Journal of Applied Genetics

, Volume 54, Issue 3, pp 309–325 | Cite as

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

  • Rabab Khairat
  • Markus Ball
  • Chun-Chi Hsieh Chang
  • Raffaella Bianucci
  • Andreas G. Nerlich
  • Martin Trautmann
  • Somaia Ismail
  • Gamila M. L. Shanab
  • Amr M. Karim
  • Yehia Z. Gad
  • Carsten M. Pusch
Human Genetics • Original Paper

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 

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Copyright information

© Institute of Plant Genetics, Polish Academy of Sciences, Poznan 2013

Authors and Affiliations

  • Rabab Khairat
    • 1
    • 2
    • 3
  • Markus Ball
    • 1
  • Chun-Chi Hsieh Chang
    • 1
  • Raffaella Bianucci
    • 4
    • 5
  • Andreas G. Nerlich
    • 6
  • Martin Trautmann
    • 7
    • 8
  • Somaia Ismail
    • 2
    • 3
  • Gamila M. L. Shanab
    • 9
  • Amr M. Karim
    • 9
  • Yehia Z. Gad
    • 2
    • 3
  • Carsten M. Pusch
    • 1
  1. 1.Institute of Human GeneticsUniversity of TübingenTübingenGermany
  2. 2.Department of Medical Molecular Genetics, Division of Human Genetics and Genome ResearchNational Research CentreCairoEgypt
  3. 3.Ancient DNA LaboratoryEgyptian MuseumCairoEgypt
  4. 4.Laboratory of Physical Anthropology, Department of Public Health and Paediatric SciencesUniversity of TurinTurinItaly
  5. 5.Division of Paleopathology, History of Medicine and Bioethics, Department of Oncology, Transplants and Advanced Technologies in MedicineUniversity of PisaPisaItaly
  6. 6.Institute of Pathology, Division of PaleopathologyAcademic Clinic München-BogenhausenMunichGermany
  7. 7.Anthropologie und OsteoarchäologiePraxis für BioarchäologieMünchenGermany
  8. 8.Institut für Forensische SachgutachtenMünchenGermany
  9. 9.Department of Biochemistry, Faculty of ScienceAin Shams UniversityCairoEgypt

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