DOI: 10.5061/dryad.r0056
title: Data from: Shotgun microbial profiling of fossil remains

description: Millions to billions of DNA sequences can now be generated from ancient
 skeletal remains thanks to the massive throughput of next-generation
 sequencing platforms. Except in cases of exceptional endogenous DNA
 preservation, most of the sequences isolated from fossil material do not
 originate from the specimen of interest, but instead reflect environmental
 organisms that colonized the specimen after death. Here, we characterize
 the microbial diversity recovered from seven ca. 200-13,000 year old horse
 bones collected from northern Siberia. We use a robust, taxonomy-based
 assignment approach to identify the microorganisms present in ancient DNA
 extracts and quantify their relative abundances. Our results suggest that
 molecular preservation niches exist within ancient samples that can
 potentially be used to characterize the environments from which the
 remains are recovered. In addition, microbial community profiling of the
 seven specimens revealed site-specific environmental signatures. These
 microbial communities appear to comprise mainly organisms that colonized
 the fossils recently. Our approach significantly extends the amount of
 useful data that can be recovered from ancient specimens using a shotgun
 sequencing approach. In future, it may be possible to correlate, for
 example, the accumulation of post-mortem DNA damage with the presence
 and/or abundance of particular microbes.
description: BaARE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample BaARE.BaB.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample BaB.BaBRE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample BaBRE.OS.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample OS.OSRE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample OSRE.Ta.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample Ta.TaRE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample TaRE.TP3.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample TP3.TP3RE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample TP3RE.Tu.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample Tu.TuRE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample TuRE.Ty.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample Ty.TyRE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample TyRE.Ya.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample Ya.YaRE.Equus_cab_mitoAlignment to the Equus caballus mitochondrial reference genome for sample YaRE.BaARE.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample BaARE.BaB.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample BaB.BaBRE.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample BaBRE.OS.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample OS.OSRE.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample OSRE.Ta.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample Ta.TaRE.Equus_cab_nuclTP3.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample TP3.TP3RE.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample TP3RE.Tu.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample Tu.TuRE.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample TuRE.Ty.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample Ty.TyRE.Equus_cab_nuclAlignment to the Equus caballus nuclear reference genome for sample TyRE.BaARE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaARE.BaB.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaB.BaBRE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaBRE.OS.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample OS.OSRE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample OSRE.Ta.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ta.TaRE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TaRE.TP3.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TP3.TP3RE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TP3RE.Tu.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Tu.TuRE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TuRE.Ty.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ty.TyRE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TyRE.Ya.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ya.YaRE.Homo_sapiens_nuclAlignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample YaRE.BaARE_metaphlanMetaPhlAn microbial profile for sample BaARE.BaB_metaphlanMetaPhlAn microbial profile for sample BaB.BaBRE_metaphlanMetaPhlAn microbial profile for sample BaBRE.OS_metaphlanMetaPhlAn microbial profile for sample OS.OSRE_metaphlanMetaPhlAn microbial profile for sample OSRE.Ta_metaphlanMetaPhlAn microbial profile for sample Ta.TaRE_metaphlanMetaPhlAn microbial profile for sample TaRE.TP1_metaphlanMetaPhlAn microbial profile for sample TP1.TP1RE_metaphlanMetaPhlAn microbial profile for sample TP1RE.TP2_metaphlanMetaPhlAn microbial profile for sample TP2.TP3_metaphlanMetaPhlAn microbial profile for sample TP3.TP3RE_metaphlanMetaPhlAn microbial profile for sample TP3RE.TuRE_metaphlanMetaPhlAn microbial profile for sample TuRE.Ty_metaphlanMetaPhlAn microbial profile for sample Ty.TyRE_metaphlanMetaPhlAn microbial profile for sample TyRE.Ya_metaphlanMetaPhlAn microbial profile for sample Ya.YaRE_metaphlanMetaPhlAn microbial profile for sample YaRE.Ancient_Horse_Metagenomics_RScriptR script for analysing microbial profiles generated by MetaPhlAn.plots_horses_MapDamagemap Damage profile of endogenous DNAplots_microbes_MapDamageMap Damage profile of bacteria