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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

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  • 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.
  • Cr(oss) Ass(embly) (Score:5, Informative)

    by tepples (727027) <tepples@gmaiBLUEl.com minus berry> on Sunday July 27, 2014 @09:38PM (#47546955) Homepage Journal

    I don't know what the "ass" part of the name signifies

    The Nat Geo article states that crAss stands for the technique used to piece together fragments of the virus's genome: "They called it crAssphage after the cross-assembly method that revealed its existence."

  • Re:CrAssphage? (Score:4, Informative)

    by nbauman (624611) on Sunday July 27, 2014 @10:42PM (#47547207) Homepage Journal

    You're new to molecular genetics.

    http://www.curioustaxonomy.net... [curioustaxonomy.net]

    http://mentalfloss.com/article... [mentalfloss.com]

    http://www.npr.org/templates/s... [npr.org]
    Fruit Fly Scientists Swatted Down Over 'Cheap Date'

  • 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.

  • 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!

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