The Microbe Discovery Project

Please join us!

This is a patient-led crowdfunding project, in support of Dr Lipkin’s study of the gut microbiome for ME/CFS patients.

Dr Lipkin’s research funding application was declined by the NIH, so we have started this patient-led crowdfunding project to support Dr Lipkin’s research.

In the short period that we have been crowdfunding, we have so far raised more than $60,000, with donations from 20 different countries and 33 US states. The project will be even more successful with your support.

We have a growing community of international supporters including on Twitter and on Facebook, and we would love you to join us.

With more of our community involved, from countries all over the world, we will demonstrate our support for Dr Lipkin and his team; we will raise the profile of the crowdfunding project; and we will raise the profile of ME/CFS in general.

The ME/CFS patient community has a chance to have a world-renowned scientist dedicate his team to our illness. Let’s grab that chance!

As a community united with a common cause, we are stronger together!

We can make a difference!


The Microbe Discovery Project

ME/CFS: a devastating neuro-immune disease as disabling as multiple sclerosis, affecting one million Americans and 17 million people worldwide.

The study: a cutting-edge hunt for the cause of symptoms in ME/CFS, studying the gut “microbiome” – the bacteria, viruses and fungi in the digestive system – led by “the world’s most celebrated virus hunter”, Dr W. Ian Lipkin at the world’s largest and most advanced center for microbe discovery and diagnosis at Columbia University in New York.

Dr Lipkin has found evidence for immune dysregulation in ME/CFS patients and believes that an infectious agent is the trigger or cause of the dysregulation. He believes the answer may lie in the gut microbiome, and is eager to study it.

The payoff: a world-class study with the potential to lead to trials of treatments using drugs, probiotics or exclusion diets.

Our challenge: to raise $1.27 million (£760,000; €910,000) to fund the project and do it fast! Dr Lipkin’s team are ready to go and can complete and publish the study within 12 months of starting. The sooner we fund it, the sooner it starts.


Please join us.

Please join us and spread the word to your family, friends, fellow patients and anyone in your network via your group mailing list, Facebook page, Twitter, or however you can.

Together, we can make a difference!​.

To find out more, please visit the website:
www.microbediscovery.org

To donate, please click here:
www.bit.ly/DonateToDrLipkin

Please join us on Facebook:
www.facebook.com/microbediscovery

And on Twitter:
https://twitter.com/MicrobeProject

Contact us:
info@microbediscovery.org


 

Posted in Blog, The Microbe Discovery Project blog series

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 9 of 9

Part 9 of 9

Dr Lipkin – Enthusiasm for ME/CFS Research

After listening to Dr Lipkin discuss his plans, expressing his enthusiasm, and his expectations, it is difficult not to also be enthused and impressed with the scope of his ambitions for ME/CFS.

DrLipkinFront

Dr Ian Lipkin. Photo courtesy of the Columbia University Center for Infection and Immunity

The ME/CFS patient community has the chance of a high-profile and world-renowned scientist to take an interest in their disease, to take hold of it with both hands, and to shake it until it gives. His ambitions are not modest. Dr Lipkin intends to get results. He is willing to explore the disease from many angles, to follow leads, and to test out ideas.

The gut microbiome study is just one study among a number of ME/CFS studies that Dr Lipkin is involved in. Dr Lipkin is not messing around, tinkering at the edges. In collaboration with the Chronic Fatigue Initiative, and other researchers, he’s searching for pathogens in the blood and spinal fluid; he intends to carry out a comprehensive search for viruses, bacteria, and fungi in the gut microbiome. (In which he will be looking for anything unusual: A single virus, or a pattern of microbes, that might indicate a difference in ME/CFS patients.) His team are also investigating immune biomarkers, gene expression, proteomics, and metabolomics.

Columbia University Medical Center campus. New York. Image: http://en.wikipedia.org/wiki/File:ColumbiaMedicalCenter.jpeg

Columbia University Medical Center campus.
New York.
Image: http://en.wikipedia.org/wiki/File:ColumbiaMedicalCenter.jpeg

Science doesn’t get better than this. The Center for Infection and Immunity has a reputation for scientific excellence, and scientific discovery. And Dr Lipkin says he is “desperately eager” to research ME/CFS. Yes, you heard correctly. Dr Lipkin, one of the world’s most eminent scientists, is “desperately eager” to support and research the underfunded, misunderstood, neglected, and forgotten illness that is known as ME/CFS.

