The past, present and future of bacterial ancient DNA
Arning, N. and D. J. Wilson (2020)
Microbial Genomics doi: 10.1099/mgen.0.000384 (pdf)
Groundbreaking studies conducted in the mid-eighties demonstrated the possibility of sequencing ancient DNA (aDNA), which has allowed us to answer fundamental questions about the human past. Microbiologists were thus given a powerful tool to glimpse directly into the inscrutable bacterial past, hitherto inaccessible due to a poor fossil record. Initially plagued by concerns regarding contamination, the field has grown alongside technical progress, with the advent of high-throughput sequencing being a breakthrough in sequence output and authentication. Albeit burdened with challenges unique to the analysis of bacteria, a growing number of viable sources for aDNA has opened multiple avenues of microbial research. Ancient pathogens have been extracted from bones, dental pulp, mummies, and historical medical specimens and have answered focal historical questions like identifying the aetiological agent of the black death as Yersinia pestis. Furthermore, ancient human microbiomes from fossilised faeces, mummies, and dental plaque have shown shifts in human commensals through the Neolithic demographic transition and industrial revolution, whereas environmental isolates stemming from permafrost samples have revealed signs of ancient antimicrobial resistance. Culminating in an ever-growing repertoire of ancient genomes, the quickly expanding body of bacterial aDNA studies has also enabled comparisons of ancient genomes to their extant counterparts, illuminating the evolutionary history of bacteria. In this review we aim to summarise the present avenues of research and contextualise them in the past of the field whilst also pointing towards questions to be answered in the future.