Your viruses are your own… in your poop

More fun news out of your intestines last week – a paper published in Nature shows that the viruses living in the bacteria living in your gut are unique to you:

Here we report sequencing of the viromes (metagenomes) of virus-like particles isolated from faecal samples collected from healthy adult female monozygotic twins and their mothers at three time points over a one-year period. We compared these data sets with data sets of sequenced bacterial 16S ribosomal RNA genes and total-faecal-community DNA. Co-twins and their mothers share a significantly greater degree of similarity in their faecal bacterial communities than do unrelated individuals. In contrast, viromes are unique to individuals regardless of their degree of genetic relatedness.

This is a pretty small study – they only looked at 4 families – so you should take these conclusions with a grain of salt. Still, the results are pretty striking. These researchers took stool samples from 4 mothers and their monozygotic (identical) twin daughters. It’s been known for a long time that mothers and their offspring share a great deal of their commensal bacteria (especially if they were born naturally as opposed to via c-section), but here they decided to look at the viruses. What they found was pretty remarkable: the variation in viruses was as large between mothers and daughters (and between twins) as it was between unrelated individuals.

As far as I can tell, there’s nothing wrong with the science here, but there are a few caveats. If you read the piece by Carl Zimmer I linked to earlier (and if you haven’t, go do it now), you’ll know that we can’t actually grow these microbes outside the human body. The scientists here extracted all the viruses (or virus-like particles), then threw them together, amplified the DNA with PCR (which can introduce biases), and then sequenced it. Finally, they used mathematical algorithms (which I don’t fully understand) to group the DNA they found with databases of known virus genomes. However, over 80% of the reads could not be matched to any known viruses, so they have to use other algorithms to predict what sorts of viruses they are and what kinds of bacteria they infect. There’s a lot of room here for biases to be introduced.

Also, as of yet there’s not functional information gained from this sort of analysis. I think the main point of the paper is to make a case that we need to look at the virus content in order to get a complete understanding of the influence that the microbes in our bodies can have on our physiology. And considering the millions of dollars that the NIH is planning to dish out for the human microbiome project in the coming years, this report couldn’t have come at a more opportune time.