Dr Lipkin repeatedly states that he is eager to get started with this project; that his laboratory is ready to go; and that he has a team of 60 whom he wishes to dedicate to the research. All he needs is the funding.


This is a series of blogs based partly on an interview with Dr Ian Lipkin by Simon McGrath in January 2014, in relation to the intended study of the gut microbiome of ME/CFS patients. (To see Simon’s article please click here.)

Please feel free to repost this blog on your own website or Facebook page, etc., but please include a link to the original blog:
http://www.microbediscovery.org/blog/2014/06/03/dr-ian-lipkin-blog-part-9-of-9/
and the donation link:
www.bit.ly/DonateToDrLipkin


Please join us.

Please join us and spread the word to your family, friends, fellow patients and anyone in your network via your group mailing list, Facebook page, Twitter, or however you can.

Together, we can make a difference!​.

To find out more, please visit the website:
www.microbediscovery.org

To donate, please click here:
www.bit.ly/DonateToDrLipkin

Please join us on Facebook:
www.facebook.com/microbediscovery

And on Twitter:
https://twitter.com/MicrobeProject

Contact us:
info@microbediscovery.org


 

Posted in The Microbe Discovery Project blog series

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 8 of 9

Part 8 of 9

Treatment

Dr Lipkin observes that ME/CFS is highly heterogeneous, which means that he believes there will probably not be a single answer for the whole ME/CFS population. Instead, Dr Lipkin is looking towards personalised medicine, whereby each patient is treated depending on their individual biomedical differences or vulnerabilities. For this, he needs to carry out large studies, collecting large amounts of data. This is why he is proposing a large study involving 100 patients and 100 controls.

Image courtesy of stockimages / FreeDigitalPhotos.net

Image courtesy of stockimages / FreeDigitalPhotos.net

Dr Lipkin predicts that his team will identify different ‘endophenotypes’ (i.e. groups of patients who show certain consistencies between them), and suggests that he might find an answer for 10% of patients at a time. Dr Lipkin has involved statisticians to refine the design of the study to support such a hypothesis.

So, for example, some groups of patients might potentially be identified by the presence of a particular virus in the gut microbiome and some might be identified by unusually high levels of a particular fungus, or by an unusual population of a certain type of bacteria within the gut.

Dr Lipkin says once you begin to narrow things down, and to identify groups of patients with a consistent pattern of gut microbes, you can then try to identify individuals who are at risk based on exposures to specific microbes, and you can also begin to think of some sort of a customised treatment.

Dr Lipkin has suggested that potential treatments might involve: various types of drugs; or antibodies directed against specific cytokines; or a course of a certain type of probiotic; or a course of antibiotics followed by probiotics. And he has discussed the possibility of fecal transplants as a potentially beneficial treatment. Although he stresses that such treatments would have to be tested in rigorous trials.

Image courtesy of Ambro / FreeDigitalPhotos.net

Image courtesy of Ambro / FreeDigitalPhotos.net

So, depending on the results of the gut microbiome study, Dr Lipkin is thinking along the lines of changing the gut microbial population, or directly treating abnormal levels of cytokines, in order to potentially have a beneficial effect on the abnormal cytokine pattern and the symptoms seen in ME/CFS.

Discussing his plans for what will happen after the gut microbiome study, he says: “we want to initiate some sort of a clinical trial where we either use probiotics, or antibiotics followed by probiotics, or some sort of an antibody directed against specific cytokines to see if we cannot improve, in a blinded trial, the condition and the status and the prognosis of people who have this disease.”

The potential treatments depend on the outcomes of the trial. For example, if high levels of a particular fungus is found in the gut, in a subset of patients, then perhaps an anti-fungal treatment could be in order for that subset. Or if an unusual virus is discovered in a subset of patients, then perhaps an anti-viral treatment could be in order for that subset.


This is a series of blogs based partly on an interview with Dr Ian Lipkin by Simon McGrath in January 2014, in relation to the intended study of the gut microbiome of ME/CFS patients. (To see Simon’s article please click here.)

Please feel free to repost this blog on your own website or Facebook page, etc., but please include a link to the original blog:
http://www.microbediscovery.org/blog/2014/06/02/dr-ian-lipkin-blog-part-8-of-9/
and the donation link:
www.bit.ly/DonateToDrLipkin


Please join us.

