Dataset Information

Bone adhered sediments as a source of target and environmental DNA and proteins

ABSTRACT: 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.

INSTRUMENT(S):

ORGANISM(S): Homo Sapiens (human) Rattus Rattus (black Rat)

SUBMITTER: Rémi Barbieri

LAB HEAD: Christiana Lyn Scheib

PROVIDER: PXD057056 | Pride | 2025-09-15

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	210219_40_Orbi2_KN_SER_G90_T120_Oras_RIB_GAM042.raw	Raw
	210305_06_Orbi2_KN_SER_G90_T120_Oras_blank_260221.raw	Raw
	210305_09_Orbi2_KN_SER_G90_T120_Oras_PSN223.raw	Raw
	210305_12_Orbi2_KN_SER_G90_T120_Oras_PSN403.raw	Raw
	210305_18_Orbi2_KN_SER_G90_T120_Oras_PSN460.raw	Raw

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Publications

Bone Adhered Sediments as a Source of Target and Environmental DNA and Proteins.

de-Dios Toni T Bonucci Biancamaria B Barbieri Rémi R Kushniarevich Alena A D'Atanasio Eugenia E Dittmar Jenna J Cessford Craig C Solnik Anu A Robb John E JE Warinner Christina C Oras Ester E Scheib Christiana L CL

Molecular biology and evolution 20250901 9

In recent years, sediments from cave environments have provided invaluable insights into ancient hominids, as well as past fauna and flora. Unfortunately, however, sediments are not always collected during excavation. In this study, we analyzed an overlooked but abundant resource in archaeological collections - sediments adhered to bone. We performed metagenomics and metaproteomics analysis on sediment from several human skeletal elements, originating from Neolithic to Medieval sites in England. ...[more]

PMID: 40856172

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