files and analysis for: Viroid-like colonists of human microbiomes
Abstract/Contents
- 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.
Description
| Date modified | January 19, 2024; January 21, 2024 |
|---|---|
| Publication date | January 19, 2024 |
Creators/Contributors
| Author | Zheludev, Ivan |
https://orcid.org/0000-0002-9572-0574
(unverified)
|
|---|---|---|
| Author | Edgar, Robert |
https://orcid.org/0000-0001-7355-2541
(unverified)
|
| Author | Lopez Galiano, Maria Jose |
https://orcid.org/0000-0002-0209-0105
(unverified)
|
| Author | de la Peña, Marcos |
https://orcid.org/0000-0002-7949-8459
(unverified)
|
| Author | Babaian, Artem |
https://orcid.org/0000-0002-4315-6262
(unverified)
|
| Author | Bhatt, Ami |
https://orcid.org/0000-0001-8099-2975
(unverified)
|
| Author | Fire, Andrew |
https://orcid.org/0000-0001-6217-8312
(unverified)
|
Subjects
| Subject | RNA metaviromics |
|---|---|
| Subject | Viroid |
| Subject | Hepatitis Delta Virus |
| Subject | Human Microbiome |
| Subject | Obelisk RNA |
| Genre | Other |
| Genre | Obelisk rnas are globally pervasive, sub-viral rnas found in human microbiomes |
Bibliographic information
| Related item | |
|---|---|
| DOI | https://doi.org/10.25740/wb363nt3637 |
| Location | https://purl.stanford.edu/wb363nt3637 |
Access conditions
- Use and reproduction
- User agrees that, where applicable, content will not be used to identify or to otherwise infringe the privacy or confidentiality rights of individuals. Content distributed via the Stanford Digital Repository may be subject to additional license and use restrictions applied by the depositor.
- License
- This work is licensed under a Creative Commons Attribution 4.0 International license (CC BY).
Preferred citation
- Preferred citation
- Zheludev, N., I., Edgar, C., R., Lopez Galiano, M., de la Peña, M., Babaian, A., Bhatt, S., A., and Fire, Z., A. (2024). Viroid-like colonists of human microbiomes. bioRxiv. Available at https://www.biorxiv.org/content/10.1101/2024.01.20.576352v1 data at https://purl.stanford.edu/wb363nt3637
Collection
Stanford Research Data
View other items in this collection in SearchWorksContact information
Also listed in
Loading usage metrics...