Please join us and spread the word to your family, friends, fellow patients and anyone in your network via your group mailing list, Facebook page, Twitter, or however you can.

Together, we can make a difference!​.

To find out more, please visit the website:
www.microbediscovery.org

To donate, please click here:
www.bit.ly/DonateToDrLipkin

Please join us on Facebook:
www.facebook.com/microbediscovery

And on Twitter:
https://twitter.com/MicrobeProject

Contact us:
info@microbediscovery.org


 

Posted in The Microbe Discovery Project blog series

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 7 of 9

Part 7 of 9

The Study.

Image courtesy of cuteimage / FreeDigitalPhotos.net

Image courtesy of cuteimage / FreeDigitalPhotos.net

The gut microbiome is the collection of microorganisms that lives within our guts, and Dr Lipkin wants to carry out a cutting edge study of the gut microbiome of 100 ME/CFS patients and 100 rigorously matched healthy controls.

We need a well powered study that examines all three trees of life: the bacteria, the viruses; the fungi. We need to compare the populations; we need to quantitate the burden; we need to do all the math to figure out what is correlated and how; we need to link that to the cytokine data. We will carry out high-throughput sequencing; follow-up real time PCR; the culture of agents; and link to the cytokine data. This is a very large project.

Dr Lipkin says he is “desperately eager” to characterise the viruses, bacteria and fungi in the gastrointestinal tract of ME/CFS patients, to attempt to identify microorganisms which he believes are likely to be triggering or causing dysregulation of the immune system.

Image courtesy of Photokanok / FreeDigitalPhotos.net

Image courtesy of Photokanok / FreeDigitalPhotos.net

Make no mistake, this is a big study, and it will produce a huge amount of data. Dr Lipkin has a team of 60 ready to carry out this study at the Center of Infection and Immunity, at Columbia University in New York, the world’s largest and most advanced academic center in microbe discovery and diagnosis. All they are waiting for is the funding.

His team will use high-throughput DNA sequencing to identify viruses, bacteria and fungi in fecal samples and will then determine the amounts of each microbe using highly accurate real-time PCR assays that are specific for that microbe.

They will then correlate any findings with levels of cytokines (immune-system messenger molecules) in each patient, determined via a blood test. This correlation is intended to discover whether any populations of gut microbes are associated with specific immune system abnormalities (cytokine patterns) in individual patients. This is an important aspect of the project and it is where some very interesting and helpful results may come about.

For example, if a subset of patients are shown to have a specific cytokine pattern, and they also have a specific type of microbial population (e.g. a proliferation of a certain fungus or unusually high levels of a certain family of bacteria), then that means that Dr Lipkin’s team may find an association between the symptoms of ME/CFS and the microbial population of the gut.

Image courtesy of ponsulak / FreeDigitalPhotos.net

Image courtesy of ponsulak / FreeDigitalPhotos.net

And then another interesting step in the study is to develop an antibody test, based on any unusual microbes found in the samples, so that the team can then look for evidence of previous infection (i.e. possible triggers) in other patients who don’t currently have signs of an ongoing infection. Then they can see whether or not a much wider group of patients have been exposed to a specific pathogen or multiple pathogens, with a simple blood test. This will help to determine whether certain groups of patients may be susceptible to a disease process after exposure to specific microbial agents or infections.


This is a series of blogs based partly on an interview with Dr Ian Lipkin by Simon McGrath in January 2014, in relation to the intended study of the gut microbiome of ME/CFS patients. (To see Simon’s article please click here.)

Please feel free to repost this blog on your own website or Facebook page, etc., but please include a link to the original blog:
http://www.microbediscovery.org/blog/2014/05/29/dr-ian-lipkin-blog-part-7-of-9/
and the donation link:
www.bit.ly/DonateToDrLipkin


Please join us.

Please join us and spread the word to your family, friends, fellow patients and anyone in your network via your group mailing list, Facebook page, Twitter, or however you can.

Together, we can make a difference!​.

To find out more, please visit the website:
www.microbediscovery.org

To donate, please click here:
www.bit.ly/DonateToDrLipkin

Please join us on Facebook:
www.facebook.com/microbediscovery

And on Twitter:
https://twitter.com/MicrobeProject

Contact us:
info@microbediscovery.org


 

Posted in The Microbe Discovery Project blog series

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 6 of 9

Part 6 of 9

The hypothesis

We have evolved to produce immune responses that slow the replication of viruses and slow the replication of other microbes, but they were designed for the short duration; they weren’t designed to be constantly active.

