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

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.

Metagenomic Analysis Reveals Presence of Treponema denticola in a Tissue Biopsy of the Iceman

“…The presence of Clostridia in Iceman’s tissue and intestinal samples was indicated in earlier molecular studies [41], [42] and our finding is consistent with previous data from the Iceman genomic survey [15]. Recently, metagenomic analysis discovered a high percentage of Firmicutes also in tissue samples of Egyptian mummies [43]. Moreover, a microbial survey of the mummies from the Capuchin Catacombs in Sicily, Italy, indicates that members of the order Clostridiales are predominant on mummified skin and muscle samples [44].…”

Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods

“…Recently, various studies were conducted on these remains, including a study on ancient Egyptian embalming resins, two ancient DNA studies and an anthropological examination of the macerated crania12181921. While the possibilities of a demographic reconstruction based on anthropological finds are naturally limited—due to incompleteness of the assemblage, the following anthropological observations were made on the assemblage: For a first assessment, computer tomographic scans of 30 mummies with soft tissue preservation were produced to describe sex (Supplementary Data 1), age at death (Supplementary Data 1) and the macroscopic health status; the six macerated mummies were examined directly.…”

“…New data obtained with high-throughput sequencing methods have the potential to overcome the methodological and contamination issues surrounding the PCR method and could help settle the debate surrounding ancient Egyptian DNA preservation8. However, the first high-throughput sequences obtained from ancient Egyptian mummies12 were not supported by rigorous authenticity and contamination tests.…”

Pharaohs and Mummies: Diseases of Ancient Egypt and Modern Approaches

“…The affected bones are enlarged, highly deformed, and show an irregular surface covered with pits, cavities, and plaques of new bone; furthermore, formation of cloacae (drainage canals) may be present in many cases. Further analysis of fragments can be undertaken through the use of next-generation sequencing technology, using specific and sensitive polymerase chain reaction protocols [10]. Some diseases that can be detected, based on changes in bone structure, include tuberculosis, leprosy and syphilis.…”