title: Insights from characterizing extinct human gut microbiomes.
abstract: In an effort to better understand the ancestral state of the human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, we pyrosequenced the 16S rDNA V3 region from duplicate coprolite samples recovered from three archaeological sites, each representing a different depositional environment: Hinds Cave (~8000 years B.P.) in the southern United States, Caserones (1600 years B.P.) in northern Chile, and Rio Zape in northern Mexico (1400 years B.P.). Clustering algorithms grouped samples from the same site. Phyletic representation was more similar within sites than between them. A Bayesian approach to source-tracking was used to compare the coprolite data to published data from known sources that include, soil, compost, human gut from rural African children, human gut, oral and skin from US cosmopolitan adults and non-human primate gut. The data from the Hinds Cave samples largely represented unknown sources. The Caserones samples, retrieved directly from natural mummies, matched compost in high proportion. A substantial and robust proportion of Rio Zape data was predicted to match the gut microbiome found in traditional rural communities, with more minor matches to other sources. One of the Rio Zape samples had taxonomic representation consistent with a child. To provide an idealized scenario for sample preservation, we also applied source tracking to previously published data for Ötzi the Iceman and a soldier frozen for 93 years on a glacier. Overall these studies reveal that human microbiome data has been preserved in some coprolites, and these preserved human microbiomes match more closely to those from the rural communities than to those from cosmopolitan communities. These results suggest that the modern cosmopolitan lifestyle resulted in a dramatic change to the human gut microbiome.
authors.affiliation: Department of Anthropology, University of Oklahoma, Norman, OK, USA.
authors.forename: Raul Y
authors.initials: RY
authors.lastname: Tito
authors.forename: Dan
authors.initials: D
authors.lastname: Knights
authors.forename: Jessica
authors.initials: J
authors.lastname: Metcalf
authors.forename: Alexandra J
authors.initials: AJ
authors.lastname: Obregon-Tito
authors.forename: Lauren
authors.initials: L
authors.lastname: Cleeland
authors.forename: Fares
authors.initials: F
authors.lastname: Najar
authors.forename: Bruce
authors.initials: B
authors.lastname: Roe
authors.forename: Karl
authors.initials: K
authors.lastname: Reinhard
authors.forename: Kristin
authors.initials: K
authors.lastname: Sobolik
authors.forename: Samuel
authors.initials: S
authors.lastname: Belknap
authors.forename: Morris
authors.initials: M
authors.lastname: Foster
authors.forename: Paul
authors.initials: P
authors.lastname: Spicer
authors.forename: Rob
authors.initials: R
authors.lastname: Knight
authors.forename: Cecil M
authors.initials: CM
authors.lastname: Lewis
mesh_terms: D000349:Africa; D001106:Archaeology; D001499:Bayes Theorem; D002648:Child; D002677:Chile; D004275:DNA, Ribosomal / Q000235:genetics; D006801:Humans; D007422:Intestines / Q000382:microbiology*; D054892:Metagenome; D008800:Mexico; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D014481:United States
chemical_list: D004275:DNA, Ribosomal; D012336:RNA, Ribosomal, 16S