biostudies-literatureWarinner CVillum FondenNIGMS NIH HHS321-356https://www.ebi.ac.uk/biostudies/studies/S-EPMC5581243biostudies-literatureUnknown18Microbial 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.Annual review of genomics and human geneticsA Robust Framework for Microbial Archaeology.PMC558124300013266R01 GM089886Weiß CLHerbig AOrlando LFellows Yates JAMann AWarinner CKrause JBurbano HAfalseA Robust Framework for Microbial Archaeology.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.2017-01-01T00:00:00Z2017 Aug2026-05-03T17:57:56.644Z2019-03-26T23:03:55ZS-EPMC55812432846019610.1146/annurev-genom-091416-035526