First NGS datasets from five Egyptian mummies and two Bolivian skeletons. Three mummies show human DNA levels matching permafrost-preserved Saqqaq. Mummies display unique metagenomic signature. Bacterial fingerprint distinguishes mummies from other warm-climate remains. Bacterial bloom occurred in biopsies stored 1.5 years without environment control. Plant DNA traces link to embalming materials. Plasmodium falciparum DNA confirms malaria infection. Toxoplasma gondii DNA confirms toxoplasmosis infection. Endogenous ancient DNA viable for future full genome sequencing. PCR replicates NGS pathogen findings. Human DNA proportions vary across mummy tissues.