Human oral metagenome
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA643812 | ENA |
REPOSITORIES: ENA
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Project description:Mineralised dental plaque (calculus) has proven to be an excellent source of ancient biomolecules. In this study we present a Mycobacterium leprae genome (6.6-fold), the causative agent of leprosy, recovered via shotgun sequencing of 16th century human dental calculus from an individual from Trondheim, Norway. Moreover, ancient mycobacterial peptides were retrieved via mass spectrometry-based proteomics, further validating the presence of the pathogen. M. leprae can readily be detected in the oral cavity and associated mucosal membranes, which likely contributed to it being incorporated into this individual’s dental calculus. This individual showed some possible, but not definitive, evidence of skeletal lesions associated with early stage leprosy. This study is the first known example of successful multi-omics retrieval of M. leprae from archaeological dental calculus. Furthermore, we offer new insights into dental calculus as an alternative sample source to bones or teeth for detecting and molecularly characterizing M. leprae in individuals from the archaeological record.
2020-10-19 | PXD017836 | Pride
Project description:Differential DNA preservation in archaeological dental calculus and dentin
| PRJNA437677 | ENA
Project description:Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan
| PRJDB8768 | ENA
Project description:Detailed investigation of extremely severe pathological conditions present in ancient human skeletons is important because they can illuminate the breadth of potential interactions between humans and disease etiologies in the past. Here, we applied palaeoproteomics to investigate the bacterial pathogenic factors and host defense response to an ancient human skeletal individual with severe oral pathology. This female skeleton, from the Okhotsk period (i.e., 5th–13th century) of northern Japan, poses abnormal deposition of large amounts of dental calculus and oral dysfunction due to severe periodontal disease. A shotgun mass-spectrometry analysis identified 81 human proteins and 15 bacterial proteins from her calculus. Two pathogenic or bio-invasive proteins originating from two of the three “red complex” bacteria, the core species associated with severe periodontal disease in modern humans, as well as additional two bio-invasive proteins of periodont-associated bacteria were identified. Human proteins associated with the defense response system were identified, but their proportion was mostly similar to that reported in ancient and modern human individuals with lower calculus deposition. These results suggest that the bacterial etiology was similar and the host defense response was not necessarily higher in ancient individuals with abnormal deposition of large amounts of dental calculus.
2024-04-01 | PXD044070 | Pride
Project description:Dental Calculus Metagenome (archaeological)
| PRJNA216965 | ENA
Project description:Ancient human dental calculus Metagenome
| PRJNA608541 | ENA
Project description:The purpose of this study was to investigate oral microbiome and host proteins in archaeological human dental tissues using a shotgun proteomics approach. The research focuses on dental calculus (mineralized plaque), dentine, a carious lesion, and an alveolar bone abscess from the medieval site of Dalheim, Germany (ca. AD 950-1200). For comparison, proteins were also analyzed from archaeological faunal dental tissues and human dental calculus samples from modern Swiss dental patient controls. Protein extraction and generation of tryptic peptides from tooth and dental calculus specimens was performed using a filter-aided sample preparation (FASP) protocol, modified for mineralized and degraded samples. Total protein extraction was performed on a total of fourteen samples: four ancient human calculus samples (indicated as: G12, B71, B61, and B78), four ancient human tooth root samples (indicated as: G12, B17, B61, and B78), one carious lesion (indicated as: B17), one alveolar bone abscess (indicated as: B17), two ancient fauna crown cementum/calculus samples (indicated as: F1 [sheep] and F5 [cattle]), and two modern dental calculus samples from clinical patients (indicated as: P1 and P2). All samples were extracted at the Centre for Evolutionary Medicine (ZEM) at the University of Zürich with the exception of dental calculus from G12, P1, and P2, which were extracted at the Center for GeoGenetics (CGG) at the University of Copenhagen. Two samples (G12 and B61 calculus) were extracted a second time in an independent laboratory at the University of York (YORK) for comparison. Sample extracts were then sequenced (LC-MS/MS) at the Functional Genomics Center Zürich (FGCZ) using an LTQ-Orbitrap Velos, at the Novo Nordisk Foundation Center for Protein Research (CPR) using a Q-Exactive Hybrid Quadrupole Orbitrap, and at the University of York’s Proteomics and Analytical Biochemistry Laboratories (PABL) using a MaXis UHR-Qq-TOF.
2014-01-29 | PXD000412 | Pride