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Human oral metagenome

ABSTRACT: Ancient DNA analysis of food remains in human dental calculus from the Edo period, Japan

PROVIDER: PRJDB8768 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	DRR201852_1.fastq.gz	Fastqsanger.gz
	DRR201852_2.fastq.gz	Fastqsanger.gz
	DRR201853_1.fastq.gz	Fastqsanger.gz
	DRR201853_2.fastq.gz	Fastqsanger.gz
	DRR201854_1.fastq.gz	Fastqsanger.gz

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human oral metagenome

Project description:Edo calculus microbiome

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Proteomic Evidence of Dietary Sources in Ancient Dental Calculus

Project description:Archaeological dental calculus has emerged as a rich source of ancient biomolecules, including proteins. Previous analyses of proteins extracted from ancient dental calculus revealed the presence of the dietary milk protein β-lactoglobulin, providing direct evidence of dairy consumption in the archaeological record. However, the potential for calculus to preserve other food-related proteins has not yet been systematically explored. Here we analyse shotgun metaproteomic data from 100 archaeological dental calculus samples ranging from the Iron Age to the post-medieval period (8thC BC - 19thC AD) in Britain, as well as dental calculus from contemporary dental patients and recently deceased individuals, to characterise the range and extent of dietary proteins preserved in dental calculus. In addition to milk proteins, we detected proteomic evidence of foodstuffs such as cereals and plant products, as well as the digestive enzyme salivary amylase. We discuss the importance of optimized protein extraction methods, data analysis approaches, and authentication strategies in the identification of dietary proteins from archaeological dental calculus. Our ability to detect dietary proteins, although limited, demonstrates the potential of these methods to robustly identify foodstuffs in the archaeological record that are under-represented due to their poor preservation.

2018-07-18 | PXD009603 | Pride

Palaeoproteomic investigation of an ancient human skeleton with abnormal deposition of dental calculus

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

Protein Extraction from Ancient Teeth and Dental Calculus Compatible with Subsequent DNA Extraction

Project description:Dental calculus is becoming a crucial material in the study of past populations, with increasing interest in its proteomic and genomic content. Here we suggest further development of protocol for analysis of ancient proteins and a combined approach for subsequent ancient DNA extraction. We tested the protocol on recent teeth. We then applied the optimised protocol to ancient teeth to limit the destruction of calculus, as it is a precious and irreplaceable source of dietary, microbiological, and ecological information in the archaeological context. Finally, the applicability of the protocol was proven on samples of ancient calculus.

2023-09-11 | PXD042668 | Pride

human oral metagenome

Project description:Dental Calculus Saladoid Metagenome

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Ancient human dental calculus

Project description:Ancient human dental calculus Metagenome

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Ancient dental calculus from Oceania

Project description:Ancient dental calculus from Oceania

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Project description:Radcliffe Infirmary ancient dental calculus

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Human Oral Metagenome

Project description:Differential DNA preservation in archaeological dental calculus and dentin

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Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus

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

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