PXD057056-1

PXD057056 is an original dataset announced via ProteomeXchange.

Title	Bone adhered sediments as a source of target and environmental DNA and proteins
Description	In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, locations with favourable conditions for ancient DNA (aDNA) preservation in sediments are scarce. In this study we analysed a set of samples obtained from sediments adhered to different human skeletal elements, originating from Neolithic to Medieval sites in England, and performed metagenomics and metaproteomics analysis. From them, we were able to reconstruct a partial human genome. The genetic profile of those human sequences matches the one recovered from the original skeletal element. Additionally, aDNA sequences matching the genomes of endogenous gut and oral microbiome bacteria were identified. We also found the presence of genetic sequences corresponding to animals and plants. In particular we managed to retrieve the partial genome and proteome of a Black Rat (Rattus rattus), sharing close genetic affinities to other medieval Rattus rattus. Our results demonstrate that material usually discarded, as it is sediments adhering to human remains, can be used to get a glimpse of the environmental conditions at the time of the death of an individual.
HostingRepository	PRIDE
AnnounceDate	2025-09-15
AnnouncementXML	Submission_2025-09-14_16:22:01.362.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Rémi Barbieri
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Rattus rattus (Black rat); NCBI TaxID: 10117;
ModificationList	(R)-5-oxo-1; monohydroxylated residue; deamidated residue; iodoacetamide derivatized residue
Instrument	Q Exactive

Revision	Datetime	Status	ChangeLog Entry
0	2024-10-22 08:42:13	ID requested
⏵ 1	2025-09-14 16:22:02	announced

de-Dios T, Bonucci B, Barbieri R, Kushniarevich A, D'Atanasio E, Dittmar J, Cessford C, Solnik A, Robb JE, Warinner C, Oras E, Scheib CL, Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins. Mol Biol Evol, 42(9):(2025) [pubmed]

10.1093/molbev/msaf202;

submitter keyword: Metagenomics,Sedimentry aDNA, environment reconstruction, rat, Metaproteomics, Paleoproteomics, Non-destructive sampling

Christiana Lyn Scheib
contact affiliation	1. Institute of Genomics, University of Tartu, Tartu, 51010, Estonia 2. St John’s College, University of Cambridge, CB2 1TP, United Kingdom 3. Department of Zoology, University of Cambridge, CB2 3EJ, United Kingdom
contact email	cls83@cam.ac.uk
lab head
Rémi Barbieri
contact affiliation	University of Tartu
contact email	remibarbieri@hotmail.fr
dataset submitter

Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2025/09/PXD057056

PRIDE project URI

• PRIDE
  1. PXD057056
     1. Label: PRIDE project
     2. Name: Bone adhered sediments as a source of target and environmental DNA and proteins