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_mito
Alignment to the Equus caballus mitochondrial reference genome for sample BaARE.
BaB.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample BaB.
BaBRE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample BaBRE.
OS.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample OS.
OSRE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample OSRE.
Ta.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample Ta.
TaRE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample TaRE.
TP3.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample TP3.
TP3RE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample TP3RE.
Tu.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample Tu.
TuRE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample TuRE.
Ty.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample Ty.
TyRE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample TyRE.
Ya.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample Ya.
YaRE.Equus_cab_mito
Alignment to the Equus caballus mitochondrial reference genome for sample YaRE.
BaARE.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample BaARE.
BaB.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample BaB.
BaBRE.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample BaBRE.
OS.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample OS.
OSRE.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample OSRE.
Ta.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample Ta.
TP3.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample TP3.
TP3RE.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample TP3RE.
Tu.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample Tu.
TuRE.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample TuRE.
Ty.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample Ty.
TyRE.Equus_cab_nucl
Alignment to the Equus caballus nuclear reference genome for sample TyRE.
BaARE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaARE.
BaB.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaB.
BaBRE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample BaBRE.
OS.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample OS.
OSRE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample OSRE.
Ta.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ta.
TaRE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TaRE.
TP3.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TP3.
TP3RE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TP3RE.
Tu.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Tu.
TuRE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TuRE.
Ty.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ty.
TyRE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample TyRE.
Ya.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample Ya.
YaRE.Homo_sapiens_nucl
Alignment to the Homo sapiens nuclear and mitochondrial reference genomes for sample YaRE.
BaARE_metaphlan
MetaPhlAn microbial profile for sample BaARE.
BaB_metaphlan
MetaPhlAn microbial profile for sample BaB.
BaBRE_metaphlan
MetaPhlAn microbial profile for sample BaBRE.
OS_metaphlan
MetaPhlAn microbial profile for sample OS.
OSRE_metaphlan
MetaPhlAn microbial profile for sample OSRE.
Ta_metaphlan
MetaPhlAn microbial profile for sample Ta.
TaRE_metaphlan
MetaPhlAn microbial profile for sample TaRE.
TP1_metaphlan
MetaPhlAn microbial profile for sample TP1.
TP1RE_metaphlan
MetaPhlAn microbial profile for sample TP1RE.
TP2_metaphlan
MetaPhlAn microbial profile for sample TP2.
TP3_metaphlan
MetaPhlAn microbial profile for sample TP3.
TP3RE_metaphlan
MetaPhlAn microbial profile for sample TP3RE.
TuRE_metaphlan
MetaPhlAn microbial profile for sample TuRE.
Ty_metaphlan
MetaPhlAn microbial profile for sample Ty.
TyRE_metaphlan
MetaPhlAn microbial profile for sample TyRE.
Ya_metaphlan
MetaPhlAn microbial profile for sample Ya.
YaRE_metaphlan
MetaPhlAn microbial profile for sample YaRE.
Ancient_Horse_Metagenomics_RScript
R script for analysing microbial profiles generated by MetaPhlAn.
plots_horses_MapDamage
map Damage profile of endogenous DNA
plots_microbes_MapDamage
Map Damage profile of bacteria