Insights from Characterizing Extinct Human Gut Microbiomes

Authors

Raul Y. Tito, University of Oklahoma
Dan Knights, University of Colorado-Boulder
Jessica Metcalf, University of Colorado-Boulder
Alexandra J. Obregon-Tito, University of Oklahoma
Lauren Cleeland, University of Oklahoma
Fares Najar, University of Oklahoma
Bruce Roe, University of Oklahoma
Karl Reinhard, University of Nebraska-LincolnFollow
Kristin Sobolik, University of Maine
Samuel Belknap, University of Maine
Morris Foster, University of Oklahoma
Paul Spicer, University of Oklahoma
Rob Knight, University of Colorado-Boulder
Cecil M. Lewis, Jr., University of Oklahoma Norman CampusFollow

Document Type

Article

Date of this Version

12-2012

Citation

Tito RY, Knights D, Metcalf J, Obregon-Tito AJ, Cleeland L, et al. (2012) Insights from Characterizing Extinct Human Gut Microbiomes. PLoS ONE 7(12): e51146. doi:10.1371/journal.pone.0051146

Comments

Copyright 2012 Tito et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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 Otzi 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.