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Annu Rev Genomics Hum Genet. 2017 Aug 31;18:321-356. doi: 10.1146/annurev-genom-091416-035526. Epub 2017 Apr 26.

A Robust Framework for Microbial Archaeology.

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Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; email:
Department of Anthropology, University of Oklahoma, Norman, Oklahoma 73019.
Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen 72076, Germany.
Centre for GeoGenetics, Natural History Museum of Denmark, 1350 Copenhagen K, Denmark.
Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université Toulouse III - Paul Sabatier, Toulouse 31000, France.


Microbial archaeology is flourishing in the era of high-throughput sequencing, revealing the agents behind devastating historical plagues, identifying the cryptic movements of pathogens in prehistory, and reconstructing the ancestral microbiota of humans. Here, we introduce the fundamental concepts and theoretical framework of the discipline, then discuss applied methodologies for pathogen identification and microbiome characterization from archaeological samples. We give special attention to the process of identifying, validating, and authenticating ancient microbes using high-throughput DNA sequencing data. Finally, we outline standards and precautions to guide future research in the field.


ancient DNA; bacteria; high-throughput sequencing; metagenomics; microbiology; microbiome; pathogens

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