New research finds genes influence the microbiome which then influences the immune system

Speaking Up About an Uncomfortable Condition – New York Times blog

New research on Inflammatory Bowel Disease, IBD, where immune cells attack the gut wall, finds that genes play a substantial role in the illness. Curiously, some of these genes have their effect indirectly, by affecting which bacteria flourish in the microbiome.

experts now know that certain genes affect the types of bacteria living in the gut; in turn, these bacteria influence the risk of getting an inflammatory bowel disease. Genes identified thus far appear to account for about 30 percent of the risk of developing an I.B.D.

It turns out the environment also plays a significant role in the disease and again the microbiome is implicated. Rates of IBD are much higher in developed countries like the US, and when people move from low risk areas such as India, to higher risk areas like the US, their chances of getting IBD increase too. Diet, and its effects on the microbiome are implicated:

Diet influences the types and balance of microbes in the gut, and different microbes produce substances that are either protective or harmful. For example, Dr. Sartor said, “Certain bacteria that can metabolize the fiber in certain vegetables and grains produce short-chain fatty acids that are believed to protect the gut. They inhibit inflammation and activate immune responses that stimulate recovery from cell injury.”

Read the full New York Time article.

Posted in Genetics, Immune system, Microbiome

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 4 of 9

Part 4 of 9

Funding Rejection

Dr Lipkin has already encountered the under-funding phenomenon that ME/CFS researchers and patients are all too familiar with. Dr Lipkin’s recent application to the National Institutes of Health (NIH) for a research grant for the intended investigation of the gut microbiome of 100 ME/CFS patients and 100 rigorously matched controls did not result in funding.

The ME/CFS patient community have become used to seeing even good quality research applications rejected by government funding institutions who simply refuse to allocate a fair amount to the disease and appear dismissive of the pressing need for answers.

However, it still came as a shock to many in the patient community to learn that this world renowned scientist (who had been called on by government agencies to answer the question of the novel retrovirus XMRV in relation ME/CFS) had had this latest application declined.

This has been happening to ME/CFS research for decades. The patient community is constantly told that the reason for the lack of funding is a lack of good-quality research applications. But good researchers drop out of the field because they can’t get funding, for reasons other than the quality of their research funding applications.

The ME/CFS community knows that it cannot rely on government agencies to fund ME/CFS research, and this is the reason that so much ME/CFS research is funded by philanthropists and patients themselves.


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/2014/05/22/dr-ian-lipkin-blog-part-4-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:
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And on Twitter:
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Posted in The Microbe Discovery Project blog series

Dr Ian Lipkin’s Study of the Gut Microbiome in ME/CFS Patients – Part 3 of 9

Part 3 of 9

Microbiome Research – A Piece of the Puzzle for ME/CFS

In collaboration with the Chronic Fatigue Initiative, Drs Lipkin and Hornig succeeded in obtaining funding for a large and rigorous investigation looking for pathogens in the blood (plasma and white blood cells) and spinal fluid of ME/CFS patients, and an initial smaller study of the gut microbiome.

Their overall research plan involves a comprehensive search for pathogens and unusual microbial agents; and an investigation of the metabolome (the complete set of small-molecule metabolites) and the proteome (the entire set of proteins); a study of genes and cytokine levels (immune system biomarkers); and an investigation of antibodies in a search for potential infectious triggers of ME/CFS.

There’s no doubt that Dr Lipkin does not settle for half-baked plans. He has embarked on a mission to find the microbial cause or causes of ME/CFS using cutting edge technology, a team of 60, and rigorously designed trials with well matched patients and healthy controls.

Commenting on a soon-to-be-published study in which his team has discovered significantly abnormal levels of cytokine levels in ME/CFS, Dr Lipkin has said: “I think we can clearly say that there is some-thing that is driving a particular series of immune responses. So I’m more keen than ever to explore all the different compartments we might, to see whether or not we can identify that trigger, whatever it happens to be.”

The gut microbiome is a piece of the puzzle that Dr Lipkin feels is needed to gain an overall picture of the illness, as part of a wide-ranging exploration of ME/CFS.


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/2014/05/21/dr-ian-lipkin-blog-part-3-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 2 of 9

Part 2 of 9

Why is Dr Lipkin so enthusiastic to be involved ME/CFS Research?

So what has piqued Dr Lipkin’s interest in ME/CFS research? Dr Lipkin was originally involved in a study of ME/CFS in 1997 with his colleague, Dr Brigitta Evengard. Dr Lipkin often describes how they discovered evidence for polyclonal B-cell activation, in roughly 75-80% of a cohort of patients that Dr Lipkin describes as very carefully characterised. These results convinced Dr Lipkin that ME/CFS is a biomedical illness with measurable biomedical abnormalities related to the immune system.

More recently, Dr Lipkin was asked by US government health agencies to settle a question in relation to the XMRV retrovirus, and another similar virus. The viruses had been detected in the blood of large proportions of ME/CFS patients, and Dr Lipkin was brought in to investigate the situation further. Dr Lipkin and the team working on the project found no evidence to support research linking the retroviruses to ME/CFS.

