Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

Abstract

Ancient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual taxa and communities of both microbes and eukaryotes. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833 ) is a collection of annotated metagenomic sample lists derived from published studies that provide basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These tables are community-curated and span multiple sub-disciplines to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks facilitate compatibility with established sequence-read archives and term-ontologies, and ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

Fig. 1

Timelines depicting the development of the sub-disciplines of ancient metagenomics as recorded in AncientMetagenomeDir as per release v20.09. (a) Number of ancient metagenomic publications per year. (b) Cumulative sum of published samples with genetic sequencing data or sequences in publicly accessible archives.

Fig. 2

Summary of temporal and spatial information of ancient metagenomic samples as recorded in AncientMetagenomeDir v20.09. (a) Maps depicting the geographic distribution of samples for each sub-discipline. (b) Histogram of sample ages for each sub-discipline. For visualisation purposes, plot axes are log-scaled, bins calculated using the ‘Freedman–Diaconis’ rule, and only samples dated to younger than 50,000 years are displayed.

Fig. 3

AncientMetagenomeDir submission and update workflow. The submission workflow is carried out on GitHub, and final releases are archived at Zenodo. Submissions go through both automated computational validation and also peer-review for consistency and accuracy.