Abstract
Groundbreaking studies conducted in the mid-1980s 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 inscrutable bacterial history, 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 such as identifying the aetiological agent of the black death as Yersinia pestis . Furthermore, ancient human microbiomes from fossilized 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 summarize the present avenues of research and contextualize them in the past of the field whilst also pointing towards questions still to be answered.
Highlights
Despite the growing wealth of genomic data since the advent of next-g eneration sequencing, some domains of life remain elusive for evolutionary biologists [1]; in particular, the past of bacteria, the oldest domain [2], is inaccessible due to a poor fossil record [3]
We aim to provide a convenient summary to serve as a primer for researchers from any field going into bacterial ancient DNA (aDNA)
Aided by benefits in preservation, and despite challenges unique to bacteria, researchers have been able to generate a tremendous amount of insight from the study of bacterial aDNA
Summary
Despite the growing wealth of genomic data since the advent of next-g eneration sequencing, some domains of life remain elusive for evolutionary biologists [1]; in particular, the past of bacteria, the oldest domain [2], is inaccessible due to a poor fossil record [3]. In lieu of fossil evidence, the study of bacterial evolution has benefited greatly from the use of ancient DNA (aDNA) extracted from archaeological specimens. ADNA has opened an increasingly larger window into the past, answered fundamental questions concerning human evolution [5] and uncovered otherwise inscrutable bacterial history. We chronologically review how paleogenetics has helped the understanding of bacterial evolution covering human pathogens and microbiomes as well as environmental microbes. As an introduction we contextualize the present state of research relative to the field’s past and highlight major breakthroughs and setbacks in its trajectory. We subsequently encapsulate the present state of the field by providing a snapshot of current findings and a catalogue of available paleogenomes. We assess the future of bacterial aDNA through possible avenues of investigation that provide potential starting points for future endeavours using bacterial aDNA
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