Environmental Contamination in Paleofecal Analysis: why soil sampling is vital for establishing ancient microbial diversity

Our study is a demonstration that it is possible, and indeed vitally important, to differentiate between the microbiota found in coprolites and the surrounding soil environment in which they were found in order to accurately portray the microbiome of an ancient sample. Ancient DNA from humans and the gut microbiome found in paleofecal material recovered from the Boomerang Rock Shelter site in southeastern Utah were analyzed and compared to the microbiome from the surrounding sediment. 16S NGS sequencing was used to develop profiles from paleofeces, as well as the particular stratigraphic soil layer from which the paleofeces was recovered. This research demonstrates that it is possible to obtain information about the ancient gut microbiome and differentiate it from the soil microbes, but future analyses should attempt to sequence both in order to ensure that cross-contamination has not occurred.