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
Well, we try not to pretend they did all the work
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 them, we can make a lot of intricate predictions about our health based on that data.
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 who is the best at predicting structure from sequence.
We also have a new modeler starting at San Diego State University in 2015 who focuses on phage capsid models, and hopefully we'll get something from that!
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
It was named after our analysis software, crAss (cross assembly) for comparing DNA sequences from different samples (called metagenomics). Here is the crAss article 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 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, 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.
The bogosity meter just pegged.
