Abstract
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.
Highlights
In 2011, the first fully reconstructed ancient bacterial genome sequence was published—that of Yersinia pestis—which confirmed at least one of the etiological agents of the Black Death pandemic [16] and put to rest years of controversy that had dogged polymerase chain reaction (PCR)–based attempts to identify the pathogen in archaeological samples [41, 57, 58, 154, 155]
This article focuses on the analysis of metagenomic data obtained from high-throughput sequencing (HTS) shotgun-sequenced or sequence-captured genes and genomes obtained from a microbiota present within a microbiome [113]
There are many well-known examples of named microbes for which the taxonomy is incongruent with phylogeny. In some cases, such discrepancies apply to clinically important taxa that differ from nonpathogenic taxa mainly because of horizontally transferred virulence factors that result in major phenotypic changes, as in the case of Yersinia pseudotuberculosis and Y. pestis [25]
Summary
See credit lines of images or other third party material in this article for license information. Keywords ancient DNA, metagenomics, microbiology, bacteria, pathogens, microbiome, high-throughput sequencing
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