title: Reducing microbial and human contamination in DNA extractions from ancient bones and teeth.
abstract: Although great progress has been made in improving methods for generating DNA sequences from ancient biological samples, many, if not most, samples are still not amenable for analyses due to overwhelming contamination with microbial or modern human DNA. Here we explore different DNA decontamination procedures for ancient bones and teeth for use prior to DNA library preparation and high-throughput sequencing. Two procedures showed promising results: (i) the release of surface-bound DNA by phosphate buffer and (ii) the removal of DNA contamination by sodium hypochlorite treatment. Exposure to phosphate removes on average 64% of the microbial DNA from bone powder but only 37% of the endogenous DNA (from the organism under study), increasing the percentage of informative sequences by a factor of two on average. An average 4.6-fold increase, in one case reaching 24-fold, is achieved by sodium hypochlorite treatment, albeit at the expense of destroying 63% of the endogenous DNA preserved in the bone. While both pretreatment methods described here greatly reduce the cost of genome sequencing from ancient material due to efficient depletion of microbial DNA, we find that the removal of human DNA contamination remains a challenging problem.
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Petra
authors.initials: P
authors.lastname: Korlević
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Tobias
authors.initials: T
authors.lastname: Gerber
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Marie-Theres
authors.initials: MT
authors.lastname: Gansauge
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Mateja
authors.initials: M
authors.lastname: Hajdinjak
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Sarah
authors.initials: S
authors.lastname: Nagel
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Ayinuer
authors.initials: A
authors.lastname: Aximu-Petri
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Meyer
mesh_terms: D001419:Bacteria; D001842:Bone and Bones; D059018:DNA Contamination; D003666:Decontamination / Q000379:methods; D005580:Fossils; D015723:Gene Library; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D010161:Paleodontology / Q000379:methods; D014070:Tooth
keywords: DNA contamination removal; DNA extraction; ancient DNA; paleogenomics