Ancient pathogen genomics
field in science
Ancient pathogen genomics is a scientific field related to the study of pathogen genomes recovered from ancient human, plant or animal remains. Ancient pathogens are microorganisms, now extinct, that in the past centuries caused several epidemics and deaths worldwide. Their genome, referred to as ancient DNA (aDNA), is isolated from the burial's remains (bones and teeth) of victims of the pandemics caused by these pathogens.
The analysis of the genomic features of ancient pathogen genomes allows researchers to understand the evolution of modern microbial strains that can hypothetically generate new pandemics or outbreaks. The analysis of aDNA is carried out by bioinformatic tools and molecular biology techniques to compare ancient pathogens with the modern descendants. The comparison also provides phylogenetic information of these strains.
Reconstructing ancient pathogen genomes through NGS technologies
Pathogen DNA detection in ancient remains can be achieved with laboratory or computational methods. In both cases, the procedure starts with the extraction of DNA from ancient specimens. The laboratory methods are based on the construction of NGS libraries and the subsequent capture-based screening. Computational tools are used to map the reads obtained by NGS against a single- or multi-genome reference (targeted approach); alternatively, metagenomic profiling or taxonomic assignment of shotgun NGS reads methods can be applied (broad approach).
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