Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

Datos Bibliográficos

ID8317881
AutoresRichard W Hagan (Max Planck Institute for the Science of Human History Jena Germany), Richard Hagan (0000-0003-1270-100X, Max Planck Institute for the Science of Human History), Courtney A Hofman (0000-0002-6808-3370, Laboratories of Molecular Anthropology and Microbiome Research University of Oklahoma Norman Oklahoma), Austin Hubner (0000-0003-3572-9996, Max Planck Institute for the Science of Human History), Alexander Hübner (0000-0002-1358-1284, Max Planck Institute for the Science of Human History Jena Germany), K Reinhard (0000-0003-1653-9329, University of Nebraska–Lincoln), Stephanie L Schnorr (0000-0002-3742-0565, University of Nevada, Las Vegas), Stephanie Schnorr (Laboratories of Molecular Anthropology and Microbiome Research University of Oklahoma Norman Oklahoma), Cecil M Lewis (0000-0002-2198-3427, Laboratories of Molecular Anthropology and Microbiome Research University of Oklahoma Norman Oklahoma), Krithivasan Sankaranarayanan (0000-0002-4767-311X, Laboratories of Molecular Anthropology and Microbiome Research University of Oklahoma Norman Oklahoma), Christina Warinner (0000-0002-4528-5877, Max Planck Institute for the Science of Human History Jena Germany, autor de correspondencia)
Año2020
Volumen171
Número2
Páginas275-284
Fecha de publicación2020-02-01
Peer ReviewedSí
Open AccessSí
TipoARTICLE
RevistaAmerican Journal of Physical Anthropology (JOURNAL)
Identificadores de la revistaISSN: 0002-9483 • E-ISSN: 1096-8644
EditorialWiley (PUBLISHER • GB)
DOI10.1002/ajpa.23978
PMID31785113
OpenAlexW2989992929
IdiomaEN
Citas recibidas7
Referencias citadas30

OBJECTIVES: Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases. METHODS: In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP). RESULTS: Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA. CONCLUSIONS: These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies

Ancient DNA · Bioinformatics · Biology · Computational biology · DNA · DNA extraction · Evolutionary biology · Gene · Gut microbiome · Human microbiome · Human Microbiome Project · Metagenomics · Microbiome · Polymerase chain reaction · Population · Shotgun · Archaeology and ancient environmental studies · Ecology · Forensic and Genetic Research · Genetics · Gut microbiota and health