Mysterious virus-like 'Obelisks' found in the human gut and mouth

Scientists have uncovered a never-before-seen class of virus-like entities hiding in the human gut and mouth, and these "viroids" may influence the gene activity within the human microbiome, Science reported.

The researchers confirmed one host for these viroids, namely, a common bacterium found in the mouth called Streptococcus sanguinis. They've yet to confirm additional hosts, but they suspect at least a fraction are bacteria.

Viroids are tiny loops of RNA, a genetic cousin of DNA, and they've been found to infect primarily plants, such as potatoes. Viroids differ from larger, RNA-based viruses in several ways. First, they're naked, lacking the protective shells that viruses use to hold their genetic material. Second, their RNA doesn't contain instructions to build proteins; whereas viruses carry instructions for their outer shells and for certain enzymes they need to replicate, viroids co-opt these enzymes from their hosts. 

Although viroids were once thought to infect only plants, recent studies suggest they may infect additional hosts, such as animals, fungi or bacteria. In the new study, researchers searched for possible viroids among the genes of microbes that reside in the human body.

Related: 70,000 never-before-seen viruses found in the human gut 

In a report published Jan. 21 to the preprint database bioRxiv, the team introduced "Obelisks," a newly named class of viroid they discovered in the human gut and mouth. In all, they identified nearly  29,960 examples of the viroids. (The work has not yet been peer-reviewed or published in a scientific journal.) 

They named them Obelisks because the viroids' secondary structure — a 3D shape they assume by folding onto themselves — is predicted to look like a thin rod. 

Using previously published data, the researchers combed through readouts of gene activity in different microbial communities within the body. These gene-activity summaries are known as "metatranscriptomes." 

They found that Obelisks were present in roughly 7% of the metatranscriptomes from human feces. These stool samples give a snapshot of gene activity in the gut microbiome. The team also found the newly named viroids in 17 out of 32, or about 53%, of the mouth metatranscriptomes they screened.

In further analyses, the team was able to match an Obelisk with its host, S. sanguinis. "While we don't know the 'hosts' of other Obelisks, it is reasonable to assume that at least a fraction may be present in bacteria," they wrote in the preprint.

Interestingly, some of the newfound Obelisks seemed to contain instructions for enzymes needed for replication, making them more complex than viroids that had been described previously, Science reported. Like most viroids, though, they still lacked instructions for a protective outer shell.

It's still unknown how or whether these viroids affect human health, although they may shape the human microbiome, since at least some infect bacteria. There's also ongoing discussion of whether viruses evolved from viroids or if viroids actually evolved from viruses, so this new discovery may help fuel that debate.

Read more in Science.

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