowdfunding project is progressing? Are there updates on another thread that I'm not aware of? I wish I could help, but I can't do anything other than contribute funds, and I'm a bit anxious that we not lose momentum.
Evening Gerald,

We are I think able to confirm that we should have our primary plaforms - website and Facebook pages and twitter feeds - launched before the US conferences begin 19/20 March at which both Montoya and Lipkin et al will all be presenting. Hopefully, the presentations and interviews, will provide a boost to the campaign efforts so we wanted to ensure the platforms were in place by then. Also if any announcements are made with regard to publication of papers pertaining to the CDC Broadcast last year from Lipkin, or Montoya's more recent seminar on the subject, then the campaign would - we think - also benefit. Any announcement would of course likely be made at these conferences.

So, we are resolving issues relating to: name, platforms, donation methods, content, logo's and images, lining up interviews on video etc. etc. and expanding our network of contacts to reach a much wider community across the world. We will shortly be engaging with members of the medical community who we'll be hoping to bring on board including those who were involved with the blood study, that Lipkin spoke about in his CDC broadcast.

The conference presentations will be followed up with articles that can help continue to raise awareness of the campaign, and we have people at both conferences to record and pass back information as it happens.

We have also posted this article above to co-cure, and we have a Spanish translation that I will hopefully publish this week. Further translations of the campaign work - and the campaign itself - are something we would like to work on and are approaching others to help us do this.

So, hopefully, you should see the fruits of this voluntary labour in coming weeks and as a result we hope the campaign contributions will really start to stack-up.

Hope that helps.
Last edited: