Stanford shocker: 99% of human microbes unknown to science

Researchers at Stanford University have found something fundamental and a little shocking: 99 percent of the organisms whose DNA floats in our blood stream are unknown to science.

In addition to DNA from our own body’s cells, human blood contains DNA fragments from viruses, bacteria and other microbes that have infected us over the years or that we’ve been born with. In the process of looking for a way to better predict when an organ transplant has been rejected, the Stanford scientists conducted full-DNA screenings on blood samples from more than 180 transplant patients and pregnant women.

What they found is that there are far more critters in our bodies than anyone knew, and most of them have never been studied, classified or named. Said Stephen Quake, the paper’s lead author: “We found the gamut…. We found things that are related to things people have seen before, we found things that are divergent, and we found things that are completely novel.”

Quake and team’s results are published in Proceedings of the National Academy of Sciences.

The scientists entered the project with a straightforward objective: To find an alternative to the needle biopsy and hospitalization usually required to tell if a patient’s body is rejecting an organ. They thought if high levels of the donor’s DNA were found in the recipient’s blood, that would be a pretty good indicator the body was not accepting the transplant.

So they took blood samples and processed all the DNA they found. Excluding human DNA from either the patient or donor, 99 percent of the DNA failed to match anything in genetic databases.

Most of it broadly came from a phylum known as proteobacteria, which includes species such as E. coli and Salmonella. The largest group of viruses came from previously unknown species in the torque teno family.

Torque teno viruses aren’t usually associated with disease but do show up in people with compromised immune systems. The viruses tend to belong to one of two groups, infecting either animals or humans. But the Stanford work found ones that fit neither group. Said Quake: “We’ve now found a whole new class of human-infecting ones that are closer to the animal class than to the previously known human ones, so quite divergent on the evolutionary scale.”

So how could so much bacteria and viruses have escaped attention until now? “I’d say it’s not that baffling in some respects because the lens that people examined the microbial universe was one that was very biased,” Quake said. Researchers usually laser in on the microbiome of a single part of the body, like the gut or skin. The beauty of blood samples of the sort Quake used is that they “go deeply everywhere at the same time,” he said.

Quake’s lab will now turn its sites to the microbiomes of other organisms, with an eye especially on any viruses or bacteria that could lead to a human pandemic. “There’s all kinds of viruses that jump from other species into humans, a sort of spillover effect, and one of the dreams here is to discover new viruses that might ultimately become human pandemics,” he said. “What this does is it arms infectious disease doctors with a whole set of new bugs to track and see if they’re associated with disease.”

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