Human Genetics • Original Paper

Journal of Applied Genetics

, Volume 54, Issue 3, pp 309-325

First insights into the metagenome of Egyptian mummies using next-generation sequencing

  • Rabab KhairatAffiliated withInstitute of Human Genetics, University of TübingenDepartment of Medical Molecular Genetics, Division of Human Genetics and Genome Research, National Research CentreAncient DNA Laboratory, Egyptian Museum
  • , Markus BallAffiliated withInstitute of Human Genetics, University of Tübingen
  • , Chun-Chi Hsieh ChangAffiliated withInstitute of Human Genetics, University of Tübingen
  • , Raffaella BianucciAffiliated withLaboratory of Physical Anthropology, Department of Public Health and Paediatric Sciences, University of TurinDivision of Paleopathology, History of Medicine and Bioethics, Department of Oncology, Transplants and Advanced Technologies in Medicine, University of Pisa
  • , Andreas G. NerlichAffiliated withInstitute of Pathology, Division of Paleopathology, Academic Clinic München-Bogenhausen
  • , Martin TrautmannAffiliated withAnthropologie und Osteoarchäologie, Praxis für BioarchäologieInstitut für Forensische Sachgutachten
  • , Somaia IsmailAffiliated withDepartment of Medical Molecular Genetics, Division of Human Genetics and Genome Research, National Research CentreAncient DNA Laboratory, Egyptian Museum
  • , Gamila M. L. ShanabAffiliated withDepartment of Biochemistry, Faculty of Science, Ain Shams University
  • , Amr M. KarimAffiliated withDepartment of Biochemistry, Faculty of Science, Ain Shams University
    • , Yehia Z. GadAffiliated withDepartment of Medical Molecular Genetics, Division of Human Genetics and Genome Research, National Research CentreAncient DNA Laboratory, Egyptian Museum
    • , Carsten M. PuschAffiliated withInstitute of Human Genetics, University of Tübingen Email author 

Rent the article at a discount

Rent now

* Final gross prices may vary according to local VAT.

Get Access

Abstract

We applied, for the first time, next-generation sequencing (NGS) technology on Egyptian mummies. Seven NGS datasets obtained from five randomly selected Third Intermediate to Graeco-Roman Egyptian mummies (806 BC–124AD) and two unearthed pre-contact Bolivian lowland skeletons were generated and characterised. The datasets were contrasted to three recently published NGS datasets obtained from cold-climate regions, i.e. the Saqqaq, the Denisova hominid and the Alpine Iceman. Analysis was done using one million reads of each newly generated or published dataset. Blastn and megablast results were analysed using MEGAN software. Distinct NGS results were replicated by specific and sensitive polymerase chain reaction (PCR) protocols in ancient DNA dedicated laboratories. Here, we provide unambiguous identification of authentic DNA in Egyptian mummies. The NGS datasets showed variable contents of endogenous DNA harboured in tissues. Three of five mummies displayed a human DNA proportion comparable to the human read count of the Saqqaq permafrost-preserved specimen. Furthermore, a metagenomic signature unique to mummies was displayed. By applying a “bacterial fingerprint”, discrimination among mummies and other remains from warm areas outside Egypt was possible. Due to the absence of an adequate environment monitoring, a bacterial bloom was identified when analysing different biopsies from the same mummies taken after a lapse of time of 1.5 years. Plant kingdom representation in all mummy datasets was unique and could be partially associated with their use in embalming materials. Finally, NGS data showed the presence of Plasmodium falciparum and Toxoplasma gondii DNA sequences, indicating malaria and toxoplasmosis in these mummies. We demonstrate that endogenous ancient DNA can be extracted from mummies and serve as a proper template for the NGS technique, thus, opening new pathways of investigation for future genome sequencing of ancient Egyptian individuals.

Keywords

Ancient DNA DNA survival Egyptian mummies Embalming material MEGAN Metagenomics Next-generation sequencing Preservation Temperature