Phylotyping and Functional Analysis of Two Ancient Human Microbiomes

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dc.contributor.authorRaúl Y. Titoen_US
dc.contributor.authorSimone Macmilen_US
dc.contributor.authorGraham Wileyen_US
dc.contributor.authorFares Najaren_US
dc.contributor.authorLauren Cleelanden_US
dc.contributor.authorChunmei Quen_US
dc.contributor.authorPing Wangen_US
dc.contributor.authorFrederic Romagneen_US
dc.contributor.authorSylvain Leonarden_US
dc.contributor.authorAgustín Jiménez Ruizen_US
dc.contributor.authorKarl Reinharden_US
dc.contributor.authorBruce A. Roeen_US
dc.contributor.authorCecil M. Lewis Jr.en_US
dc.date.accessioned2015-01-23T17:17:28Z
dc.date.accessioned2016-03-30T15:35:49Z
dc.date.available2015-01-23T17:17:28Z
dc.date.available2016-03-30T15:35:49Z
dc.date.issued2008-11-11en_US
dc.descriptionWe appreciate comments received by anonymous reviewers at earlier stages of this study.en_US
dc.descriptionConceived and designed the experiments: RT SM GW FZN BAR CMLJ. Performed the experiments: RT SM GW LC CQ PW CMLJ. Analyzed the data: RT FZN SL FR CMLJ. Contributed reagents/materials/analysis tools: FAJ KR BAR CMLJ. Wrote the paper: RT CMLJ.en_US
dc.description.abstractBackgroundThe 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 FindingsWe 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/SignificanceWe 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.en_US
dc.description.peerreviewYesen_US
dc.description.peerreviewnoteshttp://www.plosone.org/static/editorial#peeren_US
dc.identifier.citationTito RY, Macmil S, Wiley G, Najar F, Cleeland L, et al. (2008) Phylotyping and Functional Analysis of Two Ancient Human Microbiomes. PLoS ONE 3(11): e3703. doi:10.1371/journal.pone.0003703en_US
dc.identifier.doi10.1371/journal.pone.0003703en_US
dc.identifier.urihttp://hdl.handle.net/11244/14060
dc.language.isoen_USen_US
dc.publisherPLos Oneen_US
dc.relation.ispartofseriesPLoS ONE 3(11):e3703en_US
dc.relation.urihttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0003703en_US
dc.rightsAttribution 3.0 United Statesen_US
dc.rights.requestablefalseen_US
dc.rights.urihttp://creativecommons.org/licenses/by/3.0/us/en_US
dc.subjectPLOSen_US
dc.subjectPublic Library of Scienceen_US
dc.subjectOpen Accessen_US
dc.subjectOpen-Accessen_US
dc.subjectScienceen_US
dc.subjectMedicineen_US
dc.subjectBiologyen_US
dc.subjectResearchen_US
dc.subjectPeer-reviewen_US
dc.subjectInclusiveen_US
dc.subjectInterdisciplinaryen_US
dc.subjectAnte-disciplinaryen_US
dc.subjectPhysicsen_US
dc.subjectChemistryen_US
dc.subjectEngineeringen_US
dc.titlePhylotyping and Functional Analysis of Two Ancient Human Microbiomesen_US
dc.typeResearch Articleen_US

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