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  2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals

Neukamm, J., Pfrengle, S., Molak, M., Seitz, A., Francken, M., Eppenberger, P., et al. (2020). 2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals. BMC Biology, 18(1): 108. doi:10.1186/s12915-020-00839-8.

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Item Permalink: http://hdl.handle.net/21.11116/0000-0006-F6DD-C Version Permalink: http://hdl.handle.net/21.11116/0000-0007-2D53-A
Genre: Journal Article

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 Creators:
Neukamm, Judith, Author
Pfrengle, Saskia, Author
Molak, Martyna, Author
Seitz, Alexander, Author
Francken, Michael, Author
Eppenberger, Partick, Author
Avanzi, Charlotte, Author
Reiter, Ella, Author
Urban, Christian, Author
Welte, Beatrix, Author
Stockhammer, Philipp W.1, 2, Author              
Teßmann, Barbara, Author
Herbig, Alexander1, Author              
Harvati, Katerina, Author              
Nieselt, Kay, Author
Krause, Johannes1, 2, Author              
Schuenemann, Verena J., Author
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              
2MHAAM, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2541699              

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Free keywords: Ancient DNA, Egyptian mummified individuals, Metagenomics, Leprosy, Hepatitis B virus
 Abstract: BACKGROUND: Recent advances in sequencing have facilitated large-scale analyses of the metagenomic composition of different samples, including the environmental microbiome of air, water, and soil, as well as the microbiome of living humans and other animals. Analyses of the microbiome of ancient human samples may provide insights into human health and disease, as well as pathogen evolution, but the field is still in its very early stages and considered highly challenging. - RESULTS: The metagenomic and pathogen content of Egyptian mummified individuals from different time periods was investigated via genetic analysis of the microbial composition of various tissues. The analysis of the dental calculus’ microbiome identified Red Complex bacteria, which are correlated with periodontal diseases. From bone and soft tissue, genomes of two ancient pathogens, a 2200-year-old Mycobacterium leprae strain and a 2000-year-old human hepatitis B virus, were successfully reconstructed. - CONCLUSIONS: The results show the reliability of metagenomic studies on Egyptian mummified individuals and the potential to use them as a source for the extraction of ancient pathogen DNA.

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Language(s): eng - English
 Dates: 2020-08-28
 Publication Status: Published online
 Pages: 18
 Publishing info: -
 Table of Contents: Background

Results
- Sample information and dating
- General metagenomic assessment
- Mycobacterium leprae (individual Abusir1630)
- Hepatitis B virus (individual Abusir1543)
- Oral microbiome assessment

Discussion

Conclusions

Methods
- Sample extraction and radiocarbon dating
- Sample extraction and library preparation
- Metagenomic screening
- Authentication of ancient DNA
- Content of endogenous DNA (SourceTracker2)
- Data processing of sample Abusir1630b (M. leprae)
-- Read processing, mapping, and variant calling
-- SNP typing
-- Anthropological analysis
-- Phylogeny
-- Beast analysis
-- Temporal signal
- Data processing individual Abusir1543 (hepatitis B virus)
-- Read processing, mapping, and variant calling
-- Phylogeny
-- Recombination analysis
-- Beast analysis
-- Temporal signal
 Rev. Type: -
 Identifiers: DOI: 10.1186/s12915-020-00839-8
Other: shh2694
 Degree: -

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Title: BMC Biology
Source Genre: Journal
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Publ. Info: Berlin ; Heidelberg : Springer
Pages: - Volume / Issue: 18 (1) Sequence Number: 108 Start / End Page: - Identifier: ISSN: 1741-7007
CoNE: https://pure.mpg.de/cone/journals/resource/111071069889000