Paleoparasitology in the Old World has mainly concerned the study of latrine sediments and coprolites collected from mummified bodies or archaeological strata, mostly preserved by natural conditions. Human parasites recovered include cestodes, trematodes, and nematodes. The well preserved conditions of helminth eggs allowed paleoepidemiological approaches taking into account the number of eggs found by archaeological stratum. Tentatively, sanitation conditions were assessed for each archaeological period.

The identification of parasites in ancient human faeces is compromised by differential preservation of identifiable parasite structures. However, protein molecules can survive the damage of the environment and can be detected even after centuries. In this paper it is shown that is possible to detect copro-antigen of Entamoeba histolytica in historic and prehistoric human faecal remains, using a commercially available enzyme immunoassay (ELISA) kit. The kit uses monoclonal antibody-peroxidase conjugate specific for E. histolytica adhesin. A total of 90 specimens of desiccated faeces found in mummies and ancient organic sediment from South America, North America, Africa, and Europe were examined. The ELISA detected 20 positive samples, dated to about 5300 years before present to the 19th Century ad. The positive samples are from archaeological sites in Argentina, USA, France, Belgium, and Switzerland. The detection of protozoan antigen using immunoassays is a reliable tool for the studies of intestinal parasites in the past.

Coprolites are fossilized fecal material that can reveal information about ancient intestinal and environmental microbiota. Viral metagenomics has allowed systematic characterization of viral diversity in environmental and human-associated specimens, but little is known about the viral diversity in fossil remains. Here, we analyzed the viral community of a 14th-century coprolite from a closed barrel in a Middle Ages site in Belgium using electron microscopy and metagenomics. Viruses that infect eukaryotes, bacteria, and archaea were detected, and we confirmed the presence of some of them by ad hoc suicide PCR. The coprolite DNA viral metagenome was dominated by sequences showing homologies to phages commonly found in modern stools and soil. Although their phylogenetic compositions differed, the metabolic functions of the viral communities have remained conserved across centuries. Antibiotic resistance was one of the reconstructed metabolic functions detected.