AncientMetagenomeDir is a community curated resource of lists of all published shotgun-sequenced ancient metagenome or microbial genome-level enriched samples and libraries.
It is primarily meant to act as a reference guide to help point researchers toward any relevant public data for comparative analysis. It is hoped it will help researchers track growth and development of the field of ancient metagenomics over time.
These lists contain information of ancient metagenomic samples such as publication, sample name, sample type, geographic location, dates and DOIs and other accession numbers to raw data in establised sequencing data databases.
We define here 'metagenome' in a broad sense, primarily focusing any data where the whole DNA content is analysed and explored. Examples for this are (but not limited to) ancient microbiomes (host associated metagenome), ancient sedimentary DNA (environmental) and also samples used for ancient pathogen screening (single genomes).
The lists also contain metadata about all sequencing libraries generated from the corresponding samples.
See the README of each list for more detailed descriptions of the contents of each list. Further modification and expansion of these categories can be proposed to the SPAAM community for further consideration.
The purpose of this repository is not meant to be a comprehensive set of all metadata about every ancient metagenome, but the aim is to have a lightweight set of minimal information but with sufficient links to original sources of detailed information. Keeping the repository simple and lightweight will promote continual updating of the lists over a long period of time. That said, we will design lists as far as possible to follow larger database metadata specifications e.g. MIxS for compatibility.
Finally, we aim to make releases of this at regular intervals, and assign each release a citeable DOI. Each release will also include a changelog to record all additions and any corrections or modifications. Therefore researchers are free to use the information in their own publications, as per the CC-BY 4.0 licence.
ℹ️ A table for ancient anthropogenic metagenomes was included up until release v21.09 (Taputapuātea). However this was dropped in release "Pyu Cities" due to lack of interest from the community. It may be reinstated in the future.
Vector (.svg) versions of all images and interactive map (.geojson) are available under assets/images/figures. R code for all plots are freely available for modification in this repository under assets/analysis/
(Viewable on the AncientMetagenomeDir Website or here)
Legend: Green: Environmental Metagenome, Light Blue: Host Associated Metagenome, Pink: Host Associated Single Genome
This is a community project open to anyone. If you would like to get involved, you can join our community on archaeo.social. A guide to join can be found here.
Guides on how to use AncientMetagenomeDir can be found here.
Guides on how to contribute to AncientMetagenomeDir can be found here.
📖 For general use of the project, please use the publication citation below.
For a specific release citation (e.g. the version used for analysis), go to Releases and use the DOI in the badge of the given release's description, or check the corresponding Zenodo entry
Alongside the Zenodo ID of the release version, please also cite:
Fellows Yates, J. A., Andrades Valtueña, A., Vågene, Å. J., Cribdon, B., Velsko, I. M., Borry, M., Bravo-Lopez, M. J., Fernandez-Guerra, A., Green, E. J., Ramachandran, S. L., Heintzman, P. D., Spyrou, M. A., Hübner, A., Gancz, A. S., Hider, J., Allshouse, A. F., Zaro, V., & Warinner, C. (2021). Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir. Scientific Data, 8(1), 31. DOI: 10.1038/s41597-021-00816-y
!> WARNING You must also cite each paper you use data from, citing AncientMetagenomeDir is not sufficient on it's own!
ℹ️ The AncientMetagenomeDir community curates this data on a voluntary basis, and therefore provides no warranty or completeness or accuracy of the data. If in doubt, refer to the original publication of a given sample. Corrections are accepted, and thus later versions may have different values.
The Core Team of AncientMetagenomeDir is responsible for the mantainance of the repository, the organisation of training and hackathons events, as well as lead initiatives to improve AncientMetagenomeDir. The current members of the Core Team are:
- Alex Hübner (@alexhbnr)
- James Fellows Yates (@jfy133)
- Diana Spurite (@DianaSpurite)
- Yuejiao Huang (@YuejiaoHuang)
- Bianca Maria Bonucci (@biancamariabonucci)
- Piotr Rozwalak (@rozwalak)
- Bjørn Peare Bartholdy (@bbartholdy)
- Aida Andrades Valtueña (@aidaanva)
