Viroid-like colonists of human microbiomes 2024 Zheludev et al

Andy

Andy

Retired committee member
Link to post with published version

Preprint
Abstract

Here, we describe the “Obelisks,” a previously unrecognised class of viroid-like elements that we first identified in human gut metatranscriptomic data. “Obelisks” share several properties: (i) apparently circular RNA ∼1kb genome assemblies, (ii) predicted rod-like secondary structures encompassing the entire genome, and (iii) open reading frames coding for a novel protein superfamily, which we call the “Oblins”.

We find that Obelisks form their own distinct phylogenetic group with no detectable sequence or structural similarity to known biological agents. Further, Obelisks are prevalent in tested human microbiome metatranscriptomes with representatives detected in ∼7% of analysed stool metatranscriptomes (29/440) and in ∼50% of analysed oral metatranscriptomes (17/32). Obelisk compositions appear to differ between the anatomic sites and are capable of persisting in individuals, with continued presence over >300 days observed in one case. Large scale searches identified 29,959 Obelisks (clustered at 90% nucleotide identity), with examples from all seven continents and in diverse ecological niches. From this search, a subset of Obelisks are identified to code for Obelisk-specific variants of the hammerhead type-III self-cleaving ribozyme.

Lastly, we identified one case of a bacterial species (Streptococcus sanguinis) in which a subset of defined laboratory strains harboured a specific Obelisk RNA population. As such, Obelisks comprise a class of diverse RNAs that have colonised, and gone unnoticed in, human, and global microbiomes.

https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1
 
Last edited by a moderator:
‘It’s insane’: New viruslike entities found in human gut microbes

As they collect and analyze massive amounts of genetic sequences from plants, animals, and microbes, biologists keep encountering surprises, including some that may challenge the very definition of life. The latest, reported this week in a preprint, is a new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. These “obelisks,” as they’re called by the Stanford University team that unearthed them, have genomes seemingly composed of loops of RNA and sequences belonging to them have been found around the world.

Other scientists are delighted by obelisks’ debut. “It’s insane,” says Mark Peifer, a cell and developmental biologist at the University of North Carolina at Chapel Hill. “The more we look, the more crazy things we see.”

It’s not yet known whether obelisks affect human health, says Matthew Sullivan, an integrative biologist at Ohio State University, but they could alter the genetic activity of their bacterial hosts, which in turn could affect human genes.

https://www.science.org/content/article/it-s-insane-new-viruslike-entities-found-human-gut-microbes
 
Merged thread

‘It’s insane’: New viruslike entities found in human gut microbes
https://www.science.org/content/article/it-s-insane-new-viruslike-entities-found-human-gut-microbes

As they collect and analyze massive amounts of genetic sequences from plants, animals, and microbes, biologists keep encountering surprises, including some that may challenge the very definition of life. The latest, reported this week in a preprint, is a new kind of viruslike entity that inhabits bacteria dwelling in the human mouth and gut. These “obelisks,” as they’re called by the Stanford University team that unearthed them, have genomes seemingly composed of loops of RNA and sequences belonging to them have been found around the world.
...
Among the human microbial databases examined, obelisk sequences were found in 7% of human gut bacteria and in half the bacteria in the human mouth. And the obelisks in microbes from different parts of the body have distinctive sequences, Fire and colleagues report in their preprint, which was posted on 21 January on bioRxiv. Because obelisks contain genes that are unlike any discovered so far in other organisms, they “comprise a class of diverse RNAs that have colonized, and gone unnoticed in, human, and global microbiomes,” the team writes. (Fire and other co-authors on the preprint declined to comment on their work.)​

(The paper is sadly not linked or named in the article)
 
Last edited by a moderator:
Now published in Cell —

Viroid-like colonists of human microbiomes
Ivan N. Zheludev; Robert C. Edgar; Maria Jose Lopez-Galiano; Marcos de la Peña; Artem Babaian; Ami S. Bhatt; Andrew Z. Fire

SUMMARY
Here, we describe "obelisks," a class of heritable RNA elements sharing several properties: (1) apparently circular RNA ∼1 kb genome assemblies, (2) predicted rod-like genome-wide secondary structures, and (3) open reading frames encoding a novel "Oblin" protein superfamily. A subset of obelisks includes a variant hammerhead self-cleaving ribozyme. Obelisks form their own phylogenetic group without detectable similarity to known biological agents.

Surveying globally, we identified 29,959 distinct obelisks (clustered at 90% sequence identity) from diverse ecological niches. Obelisks are prevalent in human microbiomes, with detection in ∼7% (29/440) and ∼50% (17/32) of queried stool and oral metatranscriptomes, respectively. We establish Streptococcus sanguinis as a cellular host of a specific obelisk and find that this obelisk's maintenance is not essential for bacterial growth.

Our observations identify obelisks as a class of diverse RNAs of yet-to-be-determined impact that have colonized and gone unnoticed in human and global microbiomes.

HIGHLIGHTS
• Obelisks are a phylogenetically distinct group of microbiome-associated, viroid-like RNAs

• Found globally in diverse niches, obelisks also occur in human stool and oral microbiomes

• The human oral bacterium Streptococcus sanguinis SK36 harbors a distinct “obelisk-S.s”

• Under replete growth conditions, obelisk-S.s appears to be disposable for SK36 growth

Link | PDF (Cell) [Paywall]
 
You must log in or register to reply here.
Back
Top Bottom