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Prof Trevor Marshall
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Amy was invited to write the chapter on "Autoimmune Disease in the Era of the Metagenome" for JCVI's new textbook - Metagenomics of the Human Body.

The book chapters have just been put online for purchase. So we can now put a copy of our preprint up so you can all read it, and print a copy for Doc :)

You will find the preprint at:

http://Autoimmunityresearch.org/preprints/Proal_MHB_Chapter_preprint.pdf

Info on JCVI is at http://www.JCVI.org

This is obviously a big step forward for all of us. Being invited to write a chapter in a prestigious textbook from a prestigious organization says a lot about the acceptability of our science, and the forty-plus printed pages show that the science is no longer just an outline - we have gotten it pretty well detailed-out at this point.
 
Enjoy!
 
UPDATE: The book can be browsed and searched at Amazon.com

http://www.amazon.com/Metagenomics-Human-Body-Karen-Nelson/dp/1441970886#reader_1441970886

Last edited on Fri Dec 3rd, 2010 10:31 by Prof Trevor Marshall

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CONGRATULATIONS!!!!!  :D:D:D:D

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WTG! :D:D:cool:

Thanks again for all of your hard work in preparing and producing this latest achievement. After looking forward to the release for so long, it's finally here. :)

Kudos to Amy, Paul, and Trevor for continuing to move this exciting research forward and share it with the world.
Cheers,
Marysue

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CONGRATULATIONS DR MARSHALL !!
"big red green and yellow balloons"
" tons of colorful confetti"
followed by "loud trumpets of victory like music"
500+ Exclamation marks !!!
Followed by more CONGRATULATIONS to AMY & PAUL !!!!
PS. Sorry you two are under all the confetti. But I was excited and wanted to go all out. Thanks to all who who worked so hard on this awesome breakthrough.
As always, Best-- Terry

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CONGRATULATIONS, Amy, Paul, and Trevor!  I join the others in celebrating the team's efforts of yet another very important milestone!  THANK YOU for all that you have done and continue to do! With appreciation . . . Carole  :)

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This is a milestone for the Autoimmunity Research Foundation ARF and everyone on the Marshall Protocol.

I read the whole paper this evening; that feat was impossible before starting the MP.

Congraulations to everyone on a job well done.

Sherry

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Congratulations to Dr Marshall, Amy, Paul and all who assisted in writing this important chapter!  I skimmed it as it was late tonight when I noticed this was posted.  I look forward to a thorough reading tomorrow though! 

This is indeed an important milestone for the MP!  Let us all hope this speeds the adoption of the MP into mainstream medical practice. 

Last edited on Wed Nov 17th, 2010 02:08 by ChrisMavo

lymeinohio
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This article helps me a lot in understanding my own chronic disease process.  Also, it gives me more hope to carry on despite all the difficulties.  Thank-you! Thank-you! I will pass it on to others.  Jackie

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Congratulations!:D

I'm so excited about this milestone. Thank you for all your hard work in getting MP one step closer to mainstream medicine. I already pre-ordered the book; can't wait to get it!

Cathy:)

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Congratulations Amy, Paul And Dr Marshall

I can't wait to take a copy to My Doctor and My Girlfriends Pulmonologist at National Jewish Hospital. We have discuss the Marshall Protocol More than once she is always nice, But I don't think she understands how much science there really is and Thanks To Amy, Paul And Trevor now I can show her if she will read it. Cogratulation Again on such a Major Acomplishment and For all You have done to Make this day Possible and Giving Me Hope That There is life after Sarcoid  Thank You All More Than You Will Ever Know, Bob

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Congratulations and thanks to you all on your superb achievement!

Well done - what a tour de force!

Morag

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Unbelievably impressive! I really hope those who read it will be inspired to work that much harder to advance our understanding of the human microbiome and how it relates to human disease. Thank all three of you on behalf of the future generations who will benefit from your hard work and persistence in shining light where no one has been looking for so long.

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I keep thinking back to the original picture of Amy on this website...she was just a kid!!! It's wonderful to see her progress. Congratulations to all of you.

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Congratulations Amy, Paul and Trevor! As they say on teh internets: EPIC WIN!!! :)

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Well done! Great chapter. IngeD:cool:

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CONGRATULATIONS, and thank you for all your hard work what an important milestone this is, I am sure that this article will help so many more people to understand the process of chronic disease.  Again thank you Trevor,  Amy and Paul for working so hard on all our behalf.
margo

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CONGRATULATIONS!!!!

This really is an exciting time for the MP!!

Thank you Dr. Marshall, Amy and Paul for all you have done to bring about this historical moment........and I am so grateful to be a part of it!!!


