Insights from Characterizing Extinct Human Gut Microbiomes

• DOI: 10.1371/journal.pone.0051146
• Publication Date: 2012-12-12T22:13:21Z
• Authors: Raul Y. Tito; Dan Knights; Jessica Metcalf; Alexandra J. Obre...; Lauren Cleeland; Fares Najar; Bruce Roe; Karl Reinhard; Kristin Sobolik; Samuel Belknap; Morris Foster; Paul Spicer; Rob Knight; Cecil M. Lewis
• Keywords: History; 590; Social and Behavioral Sciences; Ante-disciplinary; Inclusive; Engineering; Sociology; RNA, Ribosomal, 16S; Chile; Child; 0303 health sciences; Physics; Q; Natural Resources Management and Policy; R; Biological Sciences; Peer-review; Intestines; Chemistry; Public Library of Science; Archaeology; Medicine; Other Environmental Sciences; Research Article; 570; 16S; General Science & Technology; Science; DNA, Ribosomal; Open Access; 03 medical and health sciences; Interdisciplinary; Natural Resources and Conservation; Genetics; Humans; Heritage and Archaeology; Biology; Mexico; PLOS; Ribosomal; Research; Human Genome; 028; Bayes Theorem; DNA; 15. Life on land; United States; Open-Access; Anthropology; Africa; RNA; Metagenome; Environmental Sciences

In an effort to better understand the ancestral state of human distal gut microbiome, we examine feces retrieved from archaeological contexts (coprolites). To accomplish this, pyrosequenced 16S rDNA V3 region duplicate coprolite samples recovered three sites, each representing a different depositional environment: Hinds Cave (∼8000 years B.P.) in southern United States, Caserones (1600 northern Chile, and Rio Zape Mexico (1400 B.P.). Clustering algorithms grouped same site. Phyletic representation was more similar within sites than between them. A Bayesian approach source-tracking used compare data published known sources that include, soil, compost, rural African children, gut, oral skin US cosmopolitan adults non-human primate gut. The largely represented unknown sources. samples, directly natural mummies, matched compost high proportion. substantial robust proportion predicted match microbiome found traditional communities, with minor matches other One had taxonomic consistent child. provide idealized scenario for sample preservation, also applied source tracking previously Ötzi Iceman soldier frozen 93 on glacier. Overall these studies reveal has been preserved some coprolites, microbiomes closely those communities communities. These results suggest modern lifestyle resulted dramatic change microbiome.