A Robust Framework for Microbial Archaeology

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


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.

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

Publication types

  • Review
  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Archaea / genetics
  • Archaea / isolation & purification*
  • Archaeology / methods
  • Bacteria / genetics
  • Bacteria / isolation & purification*
  • DNA, Ancient / analysis*
  • Genome, Archaeal
  • Genome, Bacterial
  • Humans
  • Metagenomics / methods*
  • Microbiota / genetics*
  • Sequence Analysis, DNA / methods*


  • DNA, Ancient