Ancient host-associated microbes obtained from mammoth remains

資料紀錄

此資源出現紀錄的資料已發佈為達爾文核心集檔案（DwC-A），其以一或多組資料表構成分享生物多樣性資料的標準格式。 核心資料表包含 35 筆紀錄。

亦存在 3 筆延伸集的資料表。延伸集中的紀錄補充核心集中紀錄的額外資訊。 每個延伸集資料表中資料筆數顯示如下。

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如何引用

研究者應依照以下指示引用此資源。:

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.

權利

研究者應尊重以下權利聲明。:

此資料的發布者及權利單位為 Centre for Palaeogenetics。 This work is licensed under a Creative Commons Attribution (CC-BY 4.0) License.

GBIF 註冊

此資源已向GBIF註冊，並指定以下之GBIF UUID: fe104fc9-c453-49e0-90c0-5d71564289a4。  Centre for Palaeogenetics 發佈此資源，並經由GBIF Sweden同意向GBIF註冊成為資料發佈者。

關鍵字

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

聯絡資訊

地理涵蓋範圍

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)

分類群涵蓋範圍

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.

計畫資料

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)

參與計畫的人員:

取樣方法

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.

方法步驟描述:

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

引用文獻

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

額外的詮釋資料