Dian

Last edited on Mon Nov 29th, 2010 10:22 by minski2

Prof Trevor Marshall
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I just noticed that the JCVI book is online for browsing at Amazon. I went to this URL:

http://www.amazon.com/Metagenomics-Human-Body-Karen-Nelson/dp/1441970886#reader_1441970886

and was able to read the introductory chapters.

You can also search the book for keywords :)

..trevor..

eClaire
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Thanks! What a great chapter. I was able to get to page 8 when I needed a break (this is a great improvement for me). I plan to read the rest. In the meantime, thanks so much for all the work you do!!!

Prof Trevor Marshall
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I just got an email for Amazon to say that my copy has shipped - will be here Tuesday :)

A little splurge for the Holidays :)
 
 

Prof Trevor Marshall
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My copy of the book arrived from Amazon yesterday, Monday 6th December :)

Total number of pages 337, of the 16 chapters ours is the most detailed, at 46 pages :)

The best way to read the parts you are most interested is via Amazon.com's preview. Remember that you will have to erase the Amazon cookies every time they decide you have read enough for free :)

http://www.amazon.com/Metagenomics-Human-Body-Karen-Nelson/dp/1441970886#reader_1441970886

..Trevor..
ps: I note some of the information is out of date. For example, the chapter on the lung microbiome was written before the COPD study showed that healthy lungs had a prolific microbiome. The chapter says there is no healthy lung microbiota. It is a pity when mistakes like this get through to final print, but this is a rapidly moving field, and the preliminary COPD lung data has only been presented at a conference...
 

eClaire
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Given your comment then it is safe to assume that you now think that there might be "healthy" bacteria?

Prof Trevor Marshall
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 All genomes will have both negative and positive interactions with the human genome. Based on what we know now, I would prefer no pathogens at all, so that the human genome can get on with doing what it evolved to do...

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Trevor,

Did not the Human Genome evolve from  early bacterial life forms?   And does it not continue to evolve in concert with the baterial metagenome

The other day I was sitting and thinking about our modern society, evolutionary biology, epigenetics and the metagenome.  I could not help thinking that with the advent of and overuse of antobiotics, the human genome has undergone such transformatios due to epigenetic changes resulting from pathogenic microbes, that within mine and my children's generation we have created a human race that will continue to exhibit chronic illness symptoms earlier and earlier in their lifetimes.

Much more research needs to be focused on earlier intervention to avoid impending future health disasters.


Teresa

Prof Trevor Marshall
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First, the word "epigenetic" does not necessarily fit into the argument you are making.

I think the biggest single contributing factor to the surge in chronic disease is the globalization of food supplies, especially meat, the surge in travel, especially International travel, and a total lack of understanding about how the microbiota are spread between an increasingly social modern population.

Yes, use of antibiotics which were never properly test in-vivo, is also a problem. How can it be that, just today, a paper comes out disclosing that a 1968 antibiotic -- minocycline -- has a direct affect on cancer autophagy, on apoptosis:

http://www.ncbi.nlm.nih.gov/pubmed/21079420

Antibiotics were thought to just kill bugs. Nobody bothered to see if they had any other actions in the human body. This was a terrible mistake.

Finally, the introduction of Vitamin-D supplementation of milk on a grand scale by Nestle in the 1950s, such that essentially all shipment of milk to less developed nations has been heavily supplemented since that date, gave the Th1 microbiota a big help in knocking out the human innate immune system, and paving the way for HIV, EBV, and other VDR-centric organisms to flourish.
 

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Here's an image from a presentation by Karesh on the globalization of food.

Grateful Survivor
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Wow, Paul, what a fabulous illustration of Trevor's point about the globalization of food supplies! It's a great map, and would do Edward Tufte* proud.

*author of the classic The Visual Display of Quantitative Information

Thanks for sharing it so promptly!

All best,
Dody
geography major and GIS (geographic info systems) analyst

paulalbert
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I love Edward Tufte. :)

Lottis
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In a nutshell! :)


Dr Trevor Marshall wrote:

...
I think the biggest single contributing factor to the surge in chronic disease is the globalization of food supplies, especially meat, the surge in travel, especially International travel, and a total lack of understanding about how the microbiota are spread between an increasingly social modern population.

Yes, use of antibiotics which were never properly test in-vivo, is also a problem. How can it be that, just today, a paper comes out disclosing that a 1968 antibiotic -- minocycline -- has a direct affect on cancer autophagy, on apoptosis:

http://www.ncbi.nlm.nih.gov/pubmed/21079420

Antibiotics were thought to just kill bugs. Nobody bothered to see if they had any other actions in the human body. This was a terrible mistake.

Finally, the introduction of Vitamin-D supplementation of milk on a grand scale by Nestle in the 1950s, such that essentially all shipment of milk to less developed nations has been heavily supplemented since that date, gave the Th1 microbiota a big help in knocking out the human innate immune system, and paving the way for HIV, EBV, and other VDR-centric organisms to flourish.

