2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals
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RESEARCH ARTICLE
Open Access
2000-year-old pathogen genomes reconstructed from metagenomic analysis of Egyptian mummified individuals Judith Neukamm1,2,3, Saskia Pfrengle1,2, Martyna Molak4,5, Alexander Seitz3, Michael Francken6,7, Partick Eppenberger1, Charlotte Avanzi8, Ella Reiter2, Christian Urban1, Beatrix Welte9, Philipp W. Stockhammer10,11, Barbara Teßmann12,13, Alexander Herbig11, Katerina Harvati6,7,14, Kay Nieselt3, Johannes Krause11,2,6* and Verena J. Schuenemann1,2,6*
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-yearold 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. Keywords: Ancient DNA, Egyptian mummified individuals, Metagenomics, Leprosy, Hepatitis B virus
Background Over the last decade, advances in next-generation sequencing technologies and the reduction of the associated costs have enabled DNA shotgun sequencing data to be analyzed on a larger scale [1]. These developments fostered the field of metagenomics to provide insights into the composition of the human microbiome and the identification of diseases from which an individual suffers [2, 3]. While most studies * Correspondence: [email protected]; [email protected] 11 Max Planck Institute for the Science of Human History, Kahlaische Str. 10, 07745 Jena, Germany 1 Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland Full list of author information is available at the end of the article
focus on the microbiome of the human gut [4], the oral cavity [5], or skin [6] in healthy or diseased modern individuals, the analysis of microbiomes could also provide insights into the health status of individuals in the past. Although the analysis is limited by the preservation of the samples and environmental contamination, e.g., by soil bacteria, studies have confirmed exceptionally well-preserved microbial and human mitochondrial DNA in dental calculus [7–9], which enables the simultaneous investigation of pathogen activity a
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