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Medicine Science

Newly Discovered Virus Widespread in Human Gut 100

Posted by timothy from the right-under-their-noses-and-stomachs dept.
A newly discovered virus has been found by a San Diego State University team to live inside more than half of all human gut cells sampled. Exploring genetic material found in intestinal samples, the international team uncovered the CrAssphage virus. They say the virus could influence the behaviour of some of the most common bacteria in our gut. Researchers say the virus has the genetic fingerprint of a bacteriophage - a type of virus known to infect bacteria. Phages may work to control the behaviour of bacteria they infect - some make it easier for bacteria to inhabit in their environments while others allow bacteria to become more potent. [Study lead Dr. Robert] Edwards said: "In some way phages are like wolves in the wild, surrounded by hares and deer. "They are critical components of our gut ecosystems, helping control the growth of bacterial populations and allowing a diversity of species." According to the team, CrAssphage infects one of the most common types of bacteria in our guts. National Geographic gives some idea why a virus so common in our gut should have evaded discovery for so long, but at least CrAssphage finally has a Wikipedia page of its own.
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Newly Discovered Virus Widespread in Human Gut More

Newly Discovered Virus Widespread in Human Gut

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  • CrAssphage? (Score:5, Funny)

    by Anonymous Coward on Sunday July 27, 2014 @08:48PM (#47546723)

    come on...

  • That's all, did you expect a joke?

  • The Phage (Score:5, Funny)

    by Chad Smith ( 3448823 ) on Sunday July 27, 2014 @08:53PM (#47546757)
    Vidiians are going to be pissed.

  • crAss (Score:5, Informative)

    by GrahamCox ( 741991 ) on Sunday July 27, 2014 @08:55PM (#47546759) Homepage
    OK, I wondered. I'm sure you did. It is short for 'cross Assembler' - the software used to sequence the genome (I skimmed the paper). Not what you thought. No.

    No shit.

    • Re:crAss (Score:5, Funny)

      by Nemyst ( 1383049 ) on Sunday July 27, 2014 @09:05PM (#47546805) Homepage
      It's still a pretty shitty name though. I wonder if the scientists are bummed about the realization.
      • This is bottom-grade science. Too much Farquharson around at SDSU. Even the Wikipedia page is bog standard.

      • FRY: This is a great, as long as you don't make me smell Uranus. ... I'm sorry, Fry, but astronomers renamed Uranus in 2620 to end that stupid joke once and for all. FRY: Oh. What's it called now? PROFESSOR FARNSWORTH: Urectum.

    • I read that. I think it's full of shit. They can claim it's an accident all they want, but they're obviously blowing smoke up our ass.

    • Is this the cause of (cr)Assburger's?

      • Re: (Score:1)

        by tepples ( 727027 )
        Just because vaccines don't cause autism doesn't mean that a wild virus (the opposite of a vaccine) necessarily causes it.

        • Re: (Score:3)

          by alzoron ( 210577 )

          Actually regular viruses can act as vaccines as well, for instance contracting cowpox can result in an immunity to smallpox.

    • Yeah, in the same way GIMP stands for Gnu Image Manipulation Program

    • And their reason not to choose xasm was...

  • it smell like ASS up in here!

  • My pandemic (Score:4, Funny)

    by cablepokerface ( 718716 ) on Sunday July 27, 2014 @09:12PM (#47546835)
    Lol, so you guys finally discovered it! Well you're too late, haha. I am now going to invest my points in heart failure and liver failure and your doctors will never have a cure in time!

  • Chromium Assphage (Score:1)

    by Anonymous Coward

    My new heavy metal band, come check us out on tuesday nights, $2 PBRs

  • So does this mean that as well as the bacteria that we have living in a symbiotic relationship with us, there's viruses in our internal ecosystems that we need to keep us alive as well now?
  • Looks like the virus acts as a catalyst; Helping other viruses in reacting fast and become more potent !!!
    • Any virus is a form of life, in that it is negative entropy, in an entropy tending universe. Life seeks to create order, and maintain order, oftentimes in a fight, at an expense of another life form. A virus, because it cannot sustain itself on its own, has no functioning cell or nucleus, it is a parasite, a predator of other life. A predators function in an ecology is extremely complex, but there is one rule to any long term successful predator or parasite, is that you don't exterminate your food supply, y

  • Most of you have it... (Score:5, Informative)

    by robedwards ( 134136 ) on Monday July 28, 2014 @07:27AM (#47548611) Homepage

    I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department [sdsu.edu] at SDSU [sdsu.edu] ...

    It was named after our analysis software, crAss (cross assembly) for comparing DNA sequences from different samples (called metagenomics [wikipedia.org]). Here is the crAss article [nih.gov] that was published in 2012. Everyone else had missed this virus that was in their DNA samples, most of which have been published (many in high profile journals like Science and Nature). However, it wasn't until we used crAss that we recognized the virus was abundant and everywhere. When we looked at the NCBI [nih.gov] database of nucleotide sequences the virus is there and scientists had seen it before in fragments but not been able to piece it together to a whole genome.