Sallie Q
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forget Julian Assange 'in the frame' for Wikileaks'
I'd like to see a class action against Nestle for cruelty to children
Sallie

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Hi !

I did not know who Craig Venter (of the Craig Venter institute that is responsible for the book we are discussing in this thread) was.

Some time ago someone here on the site posted a link to a Ted-conference-talk about people whose taste is in color.

That presentation was so incredibly interesting that I have been watching all sorts of presentations on TED.com since then.

To my astonishment I ran into a presentation of Craig Venter !

It blew my mind, a must see:
- http://tinyurl.com/nxo4wu

It gives me a good feeling to see that a pioneering organisation like JCVI gives credibility to the MP-pathogenesis.

There are more presentations of Craig Venter on TED.com  btw.

Best, Frans

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This study indicates that a nutrient, choline or lecithin (often found in supplements, but also in fish and some other foods), when combined with a particular gut microorganism, can produce a pro atherogenic substance:

http://www.sciencedaily.com/releases/2011/04/110406131814.htm

Just showing another link between the microbiome and health, adding complexity to figuring out effects of things we ingest.

Joyce Waterhouse

Prof Trevor Marshall
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Frans,
Here are two more excellent videos:

http://www.charlierose.com/view/interview/11024

http://www.youtube.com/watch?v=HLP6x4h1tOM

..Trevor..
 

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These are very thought provoking videos, and Thank you for the link.

The work does raise ethical and philosophical questions:  is the computer the "parent" of this new synthetic life form, or is the true "parent" the intelligence and creativity of human beings?  Isn't the computer merely a tool?

Excellent videos.

Sherry

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The computer is merely a tool. It slavishly does what I tell it to do. It is up to me to tell it what I want to look at, and up to me to interpret the results when they are displayed. Other scientists look at the videos I show them and they see nothing. They notice nothing. They learn nothing.

At the Nuclear Receptors conference I was showing a video emulation of exactly how the VDR activates, how each helix has to be displaced. Nobody was interested. The movie was not something they could relate to. To this day I am the only person I have met who understands precisely how 1,25-D and Olmesartan deform the VDR in order to enhance binding to DRIP205. Even though the 4 key hydrogen bonds are shown on this poster from 2007:

http://AutoimmunityResearch.org/transcripts/dmm2007-harvard.pdf
 

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I agree, very interesting videos ... thanks for posting them!

It must be very frustrating Dr Marshall to have your discoveries fall on deaf ears of scientists!  They just do not grasp how monumental a breakthrough you have achieved.  There is a LOT of ego in the scientific world!! 

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Thanks Joyce and Trevor for posting these links.  Lots of fascinating stuff!

Here's another youtube video of Venter speaking at CalTech just a few months ago.  It might have been posted elsewhere, but this is the first time I saw it.

http://www.youtube.com/watch?v=HdgfzdlgUHw
:)
Marysue

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Why do you think that is, Trevor? The lack of interest and inability to grasp ...  Are medical scientists intimidated by computer models or are your explanations/theories just too contradictory to what they know/believe/learned that they just instinctively dismiss it?

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In the "science" of creating a learning environment, it is my understanding that the first order of business is to help the student feel at ease (safe) because only then is the brain in the proper state to take in new information. The second is to provide a context for the student so that they see the value in the knowledge presented.

Perhaps the first part that is why civility on our forums is so important to me personally. :)

Of course, those checking us out online are most likely very motivated to discern if what we are reporting can help them, or a loved one, with a medical condition that has not turned around with standard of care, so the second part is easier for the patient than it is for the researcher of health professional to grasp. You think?

Prof Trevor Marshall
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Rico wrote: Are medical scientists intimidated by computer models or are your explanations/theories just too contradictory to what they know/believe/learned that they just instinctively dismiss it?
All of the above. Different emphasis in different people. Nobody likes change. Medicine (as a whole) really hasn't come to grips with Helicobacter pylori yet, let alone the Microbiome.
 

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Here's another one on 3 types of gut microbiomes

Joyce

http://bit.ly/erT660

naturenews

Published online 20 April 2011

Nature

doi:10.1038/news.2011.249

Gut study divides people into
three types

Bacterial populations fall into three distinct
classes that could help to personalize
medicine.

Nicola Jones

Just as there are a few major blood types that divide
up the world, so too, a study has found, there are
just three types of gut-microbe populations.

The result could help to pinpoint the causes of
obesity and inflammatory bowel disease, and to
personalize medicine.

"This is important. Say you want to compare ill
people and healthy people; you better match them
properly [by gut type],"

Dusko Ehrlich told Nature at a human microbiome
conference in Vancouver, Canada, in March.

Ehrlich, a senior researcher on the paper published in
Nature today1, is director of the Microbial Genetics
Research Unit at the National Institute for
Agricultural Research in Jouy-en-Josas, France, and
part of a European consortium aiming to unpick links
between gut microbes and disease.

