The study suggests that our bodies contain vastly more diverse microbes than anyone previously understood.
"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," said Stephen Quake, a professor at Stanford University.
Researchers collected samples from 156 heart, lung and bone marrow transplant recipients, along with 32 pregnant women.
Of all the non-human DNA fragments the team gathered, 99 per cent of them failed to match anything in existing genetic databases the researchers examined.
The "vast majority" of it belonged to a phylum called proteobacteria, which includes, among many other species, pathogens such as E coli and Salmonella.
Previously unidentified viruses in the torque teno family, generally not associated with disease but often found in immunocompromised patients, made up the largest group of viruses.
"We've doubled the number of known viruses in that family through this work," Quake said.
Perhaps more important, researchers found an entirely new group of torque teno viruses. Among the known torque teno viruses, one group infects humans and another infects animals, but many of the ones the researchers found did not fit in either group.
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