Comprehensive analysis of microorganisms accompanying human archaeological remains. Homo sapiens

We used metagenomic approaches to perform comparative analyses of microorganism communitiespresent in 161 archaeological human remains. DNA samples were isolated from the teeth of human skeletons dated from 100 AD to 1,200 AD. The skeletons or their fragments were collected from seven archaeological sites in Central Europe and stored under different conditions. The majority of identified microbes were ubiquitous environmental bacteria that most likely colonized the host remains not long ago. We observed that the composition of microbial communities is sample-specific and not correlated with its temporal or geographical origin. Bacteria and archaea typically found in human oral and gut flora as well as potential pathogens were identified in two-thirds of the samples. The genetic material of these human-related species, in contrast to the environmental species, revealed aDNA damage pattern comparable with endogenous human aDNA, which strongly suggests that these microbes may have accompanied the individual even before death. Our study showed that the microbiome observed in an individual sample is not reliant on the method or duration of sample storage. Moreover, shallow sequencing of DNA extracted from ancient specimens and subsequent bioinformatics analysis allow the differentiation of ancient microbial species, including pathogens, from contemporary species thatcolonized human remains more recently.