Paleomicrobiology: Revealing Fecal Microbiomes of Ancient Indigenous Cultures

Abstract

Coprolites are fossilized feces that can be used to provide information on the composition of the intestinal microbiota and, as we show, possibly on diet. We analyzed human coprolites from the Huecoid and Saladoid cultures from a settlement on Vieques Island, Puerto Rico. While more is known about the Saladoid culture, it is believed that both societies co-existed on this island approximately from 5 to 1170 AD. By extracting DNA from the coprolites, followed by metagenomic characterization, we show that both cultures can be distinguished from each other on the basis of their bacterial and fungal gut microbiomes. In addition, we show that parasite loads were heavy and also culturally distinct. Huecoid coprolites were characterized by maize and Basidiomycetes sequences, suggesting that these were important components of their diet. Saladoid coprolite samples harbored sequences associated with fish parasites, suggesting that raw fish was a substantial component of their diet. The present study shows that ancient DNA is not entirely degraded in humid, tropical environments, and that dietary and/or host genetic differences in ancient populations may be reflected in the composition of their gut microbiome. This further supports the hypothesis that the two ancient cultures studied were distinct, and that they retained distinct technological/cultural differences during an extended period of close proximity and peaceful co-existence. The two populations seemed to form the later-day Taínos, the Amerindians present at the point of Columbian contact. Importantly, our data suggest that paleomicrobiomics can be a powerful tool to assess cultural differences between ancient populations.

Fungi in the healthy human gastrointestinal tract

“…Malassezia has also been reported in significant abundance in fecal samples and may play a role in the gut. 29,30,23 To determine whether any Malassezia is indigenous to the gut would require more invasive sampling techniques than the standard fecal collection, to eliminate the possibility of inoculation of the feces by skin flora.…”

Ancient bacteria of the Ötzi’s microbiome: a genomic tale from the Copper Age

“…Similar approaches have been applied to characterize the microbiota composition of ancient biological samples retrieved from mummies [9–11]. Several types of ancient specimens, including both coprolites as well as human remains, have been studied during recent years in order to elucidate their microbial associations [11, 12]. In this context, the oral cavity [13, 14] and distal gut microbiota have been extensively analyzed [9, 10].…”

Paleomicrobiology: a Snapshot of Ancient Microbes and Approaches to Forensic Microbiology

“…and Enterobius spp., were preserved for thousands of years, although it was not clear if they were still infective. Paleoparasitological studies of coprolites were among the first to suggest that dietary habits, and even lifestyles, of ancient cultures (e.g., hunter-gatherer people vs. agriculturalists) could be discerned from ancient samples (73–76). …”

“…In addition, given that the gut microbiomes of modern human societies seem to be a reflection of diet and culture (77), recent paleomicrobiology studies have discerned dietary habits and even cultural differences by characterizing the coprolite microbiome using high-throughput sequencing of the 16S rDNA fragments (72). While coprolites possess a core microbiome that is comparable to extant human gut microbiomes, the proportions of certain microbial groups (both bacterial and fungal) have been found to be diet specific and thus may be ethnic group specific (76, 78). …”

“…are present in soil (93–95). As with any archaeological sample, soil and its associated microbiota will most likely be present as contaminants; thus, it is crucial to ensure optimal sample handling and, whenever possible, discard the exterior layers of the sample, focusing all analyses on sample cores, which contain less of the environment-associated microbiota (76). …”