10.5061/DRYAD.R0056
Der Sarkissian, Clio
University of Copenhagen
Ermini, Luca
University of Copenhagen
Jónsson, Hákon
University of Copenhagen
Alekseev, Anatoly N.
North-Eastern Federal University
Crubézy, Éric
Paul Sabatier University
Shapiro, Beth
University of Copenhagen
Orlando, Ludovic
University of Copenhagen
Data from: Shotgun microbial profiling of fossil remains
Dryad
dataset
2014
Metagenomics
2014-02-06T19:53:00Z
2014-02-06T19:53:00Z
en
https://doi.org/10.1111/mec.12690
1943596454 bytes
1
CC0 1.0 Universal (CC0 1.0) Public Domain Dedication
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.
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