Friday, April 06, 2007

Scientist Reveals Secret of the Ocean: It's Him

Published: April 1, 2007

Maverick scientist J. Craig Venter has done it again. It was just a few years ago that Dr. Venter announced that the human genome sequenced by Celera Genomics was in fact, mostly his own. And now, Venter has revealed a second twist in his genomic self-examination. Venter was discussing his Global Ocean Voyage, in which he used his personal yacht to collect ocean water samples from around the world. He then used large filtration units to collect microbes from the water samples which were then brought back to his high tech lab in Rockville, MD where he used the same methods that were used to sequence the human genome to study the genomes of the 1000s of ocean dwelling microbes found in each sample. In discussing the sampling methods, Venter let slip his latest attack on the standards of science – some of the samples were in fact not from the ocean, but were from microbial habitats in and on his body.

“The human microbiome is the next frontier,” Dr. Venter said. “The ocean voyage was just a cover. My main goal has always been to work on the microbes that live in and on people. And now that my genome is nearly complete, why not use myself as the model for human microbiome studies as well. ”

It is certainly true that in the last few years, the microbes that live in and on people have become a hot research topic. So hot that the same people who were involved in the race to sequence the human genome have been involved in this race too. Francis Collins, Venter main competitor and still the director of the National Human Genome Research Institute (NHGRI), recently testified before Congress regarding this type of work. He said, “There are more bacteria in the human gut than human cells in the entire human body… The human microbiome project represents an exciting new research area for NHGRI.” Other minor players in the public’s human genome effort, such as Eric Lander at the Whitehead Institute and George Weinstock at Baylor College of Medicine are also trying to muscle their way into studies of the human microbiome.

But Venter was not going to have any of this. “This time, I was not going to let them know I was coming. There would be no artificially declared tie. We set up a cutting edge human microbiome sampling system on the yacht, and then headed out to sea. They never knew what hit them. Now I have finished my microbiome.”

Reactions among scientists range from amusement to indifference, most saying that it is unimportant whose microbiome was sequenced. But a few scientists expressed disappointment that Dr. Venter had once again subverted the normal system of anonymity. Recent human microbome studies by other researchers have all involved anonymous donors. Jeff Gordon, at the Washington University in St. Louis expressed astonishment, “I have to fill out about 200 forms for every sample. It takes years to get anything done. And now Venter sails away with the prize. All I can say is, I will never listen to one of my review boards again.”

Venter had hinted at the possibility that something was amiss in an interview he gave last week for the BBC News. He said “Most of the samples we studied were from the ocean but a few were from people.” When the interviewer seemed stunned, Doug Rusch, one of Venter’s collaborators stepped in and said “Collected with the help of other people.”

Venter was apparently spurred to make the admission today that many of the samples were in fact from his own microbiome due to a video that surfaced on YouTube showing Jeff Hoffman, the person responsible for collecting the water samples, performing a tooth scraping of Venter and then replacing the ocean water filter with Venter’s tooth sample.

Venter said the YouTube video was immaterial, “Well, we wanted to wait a few more weeks to have the papers describing the human microbiome published. But in the interest of human health we are deciding to make the announcement today.”

Unlike with the human genome data however, Venter says all of the data from his personal microbiome will be made publicly available with no restrictions. “If there is one lesson I have learned it is that open access is better than closed access. The more people can access my microbiome, the more they will help me understand myself. Plus, unlike Collins and Lander, who publish only in fee-for access journals, we will be publishing our analysis in the inaugural issue of a new Open Access journal that is a joint effort between the Public Library of Science and Nature. It will be called PLoN, the Public Library of Nature.”

In making his microbiome available, Venter has yet again abandoned his genetic privacy as he did when making his own genome available. Interestingly, the microbiome helps explain one of the first findings that was announced regarding his own genome. Venter said that analysis of the samples that came from his intestine reveal that microbes may explain why even though he has an apoE4 allele in his own genome (which is associated with abnormal fat metabolism) he does not need to take fat-lowering drugs. “Apparently, I have some really good fat digesters living in my gut. They make up for what is missing in my own genome.”

Dr. Venter's reason for having his own microbiome sequenced, he said in the interview was in part scientific curiosity -- ''How could one not want to know about one's own microbes?'' As to opening himself to the accusation of egocentricity, he said, ''I've been accused of that so many times, I've gotten over it.''

The key question that remains is – which of the samples were really from the ocean and which are from Venter. Venter said “Our funding agencies, including the DOE and the Moore Foundation, have agreed that we should not explicitly reveal which samples are which as this will encourage people to develop better methods of analyzing such complex mixtures of different microbes. Next week we will be announcing an X-prize award for the person who can identify which samples are mine and where they came from in me.”

Rob Edwards, a freelance microbial genomics expert says “It won’t be difficult to tell which are which. In fact, we had already identified an anomalous sample from Venter’s previous ocean sampling work, but nobody would listen to us.”

Jonathan Eisen, an evolutionary biologist who used to work for Venter says “I am certain that a few creative evolutionary analyses can reveal which sample is which. In fact, we are starting analyzing the samples already in anticipation of the X-prize announcement.”

Others are not so confident. Ed Delong, an ocean microbiology expert from MIT says “We have spent years carefully selecting our ocean samples to make sure they are not contaminated with sewage from cruise ships or from city drains. And now this – a purposeful mixture of ocean and human. It could take years to clean up the mess.”