The finding of just three types of gut-microbe
population was an unexpected result that fell out of
the team's early analysis. The types aren't related to
age, gender, nationality or diet.

"What causes it? We don't know," says Ehrlich.

One possible explanation, which the team is testing,
is that a person's gut-microbe make-up is
determined by his or her blood type.

Alternatively, it might be determined by metabolism:
there are three major chemical pathways by which
people get rid of excess hydrogen gas created during
food fermentation in the colon, and the gut type
might be linked to those.

Or, perhaps the first microbes a baby is exposed to
as his or her immune system is developing
determines the type.

A person's gut type might help to determine whether
people can eat all they like and stay slim, whether
they will experience more gut pain than others when
sick and how well they can metabolize a certain
drug.

It's unclear whether a person's gut type might
change over time, either naturally or in response to
something such as a steady diet of probiotic yoghurt.

Little helpers

Researchers have only recently begun to appreciate
the importance of the bacterial cells that grow on
and in our bodies, outnumbering our own cells by
about ten to one.

In rodents, gut microbes are known to influence
weight and immunity against disease (see 'For mice,
swapping fecal bacteria can mean life or death':
http://bit.ly/e2CjTW ).

In the United States, the Human Microbiome Project
is aiming to catalogue all the microbes living in our
nose, mouth, skin, gut, and urinary and genital
tracts; in Europe, the Metagenomics of the Human
Intestinal Tract (MetaHIT) Consortium, the group to
which Erlich belongs, is focusing on the gut.

For this paper, the team used genetic screening to
identify the microbes present in faecal samples from
22 Europeans enrolled in other gut-microbe studies,
and compared the results with samples from 17
people in the United States and Japan.

When they looked to see how similar the samples
were, the researchers found that they clustered
neatly into three groups.

"We were very surprised," says Peer Bork of the
European Molecular Biology Laboratory in Heidelberg,
Germany, also a senior author on the paper.

Although the number of samples in this paper is
small, Bork says that his team now has results from
more than 400 samples and that the clustering is
still evident.

"I was surprised too. I thought it would be much
more chaotic," says Brett Finlay, a microbiologist at
the University of British Columbia in Vancouver.

Fat or thin

The team has named the clusters after the dominant
genus: Bacteroides, Prevotella and Ruminococcus.

Bacteroides are known to be good at breaking down
carbohydrates, so it is possible that people of this
type might, for example, struggle more with obesity,
says Bork.

Prevotella tend to degrade slimy mucus in the gut,
which could conceivably increase gut pain.

And some Ruminococcus help cells to absorb sugars,
which might contribute to weight gain.

Bork cautions, however, that each person carries a
complex mix of perhaps a few thousand bacterial
species, and too little is known to make sweeping
generalizations about the implications of the
different gut types.

The team has, however, found hints that one
particular disease — Bork won't yet say which one —
is found only in people of one microbial gut type.

The team also has a host of as-yet-unpublished
results that link specific gut-bacteria species to
individual characteristics.

"If I have a stool sample I can tell how old you are,"

says Bork.

"That seems useless because you already know how
old you are, but it's proof of principle that it could
maybe be used for all sorts of other things."

Ehrlich says that his team can diagnose obesity with
an accuracy of 80-85% from half a dozen bacterial
species.

"The real question is: what is the gene set we need
in our guts to be healthy?"

says Finlay. That has yet to be answered.

References

Arumugam, M. et al. Nature Advance online
publication doi:10.1038/nature09944 (2011).


Sallie Q
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jcwat101 wrote: ............."We were very surprised," says Peer Bork of the
European Molecular Biology Laboratory in Heidelberg,
Germany, also a senior author on the paper.
............
"If I have a stool sample I can tell how old you are,"

says Bork.

"That seems useless because you already know how
old you are, but it's proof of principle that it could
maybe be used for all sorts of other things."....................................................

The penny just dropped :D

Wouldn't it be interesting for MP research team to be able to initiate a project with Bork's team to analyse a significant number of stage 5 'Alumni' stools separately to test a hypothesis that long term MPers may gain an objective biological age below calendar age

pgeek
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That's not a penny, that's a pound :P

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Other than wondering what to put on the customs forms, that sounds like a great idea.

Deb

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How about "Hazardous Waste" :) :)

Sallie Q
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or Scraps :P

Happy Christmas, Hanukkah, New Year, Light Festivals, to Everyone
may your guardian angel or guiding star be with you in the coming year.

Here in this battered confraternity
whose borders are alternate herx and gain
Where patient after patient in their trials
abode a year or two, and went their way

with apologies to Omar Khayyam 





* We can help you understand chronic disease, but only your physician is licensed to give you medical care *

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