title: 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.
authors.affiliation: Center for Applications in Biotechnology, California Polytechnic State University, San Luis Obispo, California, United States of America.
authors.forename: Raul J
authors.initials: RJ
authors.lastname: Cano
authors.affiliation: Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.
authors.forename: Jessica
authors.initials: J
authors.lastname: Rivera-Perez
authors.affiliation: Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.
authors.forename: Gary A
authors.initials: GA
authors.lastname: Toranzos
authors.affiliation: Department of Pathology, University of California San Diego, San Diego, California, United States of America.
authors.forename: Tasha M
authors.initials: TM
authors.lastname: Santiago-Rodriguez
authors.affiliation: Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico.
authors.forename: Yvonne M
authors.initials: YM
authors.lastname: Narganes-Storde
authors.affiliation: Center for Archaeological Research, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico.
authors.forename: Luis
authors.initials: L
authors.lastname: Chanlatte-Baik
authors.affiliation: Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.
authors.forename: Erileen
authors.initials: E
authors.lastname: García-Roldán
authors.affiliation: Department of Biology, University of Puerto Rico, Mayaguez Campus, San Juan, Puerto Rico.
authors.forename: Lucy
authors.initials: L
authors.lastname: Bunkley-Williams
authors.affiliation: Department of Biology, University of Puerto Rico, San Juan, Puerto Rico.
authors.forename: Steven E
authors.initials: SE
authors.lastname: Massey
mesh_terms: D004032:Diet; D005243:Feces / Q000382:microbiology* / Q000469:parasitology; D006801:Humans; D008829:Microbiology; D064307:Microbiota; D010163:Paleontology; D044382:Population Groups; D011647:Puerto Rico / Q000208:ethnology; D012336:RNA, Ribosomal, 16S / Q000235:genetics
chemical_list: D012336:RNA, Ribosomal, 16S