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Updated: Jun 28, 2026
11:22
Microbiota Analysis Using Two-step PCR and Next-generation 16S rRNA Gene Sequencing
Published on: October 15, 2019
Phylotyping and functional analysis of two ancient human microbiomes.
Raúl Y Tito1, Simone Macmil, Graham Wiley
1Department of Anthropology, University of Oklahoma, Norman, OK, USA.
Plos One
|November 13, 2008
Summary
Ancient human gut microbiomes from Mexico reveal distinct functional profiles and suggest greater geographic structuring in pre-Columbian times compared to today. Novel methods controlled for DNA contamination in this study of extinct microbiotas.
Area of Science:
- Microbiology
- Paleogenomics
- Human Ecology
Background:
- The Human Microbiome Project (HMP) investigates gut microbiome distinctiveness, diversity factors, and functional redundancies.
- This study characterizes two extinct human microbiotas to contribute to HMP interests.
Purpose of the Study:
- To analyze ancient human microbiomes using phylotyping and functional analysis.
- To develop novel methods for controlling DNA contamination in ancient DNA research.
- To explore past microbiome biogeography and factors influencing its structure.
Main Methods:
- Analysis of two paleofecal samples from Durango, Mexico, dated to ~1300 years ago.
- Application of a novel contamination control approach for ancient DNA.
- Generation of 45,000 shotgun DNA sequencing reads for phylotyping and functional analysis.
Main Results:
- Ancient gut microbiotas showed signatures consistent with modern gut ecology.
- Inter-individual variability was observed in phenotypes but not functional pathways.
- Ancient samples exhibited more similar functional profiles to each other than to modern human profiles.
Conclusions:
- Natural selection may influence microbiome functional profiles more than species composition.
- Human microbiomes were likely more geographically structured in pre-Columbian times.
- Novel hypotheses regarding past microbiome biogeography were proposed.
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