    We only find the phage in poo samples (they usually call them fecal samples...) from people (oh, and very occasionally on the skin of people, but we suspect they don't have great hygiene). We haven't been able to find it anywhere else that we have looked, and so we don't know what its range is beyond the intestine.

    This is one of those situations where the computational biology is really driving the question and the biologists. You often head that bioinformatics is just a support science for "real biology" - that's not true. In this case, based on the questions the bioinformatics group came up with, the biology was supporting the bioinformatics analysis. The biologists were able to determine that the assembly of DNA fragments was correct, and confirm, using PCR [wikipedia.org], that it is indeed a whole genome.

    We (and others) are working on isolating the phage and designing experiments to test exactly what it does in our guts. That doesn't mean we can't speculate!

    A couple of answers to comments:
    1. Everyone (including the scientists that write grants and papers) confuses gut and fecal samples (sometimes deliberately). To be clear, almost all the samples we have are feces because it is everyone has it, it is easy to get, and everyone seems to want to share it. To get samples other than feces you need surgery, and so the non-fecal samples tend to be associated with other issues that require surgical intervention (and thus are complicated).
    2. Noriko (Nori) Cassman is a graduate student (and so doesn't have tenure yet)
    3. We were not responsible for the wikipedia page (or the twitter account)
    4. phages are viruses that attack bacteria only. There is no evidence or suggestion that this virus does anything to human cells.

    • Re:Most of you have it... (Score:4, Funny)

      by ArsenneLupin ( 766289 ) on Monday July 28, 2014 @08:14AM (#47548793)

      everyone seems to want to share it.

      ... and I just thought only monkeys behaved like this...

    • I'm really curious as to what kind of comments about the name that you got in pre-publication reviews...

      • Re:Most of you have it... (Score:5, Informative)

        by robedwards ( 134136 ) on Monday July 28, 2014 @08:47AM (#47548939) Homepage

        In one of the early versions of the paper we didn't have a name for it and just called it "the new virus". A (anonymous) reviewer said "The new virus would seem to need a name ("the new virus" is clumsy).", so we came up with crAssphage. It turns out there was an unexpected side benefit - there were essentially no Google results for crassphage until last week!

    • I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department at SDSU ...

      Quick question -- I see from your paper, do you have an idea what it looks structurally? A bunch of media sites have pictures but are using what is obviously stock art (mostly of T-even phages), but from your paper I see that it has no close phylogenetic relationship to known phages (and if your group had e-microscopy or crystallographic data, it would have been in the paper already).

      Still, I figured someone skilled in virology might be able to identify some capsid sequences or something, and be able to ma

      • We don't have that capability yet. We have not isolated the virus, yet, (we're trying hard...) and so we don't have EMs of the particle which would tell us the T-number and other information, and our computational tools are not yet able to take a raw protein sequence, like that we can predict from the DNA sequence, and predict what the structure would look like. There are lots of groups working on that prediction step, and an annual competition (Critical Assessment of protein Structure Prediction) to see wh

    • Re: (Score:2)

      by geekoid ( 135745 )

      AMA ?

    • Re: (Score:1)

      by proto ( 98893 )

      Google has just recently started a "Google X" project to create a complete picture of what a healthy human being should be. [slashdot.org] Google should be all over this if they really want a complete picture. Their commitment to studying the human genome could give afflicted people legitimate hope that their condition can be properly diagnosed. They may not find a cure for anything in X amount of years but at least they are on the right track.

      • The human genome is only a small part of what you are, the microbiome and virome (the microbial and viral components, respectively) have profound impacts on our health in ways that we really don't tet understand. However, this is an area where big data approaches that Google are good at will succeed. The only reason we found crAssphage is by comparing a lot of samples from different people. Imagine if we have genomes, microbiomes, and viromes from thousands of volunteers, together with health data about the

    • Re: (Score:2)

      by Reziac ( 43301 ) *

      Have you looked at animal samples too? Seems to me it would be easier to get those upper gut samples...

      Is it human-host only, or opportunistic wherever its favored bacteria thrive?

      Has any of this virus been incorporated in our DNA?

      Completely OT, having been preconditioned by the crAss cracks, my brain decided to parse your username as "robed wards" which made no sense. :)

      • We have looked at quite a few animal samples, and it is not that common. There are a few mouse studies, but many of those now have "humanized" gut bacteria! They actually make the mouse look like the human!

        We think it is mostly human associated, but it would sure be good to sequence some poo from chimps and apes to see if we can figure out where it is in our evolutionary tree. But that is not something we're going to do ... hopefully others will.

        • Re: (Score:2)

          by Reziac ( 43301 ) *

          Considering that wild mice who live in proximity to humans markedly prefer to eat stuff humans have touched ... I imagine you'd have to find wilderness mice to study!

          Zoo primates could be 'contaminated' as well.

          Looks like some future researcher is in for a long tramp through the back of beyond. :)

  • Hit over 50% worldwide infection rate, then start buying the symptoms that kill and spread. Just make sure you've infected the islands before they cut off water and air travel (Greenland, Iceland, Madagascar, New Guinea and New Zealand have defeated me often enough). Oh, and target the countries that are contributing the most to finding a cure.

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