Commensal and pathogenic bacteria and viruses, the human microbiota, have coexisted with humans since the dawn of our species with ongoing variable clinical manifestations, including cancer. By exploring deep-sequenced pathogen genomes from clinical and ancient samples has a potential to yield much more accurate estimates of the within-host and between-host pathogen evolutionary rates and uniquely provide data on changes in pathogen genomic stability and evolutionary responses. To better understand ancient pathogen genomic divergence and the ancient pathogen-host parallel evolutionary histories will further allow us to reconstruct the likely origin of present-day clinical pathogen infections.

That is, to investigating human pathogen genomes at deep timescales may provide crucial insights into pathogen virulence evolution and will hopefully allow us to foresee possible new environmentally induced pathogen emergence.

Here, we examined three groups of pathogens transmitted mainly through sexual contact between humans to provide insight into ancient human behavior and history with their pathogens. In addition, we discuss the importance of sound and solid ethical protocols in ancient pathogen DNA research, which should be combined with modern clinical pathogen sequence data, and provide advantages for all researchers worldwide, e.g., through shared genomic data.

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