Exploring the Pathogen Profiles of Ancient Feces

Analysis of ancient desiccated feces - termed paleofeces or coprolites - can unlock insights into the lives of ancient people. We collected desiccated feces from caves in the Rio Zape Valley in Mexico (725-920 CE). First, we extracted DNA with methods previously optimized for paleofeces. Then, we applied highly sensitive modern molecular tools (i.e., PCR pre-amplification followed by multi-parallel qPCR) to assess the presence of 30 enteric pathogens. We detected [≥]1 pathogen associated gene in each of the ten samples and a mean of 3.9 pathogens per sample. The targets detected included Blastocystis spp. (n=7), atypical enteropathogenic E. coli (n=7), Enterobius vermicularis (n=6), Entamoeba spp. (n=5), enterotoxigenic E. coli (n=5), Shigella spp./enteroinvasive E. coli (n=3), Giardia spp. (n=2), and E. coli O157:H7 (n=1). The protozoan pathogens we detected (i.e., Giardia spp. and Entamoeba spp.) have been previously detected in paleofeces via enzyme-linked immunoassay (ELISA), but have not via PCR. This work represents the first detection of Blastocystis spp. atypical enteropathogenic E. coli, enterotoxigenic E. coli, Shigella spp./enteroinvasive E. coli, and E. coli O157:H7 in paleofeces. These results suggest that sensitive modern molecular tools, such as PCR, can be used to evaluate ancient materials for genes of interest.