Nineteenth and twentieth century portrayals of the pile-dwelling communities who lived in and around the Alps during the Neolithic and Bronze Age were often romanticized, depicting a life of plenty and prosperity. But what was life really like? Living on the lake in Neolithic Europe had certain advantages, but it might also have exposed people to waterborne infectious diseases, such as typhoid, cholera, and dysentery, or vector-borne diseases, such as malaria, which are “invisible” archaeologically. Parasites also constituted a major health burden on human populations in the past and can be similarly detected using ancient DNA. We will use ancient metagenomics and metaproteomics to investigate the health status of the pile-dwelling communities and to shed light on the evolution of the human oral microbiome and specific human pathogens. As a high-risk element, we will attempt to recover ancient RNA viruses from the pitch. The recovery of ancient RNA is complicated by the fact that RNA is much less stable than double-stranded DNA and so far it has only been recovered from very well-preserved tissues but, if successful, the proposed research will revolutionize the study of ancient viral pathogens and their impact on human populations.