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New Study Finds 99% of Microbes in Human Body Previously Unknown

A new study published in the Proceedings of the National Academy of Sciences determined that our bodies are host to a number of diverse microbes that were previously unidentified.

This work was led by principal investigator, Stephen Quake, PhD, professor of bioengineering and applied physics at Stanford University. Professor Quake and his colleagues utilized shotgun sequencing and examined circulating cell-free DNA (cfDNA) from patient blood to determine the microbiome landscape. The study included 188 patients in 4 cohorts: heart transplant (76 patients, 610 samples), lung transplant (59 patients, 460 samples), bone marrow transplant (21 patients, 161 samples), and pregnancy (32 patients, 120 samples).

The authors sequenced 37 billion molecules from the cfDNA sample and found that 0.45% of the reads were non-human. Intriguingly, the authors aligned these non-human reads to known microbes in a database that consists of 8000 species of bacteria, viruses, fungi, and other organisms and found that only 1% of these reads belonged to known microorganisms. In other words, a staggering 99% of the non-human reads correspond to previously unidentified species. In an effort to find out more about these unknown species, the authors performed de novo assembly on the non-human reads using an iterative approach, making sure to screen for contaminants and artifacts.

Professor Quake and his colleagues found that approximately two-thirds of the sequences belong to bacterial species and are most similar to the phylum Proteobacteria, which include species like Escherichia coli and Vibrio cholerae. In addition, 9% of the sequences are of viral origin, the majority of which are either phages or torque teno viruses (TTVs), which include the family of anelloviruses. The TTVs identified seem to cluster around immunocompromised patients, which validates what had been previously shown in the literature. Overall, the authors determined that they observed more than 1000 new taxa and have doubled the number of anelloviruses known to be found in humans.

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