Image courtesy of cuteimage / FreeDigitalPhotos.net

Image courtesy of cuteimage / FreeDigitalPhotos.net

Dr Lipkin observes that symptoms in ME/CFS are similar to those seen “with a low-grade but persistent infection, typically with viruses but that can also occur with some bacteria.” “Our objective therefore is to determine whether infectious agents can be implicated in this syndrome.”

Dr Lipkin is interested in exploring the idea that an infectious trigger may initiate immune activation, culminating in the “debilitating fatigue and cognitive dysfunction” associated with ME/CFS.

He observes that “there may be some variety of underlying mechanisms that can be triggered by different microbial agents that act through final common pathways, resulting in the disorders that we call either ME or CFS.”

In collaboration with the Chronic Fatigue Initiative, Dr Lipkin’s overall research plans for ME/CFS involve a comprehensive investigation of blood plasma, white blood cells, spinal fluid and now the gut microbiome.

So what we want to do – we’re desperately eager to do – is to characterise the microbiome in the gastrointestinal tract to see whether or not in fact we can identify populations of bacteria, viruses or fungi – it could be fungi too – that are responsible for this dysregulation of immunity which then presents as interference with cognitive function, persistent fatigue, and so forth.

Explaining the rationale behind the gut microbiome study, Dr Lipkin has described how he is hoping to find a microbial agent, or agents, that he believes may trigger, or cause, the immune system dysregulation (i.e. abnormal cytokine levels) that he has detected in blood plasma and spinal fluid samples of ME/CFS patients which in turn may result in the symptoms of ME/CFS.

Dr Lipkin describes how different populations of fungi, bacteria, or viruses, in the gastrointestinal tract, may potentially have an impact on the immune system, which could trigger or cause the symptom complexes seen in ME/CFS.

Image courtesy of dream designs / FreeDigitalPhotos.net

Image courtesy of dream designs / FreeDigitalPhotos.net

The gut microbiome study will include a wide-ranging search for viruses, bacteria and fungi, and it will correlate any findings with cytokine levels in each patient, determined via a blood test. This correlation is intended to discover if any populations of gut microbes are associated with abnormal cytokine patterns. If an association is detected, then this may indicate that certain microbes are causing problems, which will lead to trials of potential treatments which Dr Lipkin is already thinking about.

So Dr Lipkin intends to explore whether an abnormal microbial population within the gut microbiome may trigger or cause cytokine activation which in turn causes the symptoms in ME/CFS patients.

For example, perhaps there could be an unusual fungal overgrowth in the gut of a subset of ME/CFS patients, resulting in cytokine abnormalities that may, in turn, be causing the symptoms.

Take, for example, cryptococcus neoformans, a human fungal pathogen that mainly infects individuals with compromised immune systems, such as patients undergoing transplant or those afflicted with HIV/AIDS. Acute infections with this fungus are said to be rare in those with fully functioning immune systems, but cryptococcus neoformans can infect the central nervous system and cause inflammation of the brain. Symptoms of a central nervous infection may include fever, headache, lethargy, and cognitive symptoms. Perhaps the presence of a similar fungus could cause chronic symptoms in some ME/CFS patients? At this point in time, this is just conjecture, but Dr Lipkin will be able to detect any such fungal infection, and any viral infection or unusual population of bacteria in the gut.

Image courtesy of cuteimage / FreeDigitalPhotos.net

Image courtesy of cuteimage / FreeDigitalPhotos.net

Dr Lipkin observes that ME/CFS is highly heterogeneous, which means he believes that there may not be a single answer for the whole ME/CFS population. He suggests that he might find different answers for small subsets of patients: For example, perhaps 10% of patients have an unusual population of bacteria residing in the gut microbiome, perhaps 10% have symptoms triggered by a virus in the gut microbiome, perhaps 10% have unusual levels of a fungus in the gut resulting in symptoms, and perhaps 10% have a viral infection to be found in white blood cells (i.e. in Dr Lipkin’s other research study), etc. It’s a case of steadily chipping away at the disease with top quality research.

To define subsets of ME/CFS patients, Dr Lipkin needs to carry out large studies, collecting large amounts of data. This is why he is proposing a study involving 100 patients and 100 controls.


