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

  • Human Genetics • Original Paper
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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.

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Acknowledgements

We are grateful to Heiko Prümers, Iris Trautmann and Andreas Keller for their technical support and for providing sample/library access. Financial support was provided by the Graduiertenförderung Tübingen to R.K., M.B., C.-C.H.C. and C.M.P. Further support was obtained from the DAAD-GERLS program.

Conflict of interest

The authors declare that they have no conflict of interest.

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Authors and Affiliations

  1. Institute of Human Genetics, University of Tübingen, Wilhelmstraße 27, 72074, Tübingen, Germany

    Rabab Khairat, Markus Ball, Chun-Chi Hsieh Chang & Carsten M. Pusch

  2. Department of Medical Molecular Genetics, Division of Human Genetics and Genome Research, National Research Centre, El Buhouth Street, Dokki, 12311, Cairo, Egypt

    Rabab Khairat, Somaia Ismail & Yehia Z. Gad

  3. Ancient DNA Laboratory, Egyptian Museum, El Tahrir Square, 11557, Cairo, Egypt

    Rabab Khairat, Somaia Ismail & Yehia Z. Gad

  4. Laboratory of Physical Anthropology, Department of Public Health and Paediatric Sciences, University of Turin, C.so Galileo Galilei 22, 10126, Turin, Italy

    Raffaella Bianucci

  5. Division of Paleopathology, History of Medicine and Bioethics, Department of Oncology, Transplants and Advanced Technologies in Medicine, University of Pisa, Via Roma 56, 56126, Pisa, Italy

    Raffaella Bianucci

  6. Institute of Pathology, Division of Paleopathology, Academic Clinic München-Bogenhausen, Englschalkinger Str. 77, 81925, Munich, Germany

    Andreas G. Nerlich

  7. Anthropologie und Osteoarchäologie, Praxis für Bioarchäologie, Stolzeneckstr. 7, 81245, München, Germany

    Martin Trautmann

  8. Institut für Forensische Sachgutachten, Dall‘Armistr. 16, 80638, München, Germany

    Martin Trautmann

  9. Department of Biochemistry, Faculty of Science, Ain Shams University, Cairo, Egypt

    Gamila M. L. Shanab & Amr M. Karim

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  1. Rabab Khairat
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  2. Markus Ball
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  4. Raffaella Bianucci
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  11. Carsten M. Pusch
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Correspondence to Carsten M. Pusch.

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Khairat, R., Ball, M., Chang, CC.H. et al. First insights into the metagenome of Egyptian mummies using next-generation sequencing. J Appl Genetics 54, 309–325 (2013). https://doi.org/10.1007/s13353-013-0145-1

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