At that time, Dr Lipkin was asked to get involved in ME/CFS research by the patient community and, as a scientist, Dr Lipkin says he felt compelled to continue working on ME/CFS to help the patient community and to work to unravel the mysteries of the disease.

The Chronic Fatigue Initiative, funded by the Hutchins Family Foundation, has provided resources for Dr Lipkin’s team, and others, to carry out a large scale search for pathogens and immune markers in relation to ME/CFS.

During the course of this research, Dr Lipkin, Dr Hornig, and their colleagues discovered abnormal cytokine levels in the blood and spinal fluid of ME/CFS patients. Dr Lipkin is excited about these soon-to-be-published results, and believes that the study data suggests that ME/CFS is an immune-related illness (with distinct immune abnormalities) triggered by infection with a microbial agent, such as a bacterium, virus or fungus.

The cause of ME/CFS is currently unknown, and Dr Lipkin and his team are motivated partly by the challenge of finding the cause, or causes. His research program is designed to find the agent/s that he believes are responsible for the symptoms.


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/2014/05/20/dr-ian-lipkin-blog-part-2-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 1 of 9

Part 1 of 9

Background to the Gut Microbiome Study of ME/CFS Patients

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

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

Dr. W. Ian Lipkin is director of the Centre for Infection and Immunity at Columbia University, New York, and is a world leader in terms of discovering pathogens. He has been described as “The World’s Most Celebrated Virus Hunter”, and as “A Man From Whom Viruses Can’t Hide.”

Columbia University’s website explains that Dr Lipkin & his team “have discovered or characterized more than 500 infectious agents including Borna disease virus, West Nile virus, LuJo virus, human rhinovirus C, piscine reovirus and canine hepacivirus.”

The Chronic Fatigue Initiative (CFI) is a non-profit organisation funded by the Hutchins Family Foundation, and has worked in collaboration with Dr Lipkin and his colleague, Dr Mady Hornig, and other researchers, designing and implementing a large biomedical investigation into chronic fatigue syndrome (CFS), also known as Myalgic Encephalomyelitis (ME), looking for pathogens and immune system dysregulation in blood plasma, white blood cells and spinal fluid.

Drs Lipkin and Hornig have now completed a study of blood plasma, and spinal fluid. Their team have not yet found any pathogens clearly related to the disease, but they did discover some intriguing immune biomarkers in the blood plasma and spinal fluid studies, suggesting immune dysregulation in ME/CFS patients.

Dr Mady Hornig. Photo courtesy of the Columbia University Center for Infection and Immunity

Dr Mady Hornig.
Photo courtesy of the Columbia University Center for Infection and Immunity

The results have not yet been published, but Dr Lipkin is excited by them. They relate to changes in levels of cytokines, which are immune-system messenger proteins. He says “I think the cytokine data, that we are putting out are going to clearly demonstrate there is an organic problem here.”

Dr Lipkin believes that this apparent immune system dysregulation must be caused or triggered by an infectious agent, or microbial agents, and he wants to find the agent responsible.

His team is now studying white blood cells from ME/CFS patients and he plans to study the gut microbiome as the next step in a comprehensive research program, with his colleague, Dr Mady Hornig, who is taking the role of principal investigator for the gut microbiome study.

Dr Hornig is the director of Translational Research, at the Center for Infection and Immunity, and Associate Professor of Epidemiology. She is internationally recognized for her clinical research on the role of microbes, immunity, and xenobiotics in relation to disorders such as autism, schizophrenia, PANDAS (Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal infection), attention-deficit/hyperactivity disorder, and chronic fatigue syndrome.

Dr Lipkin and Dr Hornig intend to study the gut microbiome of ME/CFS patients in a wide ranging and rigorous hunt for viruses, bacteria and fungal agents, seeking the cause of the immune dysregulation that they have detected in ME/CFS.

The gut microbiome is the collection of microorganisms that live within the gastrointestinal tract, consisting of bacteria, viruses and fungi.

Columbia University Medical Center campus. 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

 


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/2014/05/19/dr-ian-lipkin-blog-part-1-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

Brooke and Belinda raised $400 by selling books

BrookeAndBelindaThis is Brooke and Belinda (who has been diagnosed with ME/CFS and fibromyalgia since 2001).

They have recently set a book stall at their local community’s annual ‘Booktown’ event in Australia and raised $400 by selling books for Dr. Ian Lipkin’s microbiome study.

Thank you very much – what an inspiration you are!

You can  read more on our Facebook page here - and why not follow the crowdfunding developments on our Facebook page? – www.facebook.com/microbediscovery

Have you done a similar community fundraiser? Or are you planning to do one?  Please get in touch and let us know.

TOGETHER, WE CAN DO IT

Posted in Australia, Crowdfunding, Dr Ian Lipkin, Global effort

UPCOMING EVENTS

1-2 September, 2014: Dr. Lipkin will be a keynote speaker at the conference of the UK ME/CFS Research Collaborative, which will be held in Bristol.

3 September, 2014: Dr. Lipkin will give a talk in London for patients about his work: still time to book