For over a century, scientists have analyzed the vast microbial world within the human body. They’ve found bacteria, fungi, and viruses that influence our health in many ways. We thought we had a decent idea of what lies in our bodies. But nature, as it so often does, seems to have thrown us a curveball.
Hidden within the microbial communities of our gut and mouth, researchers have identified thousands of tiny, virus-like genetic entities. They’re not viruses, not bacteria, and they don’t look like anything we’ve seen before. They call them obelisks — flattened, rod-shaped loops of RNA that challenge fundamental assumptions about what constitutes life.
Some researchers have likened it to “fossils from another world.”
What Are Obelisks?
The discovery of obelisks came from a deep dive into genetic databases. Led by Ivan Zheludev and Andrew Fire at Stanford University, a team of scientists analyzed massive metatranscriptomic datasets — collections of RNA sequences extracted from human stool and saliva samples. What they found was astonishing: nearly 30,000 distinct sequences forming RNA circles that were unlike anything in recorded biology. They’re so unusual we wouldn’t even know where to put them on the tree of life.
To make things even stranger, they seem to be remarkably common. These structures have been detected in approximately 7% of gut bacteria and 50% of oral bacteria samples worldwide, suggesting a widespread presence.
Obelisks sort of look like viruses but unlike viruses, they don’t have an outer protein coat. Their structure is reminiscent of viroids — plant pathogens composed of simple RNA loops that also don’t have a protein coat. But obelisks are not found in plants. Instead, they inhabit bacterial species, including Streptococcus sanguinis, a common microbe in human mouths.
It’s also unclear what they actually do. They don’t seem to be pathogens, so they may just be benign passengers, quietly existing within bacteria without altering their hosts. Alternatively, they could play an active role in microbial genetics, potentially influencing bacterial behavior or even interacting with human cells. They could have significant impacts for digestion, immunity, or even diseases; but we don’t know.
So… what do we know about them?
The researchers also identified unique proteins, tentatively named oblins, encoded by obelisk genomes. Unlike traditional viroids, which do not encode proteins, these RNA loops seem capable of producing molecules that might interact with bacterial or even human cells. It’s hard to say what this actually means, but the fact that these proteins do exists suggests that obelisks are either something between a viroid and a virus or something entirely new.
“It’s insane,” says Mark Peifer, a cell and developmental biologist at the University of North Carolina at Chapel Hill, for Science. “The more we look, the more crazy things we see.”
They could be evolutionary relics — remnants of an ancient stage in the development of life. They could even be a missing link in the evolutionary history of viruses, suggesting that viral genomes may have once been simple RNA circles like these before evolving into more complex infectious agents.
We don’t even know if these obelisks are alive. In fact, scientists have been debating whether viruses are alive for decades (because they can’t replicate independent of a host cell’s molecules). Obelisks seem to be even simpler “creatures” and they could end up forcing us to reconsider what we even consider to be “alive.”
Yet, despite their mysterious nature, obelisks could have practical implications for medicine and microbiome research. If they play a role in regulating bacterial populations, they might influence conditions linked to the gut microbiome, such as inflammatory bowel disease, obesity, or even mental health disorders. Future research will need to explore whether obelisks interact with human health in ways that warrant medical attention — or if they are merely another hidden feature of the vast microbial world inside us.