Venter does not seem concerned. “If nobody can figure out which sample is from me and which is from the ocean, then we have no hope of making any progress in studies of either human microbiomes or oceans.”

More importantly, many scientists want to know what Venter will do next. Some want to know so that they can make sure to stay out of the way. Others probably relish the potential to go head to head with Venter. In this regard, Venter is not shy. “Biofuels. There is a great future in biofuels.”

13 comments:

  1. Is this even legal? And by "this" I mean an april fools day joke five days late.

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  2. Hey I just got it by email ... the date on the article says April 1. I just added a thing to note this.

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  3. Oh and I also got this follow up story by email:

    Collins and NHGRI Respond to Venter's Human Microbiome Gauntlet

    By NICHOLAS WADE
    Published: April 2, 2007

    The response has been quick and some would say, somewhat unusual. Yesterday, outspoken scientist Craig Venter announced that he had secretly completed a study of the microbes that live in and among the human body. Such microbes are thought to play key roles in almost every aspect of human health. Venter’s sneaking into this field under the radar has both amazed and astonished researchers in the field.

    But his old competitors from the human genome project did not take it lightly. Today, Francis Collins, Director of the National Human Genome Research Institute (NHGRI) has announced a new 500 million dollar project to produce a competing version of the human microbiome.

    “Who does he think he is?” Collins said on Meet the Press this Sunday where he was to talk about his new book on science and religion. “We went through this once before. We will not let him win this race either.”

    And as before, Collins apparently has the full weight of the government behind him. “We are announcing a new major initiative in really completing the human microbiome. As with the human genome, Venter words mean little here. The methods he used in his microbiome study simply cannot do the job well. We will have to pick up the slack once again.”

    When asked to comment Venter said “This whole thing is ridiculous. Do they not have anything better to do?”

    Tony Fauci, Director of the National Institutes of Allergy and Infectious Diseases (NIAID), said “Normally I would not comment on initiatives by other NIH agencies, but in this case I really have to. Microbes are under the NIAID umbrella. What does Francis think the ‘human” part of NHGRI means?”

    The controversy lit up the email networks yesterday, with hundreds of scientists signing a petition condemning Collins and the NHGRI for letting this prize slip through their fingers. “It is embarrassing. While the NHGRI has been spending money to sequencing a million different fungi and every type of mammal on the planet, we missed out on the most important study of our lifetimes,” said a tired and frustrated David Relman from Stanford.

    But Collins and his coworkers at NHGRI do not accept the criticism. Eric Lander, from the Broad Institute said, “Listen. Venter simply does not know what he is doing. Phil Green and I did a study last night that proves that shotgun sequencing cannot work on uncultured microbes. You simply cannot get enough material for sequencing and the microbes are way too small to collect reliably.” Lander and Green claim to have submitted a paper describing their findings early this morning.

    Collins said, “We have a commitment from all of the centers originally involved in sequencing the human genome. We will shift all our resources to finish this work as fast as God allows.”

    Perhaps the most surprising part of the whole controversy is that all of the people involved in the NHGRI microbiome effort have connections to start up companies working in the area of human microbiome research. In contrast, Venter has released the data free to the world. Yesterday Venter said “I learned my lesson with Celera. After I left there it was quite a task to get access to my own genome. So this time I put my microbiome into Genbank as quickly as possible.”

    When Collins was asked about the connections to private corporations he said, “Under Clinton, such connections were frowned upon. With Bush in office we are encouraged to build upon the public’s work through private enterprise. We specifically discussed the new program at a prayer breakfast yesterday. Bush is all for it.”

    However, it is not clear if this is really going to turn out like the human genome race. Venter, for his part says “Well, I am completely perplexed. How exactly can we have a race when we are done and have moved on to other things.” Collins says, “It is not for Venter to decide if there is a race. We are in this for the long haul. If he quits so be it.”

    This time apparently, there will be no agreement signed at the White House, and no tie declared. Lander adds “With Venter you never know. He is always five steps ahead of us in every area. But we will catch him one of these days.”

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  4. Thank His Noodliness Venter never got into cosmology. Or maybe that's next.

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  5. Oh come on - that would be the funniest thing ever. I am going to suggest it.

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  6. This comment has been removed by a blog administrator.

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  7. What a fascinating, hilarious story. By the way, how close are you to deciphering which genome comes from the ocean,which from Venter? I wonder if it is not a nobrainer...

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  8. citykitty

    fyi - it ws an april fools joke

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  9. Jonathan,

    Thanks. What a bummer! I already thought of strategies to distinguish the two kinds of microbes. As our symbiotic bacteria so often resort to horizontal transfer, this surely would have nailed it down. The other thing would have been to check the overall protein disorder. Venter's microbes probably would have a greater overall disorder. What do you think?

    But who has the idle mind to concoct such stories? This is amazing.

    ck

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  10. Well, alas, apparently, I had the time to concoct this story ...

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  11. Oh, I see now :-) There would have been a few clues to realize it. When rpm says "is this legal?" Or when Venter claims his open metagenome will get the attention of more people and they will help him understand himself better :-) Although he probably would secretly think such things he is smarter than this to avoid ridicule.

    BTW did you get any feedback from Venter?

    Anyway, congrats to your sense of humor and imagination, I was totally fooled.

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  12. I don't think this is actually that far off as a number of the original samples seem to have been contaminated with stuff off the hull of the boat ...

    http://www.ncbi.nlm.nih.gov/pubmed/15886695

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  13. truth has a strange way of matching fiction ...

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