Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

Authors

Raúl Y. Tito, University of Oklahoma,
Simone Macmil, University of Oklahoma,
Graham Wiley, University of Oklahoma,
Fares Najar, University of Oklahoma,
Lauren Cleeland, University of Oklahoma,
Chunmei Qu, University of Oklahoma,
Ping Wang, University of Oklahoma,
Frederic Romagne, University of Auvergne, France
Sylvain Leonard, University of Auvergne, France
Agustín Jiménez Ruiz, University of Nebraska State Museum,
Karl Reinhard, University of Nebaska, LincolnFollow
Bruce A. Roe, University of Oklahoma
Cecil M. Lewis, Jr., University of Oklahoma Norman CampusFollow

Date of this Version

11-11-2008

Comments

Published in PLoS ONE 3:11 (November 2008), e3703. Copyright 2008 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

Background: The Human Microbiome Project (HMP) is one of the U.S. National Institutes of Health Roadmap for Medical Research. Primary interests of the HMP include the distinctiveness of different gut microbiomes, the factors influencing microbiome diversity, and the functional redundancies of the members of human microbiotas. In this present work, we contribute to these interests by characterizing two extinct human microbiotas.

Methodology/Principal Findings: We examine two paleofecal samples originating from cave deposits in Durango Mexico and dating to approximately 1300 years ago. Contamination control is a serious issue in ancient DNA research; we use a novel approach to control contamination. After we determined that each sample originated from a different human, we generated 45 thousand shotgun DNA sequencing reads. The phylotyping and functional analysis of these reads reveals a signature consistent with the modern gut ecology. Interestingly, inter-individual variability for phenotypes but not functional pathways was observed. The two ancient samples have more similar functional profiles to each other than to a recently published profile for modern humans. This similarity could not be explained by a chance sampling of the databases.

Conclusions/Significance: We conduct a phylotyping and functional analysis of ancient human microbiomes, while providing novel methods to control for DNA contamination and novel hypotheses about past microbiome biogeography. We postulate that natural selection has more of an influence on microbiome functional profiles than it does on the species represented in the microbial ecology. We propose that human microbiomes were more geographically structured during pre-Columbian times than today.