This is a series of blogs based partly on an interview with Dr Ian Lipkin by Simon McGrath in January 2014, in relation to the intended study of the gut microbiome of ME/CFS patients. (To see Simon’s article please click here.)

Please feel free to repost this blog on your own website or Facebook page, etc., but please include a link to the original blog:
http://www.microbediscovery.org/blog/2014/05/28/dr-ian-lipkin-blog-part-6-of-9/
and the donation link:
www.bit.ly/DonateToDrLipkin


Please join us.

Please join us and spread the word to your family, friends, fellow patients and anyone in your network via your group mailing list, Facebook page, Twitter, or however you can.

Together, we can make a difference!​.

To find out more, please visit the website:
www.microbediscovery.org

To donate, please click here:
www.bit.ly/DonateToDrLipkin

Please join us on Facebook:
www.facebook.com/microbediscovery

And on Twitter:
https://twitter.com/MicrobeProject

Contact us:
info@microbediscovery.org


 

Posted in The Microbe Discovery Project blog series

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 5 of 9

Part 5 of 9

Crowdfunding

After being turned down for funding by the NIH, for this important piece of research, an ME/CFS patient approached Dr Lipkin at a conference, and suggested crowdfunding the project, to speed things up, saying that we’re all losing valuable time in our lives.

A member of the campaign team and Dr W Ian Lipkin at the Stanford ME-CFS Symposium 2014

A member of the campaign team and Dr W Ian Lipkin at the Stanford ME-CFS Symposium 2014

Dr Lipkin is keen on the idea of involving the community to help speed up the research. He has enthusiastically embraced the patient community as collaborators in seeking funds and raising the profile of ME/CFS research.

He often talks of the HIV/AIDS patient community in the 1980’s, which embarked on a vocal campaign in an effort to stimulate government response to the disease. Adding a clarification that he doesn’t suggest such an approach for ME/CFS patients, he reflects on how HIV/AIDS patients, and friends of patients, chained themselves to railings of government buildings. He reflects on what he considers to be a more withdrawn ME/CFS community.

So this is where the ME/CFS patient community finds itself. Government research funding bodies reject research funding applications, and the best researchers in the world can’t obtain funding for ME/CFS.

But this time, with a leading scientific figure such as Dr Lipkin behind them, perhaps the patient community can pull together, and make a difference.

Dr Lipkin says he is committed to ME/CFS patients, but if he cannot obtain funding the fact is that he cannot carry out the research.

Columbia University Center for Infection and Immunity Image courtesy of CII

The Center for Infection and Immunity, Columbia University Mailman School of Public Health
Image courtesy of CII

So can the ME/CFS patients community afford not to support a scientist like Dr Lipkin and his team of sixty? After having seen a severe lack of large, rigorous, and replicated research studies into ME/CFS over a period of decades, this is an opportunity for the patient community to come together to support the sort of research that the community has been seeking.

By pulling together, and supporting Dr Lipkin, not only would the community see top-quality research into their illness, but they’d also have the service of a world-class scientist who is keen to study the illness, and to whom other scientists look toward with high regard. This is a rare event for ME/CFS research. It’s surely an opportunity not to be missed.

Dr Lipkin is eager to go. He has a plan. He’s enthusiastic. He wants to get on with it, and he says he’s behind schedule because of the difficulty with funding.


This is a series of blogs based partly on an interview with Dr Ian Lipkin by Simon McGrath in January 2014, in relation to the intended study of the gut microbiome of ME/CFS patients. (To see Simon’s article please click here.)

Please feel free to repost this blog on your own website or Facebook page, etc., but please include a link to the original blog:
http://www.microbediscovery.org/blog/2014/05/27/dr-ian-lipkin-blog-part-5-of-9/
and the donation link:
www.bit.ly/DonateToDrLipkin


Please join us.

Please join us and spread the word to your family, friends, fellow patients and anyone in your network via your group mailing list, Facebook page, Twitter, or however you can.

Together, we can make a difference!​.

To find out more, please visit the website:
www.microbediscovery.org

To donate, please click here:
www.bit.ly/DonateToDrLipkin

Please join us on Facebook:
www.facebook.com/microbediscovery

And on Twitter:
https://twitter.com/MicrobeProject

Contact us:
info@microbediscovery.org


 

 

Posted in The Microbe Discovery Project blog series