There's a Hole in the Bottom of the Sea

By Elizabeth Preston
Mar 30, 2011 12:49 PMNov 5, 2019 10:11 AM


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"There's! A! Flea, on the fly, on the wart, on the frog, on the bump, on the log--" Does anyone else remember this song? Because it has been going through my head ever since I started reading about the human virome. That's the viruses that live inside the bacteria that live inside us.

First there was the genome--all the DNA in a human--which we've now got a pretty good handle on. It turned out that our smallish number of genes can be shuffled into a larger number of RNA "transcripts," so there's also the transcriptome. Those transcripts are used to make the proteins in our body, naturally known as the proteome. The microbiome is all of the microorganisms that live inside humans. (Don't look now, but there are 10 times more of their cells than yours in your body.) And the virome goes a step more microscopic, to the viruses.

The bacteria inside us have been the subject of a lot of interesting research lately. They occupy us as paying tenants, helping to digest our food and performing other mysterious functions that seem to maintain our good health. Existing around and in those bacteria are viruses that vastly outnumber even the bacterial cells.

Some scientists are starting to explore the role these viruses play in our bodies. At Washington University in St. Louis, Jeffrey Gordon and his colleagues studied the viruses inhabiting four sets of adult identical twins and their mothers. (They did this by sequencing the viral genes in their stool samples.) Previous studies had shown that twins and their mothers have more similar bacterial populations than unrelated people do. Surprisingly, though, there was no such connection between the viral populations--people have unique viromes, regardless of how related they are.

But the viral populations seemed to be stable. In three samples taken over the course of a year, the subjects' viromes were consistent. So the differences between people aren't due to a constant turnover in the types of viruses they harbor.

Furthermore, Gordon found evidence that the bacteria and the viruses that attack them (called phages) were coexisting relatively peacefully, and not engaging in the turf war that might be expected.

So what are they doing in there? Are they helping us? Hurting? Neither or both? Gordon suggests that studies of the human microbiome should include the virome, so we can find out.

One interesting preliminary result has come from another set of researchers at Washington University who are studying viruses in babies. Looking at the viral genes in babies' nasal samples, they compared healthy babies to babies with unexplained fevers. They say they found 10 times more viruses in the feverish babies. It's not clear whether the viruses are to blame for the fevers or something more complicated is going on. But if doctors learn that the virome is to blame in these cases, they could avoid prescribing unnecessary antibiotics (since antibiotics only treat bacterial infections).

It's good to avoid unnecessary antibiotic use, of course, because it encourages bacteria to develop resistance to those drugs. That brings up another point about the virome: Phages, the viruses that prey on bacteria, sometimes drag bacterial genes between their victims. A gene for antibiotic resistance, for example, could be spread among a population of bacteria in your body by the viruses there.

More alarming and interesting relationships will, no doubt, emerge as scientists continue to learn about the microscopic menageries inside us. I just hope they don't find any more "omes." Really, it's enough already.

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