title: Phylotyping and functional analysis of two ancient human microbiomes.
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.
  
  
  RESULTS
  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
  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.
authors.affiliation: Department of Anthropology, University of Oklahoma, Norman, OK, USA.
authors.forename: Raúl Y
authors.initials: RY
authors.lastname: Tito
authors.forename: Simone
authors.initials: S
authors.lastname: Macmil
authors.forename: Graham
authors.initials: G
authors.lastname: Wiley
authors.forename: Fares
authors.initials: F
authors.lastname: Najar
authors.forename: Lauren
authors.initials: L
authors.lastname: Cleeland
authors.forename: Chunmei
authors.initials: C
authors.lastname: Qu
authors.forename: Ping
authors.initials: P
authors.lastname: Wang
authors.forename: Frederic
authors.initials: F
authors.lastname: Romagne
authors.forename: Sylvain
authors.initials: S
authors.lastname: Leonard
authors.forename: Agustín Jiménez
authors.initials: AJ
authors.lastname: Ruiz
authors.forename: Karl
authors.initials: K
authors.lastname: Reinhard
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Roe
authors.forename: Cecil M
authors.initials: CM
authors.lastname: Lewis
mesh_terms: D001419:Bacteria / Q000145:classification / Q000302:isolation & purification; D004269:DNA, Bacterial / Q000032:analysis; D019143:Evolution, Molecular; D041981:Gastrointestinal Tract / Q000382:microbiology*; D016680:Genome, Bacterial; D005843:Geography; D006801:Humans; D054892:Metagenome / Q000235:genetics*; D008800:Mexico; D010802:Phylogeny
chemical_list: D004269:DNA, Bacterial