摘要:SummaryRecent studies have demonstrated the potential to recover ancient human mitochondrial DNA and nuclear DNA from cave sediments. However, the source of such sedimentary ancient DNA is still under discussion. Here we report the case of a Bronze Age human skeleton, found in a limestone cave, which was covered with layers of calcite stone deposits. By analyzing samples representing bones and stone deposits from this cave, we were able to: i) reconstruct the full human mitochondrial genome from the bones and the stones (same haplotype); ii) determine the sex of the individual; iii) reconstruct six ancient bacterial and archaeal genomes; and finally iv) demonstrate better ancient DNA preservation in the stones than in the bones. Thereby, we demonstrate the direct diffusion of human DNA from bones into the surrounding environment and show the potential to reconstruct ancient microbial genomes from such cave deposits, which represent an additional paleoarcheological archive resource.Graphical abstractDisplay OmittedHighlights•Bronze Age human skeletal remains were found unburned in Wimsener cave in Germany•The bones were covered with layers of calcite stone deposits•The ancient human and microbial DNA diffused from the bones to the stones•The mitochondrial haplogroup and sex were revealed by analyzing the stones onlyBiological sciences; Evolutionary biology; Paleobiology; Paleogenetics; Anthropology; Archeology