Ancient host-associated microbes obtained from mammoth remains

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 35 records.

3 extension data tables also exist. An extension record supplies extra information about a core record. The number of records in each extension data table is illustrated below.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

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How to cite

Researchers should cite this work as follows:

Guinet B, Oskolkov N, Moreland K, Dehasque M, Chacón-Duque J C, Angerbjörn A, Arsuaga J L, Danilov G, Kanellidou F, Kitchener A C, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Termes L, Zazula G, Mortensen P, Grigorieva L, Richards M, Shapiro B, Lister A M, Vartanyan S, Díez-Del-Molino D, Götherström A, Pečnerová P, Nikolskiy P, Dalén L, van der Valk T (2025). Ancient host-associated microbes obtained from mammoth remains. Dataset (metagenomic microbial DNA from mammoth remains). Centre for Palaeogenetics.

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Researchers should respect the following rights statement:

The publisher and rights holder of this work is Centre for Palaeogenetics. This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: fe104fc9-c453-49e0-90c0-5d71564289a4.  Centre for Palaeogenetics publishes this resource, and is itself registered in GBIF as a data publisher endorsed by GBIF Sweden.

Keywords

ancient DNA; aDNA; mammoth; metagenomics; microbial ecology; host-associated microbes; palaeogenetics

Contacts

Geographic Coverage

The dataset covers mammoth remains recovered from a broad geographic range (including Siberia, Russia; Yakutia; Yukon, Canada; Europe) spanning multiple localities. Specific sample coordinates and provenance details are provided in the associated supplementary material of the paper (TableS1)

Taxonomic Coverage

Taxa include remains of wooly and steppe mammoths and associated microbial taxa from Actinobacillus sp., Pasteurella sp. , Streptococcus sp. and Erysipelothrix sp.). The microbial DNA is identified and/or reconstructed to clade level.

Project Data

International collaborative project to sequence and analyse ancient microbial DNA from mammoth remains spanning over one million years, to reconstruct host-associated microbial lineages and explore their evolutionary history.  Funding: SciLifeLab and Wallenberg Data Driven Life Science Program (KAW 2020.0239), Knut and Alice Wallenberg Foundation, National Bioinformatics Infrastructure Sweden (NBIS) at SciLifeLab, Swedish Research Council (grants 2017-04647 and 2021-00625), European Union – ERC (PrimiGenomes, 101054984), European Union – Horizon 2020 (Marie Skłodowska-Curie grant no. 892446), European Union – Horizon Europe (Marie Skłodowska-Curie Actions Postdoctoral Fellowships, 101111414)

The personnel involved in the project:

Sampling Methods

Specimens were obtained from collections/museums and excavations (locations include Yakutia, Russia; Yukon, Canada; Europe). DNA was extracted from tissue types (e.g., bone, tooth, tusk) under ancient DNA clean-lab conditions. Metagenomic sequencing libraries were prepared, sequenced, and processed. Contaminants were filtered using standard damage-pattern screening and comparison to environmental controls.

Method step description:

1. Step 1: Collection of mammoth remains and contextual metadata (age, location, tissue type)  Step 2: Ancient DNA extraction and library preparation in clean-lab facilities  Step 3: High-throughput sequencing of metagenomic libraries  Step 4: Bioinformatic screening: mapping, contaminant filtering, damage pattern analysis  Step 5: Taxonomic assignment of microbial reads/contigs, genome reconstruction of key clades  Step 6: Phylogenetic and functional analyses of reconstructed microbial genomes  Step 7: Metadata integration and dataset assembly for publication and deposition

Bibliographic Citations

1. Guinet B, Oskolkov N, Moreland K, Dehasque M, Chacón-Duque J C, Angerbjörn A, Arsuaga J L, Danilov G, Kanellidou F, Kitchener A C, Muller H, Plotnikov V, Protopopov A, Tikhonov A, Termes L, Zazula G, Mortensen P, Grigorieva L, Richards M, Shapiro B, Lister A M, Vartanyan S, Díez-Del-Molino D, Götherström A, Pečnerová P, Nikolskiy P, Dalén L, van der Valk T. 2025. “Ancient host-associated microbes obtained from mammoth remains.” Cell. S0092-8674(25)00917-1. https://doi.org/10.1016/j.cell.2025.08.003

Additional Metadata