Data from: Shotgun microbial profiling of fossil remains
Data files
Feb 06, 2014 version files 1.94 GB
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Ancient_Horse_Metagenomics_RScript.txt
7.41 KB
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BaARE_metaphlan.txt
8.55 KB
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BaARE.Equus_cab_mito.bam
22.96 KB
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BaARE.Equus_cab_nucl.bam
24.94 MB
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BaARE.Homo_sapiens_nucl.bam
852.50 KB
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BaB_metaphlan.txt
7.66 KB
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BaB.Equus_cab_mito.bam
4.38 KB
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BaB.Equus_cab_nucl.bam
4.11 MB
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BaB.Homo_sapiens_nucl.bam
280.52 KB
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BaBRE_metaphlan.txt
13.05 KB
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BaBRE.Equus_cab_mito.bam
11.46 KB
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BaBRE.Equus_cab_nucl.bam
19.89 MB
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BaBRE.Homo_sapiens_nucl.bam
732.68 KB
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OS_metaphlan.txt
8.68 KB
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OS.Equus_cab_mito.bam
3.58 KB
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OS.Equus_cab_nucl.bam
1.90 MB
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OS.Homo_sapiens_nucl.bam
101.01 KB
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OSRE_metaphlan.txt
9.22 KB
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OSRE.Equus_cab_mito.bam
6.55 KB
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OSRE.Equus_cab_nucl.bam
3.12 MB
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OSRE.Homo_sapiens_nucl.bam
368.08 KB
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plots_horses_MapDamage.tar
2.60 MB
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plots_microbes_MapDamage.tar
870.40 KB
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Ta_metaphlan.txt
10.12 KB
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Ta.Equus_cab_mito.bam
1.60 KB
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Ta.Equus_cab_nucl.bam
4.11 MB
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Ta.Homo_sapiens_nucl.bam
203.13 KB
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TaRE_metaphlan.txt
7.30 KB
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TaRE.Equus_cab_mito.bam
15.01 KB
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TaRE.Equus_cab_nucl.bam
16.66 MB
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TaRE.Homo_sapiens_nucl.bam
646.34 KB
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TP1_metaphlan.txt
2.08 KB
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TP1RE_metaphlan.txt
6.33 KB
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TP2_metaphlan.txt
1.87 KB
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TP3_metaphlan.txt
12.06 KB
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TP3.Equus_cab_mito.bam
78.77 KB
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TP3.Equus_cab_nucl.bam
476.02 MB
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TP3.Homo_sapiens_nucl.bam
5.70 MB
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TP3RE_metaphlan.txt
10.24 KB
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TP3RE.Equus_cab_mito.bam
88.33 KB
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TP3RE.Equus_cab_nucl.bam
686.76 MB
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TP3RE.Homo_sapiens_nucl.bam
10.32 MB
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Tu.Equus_cab_mito.bam
27.28 KB
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Tu.Equus_cab_nucl.bam
87.45 MB
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Tu.Homo_sapiens_nucl.bam
2.09 MB
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TuRE_metaphlan.txt
3.88 KB
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TuRE.Equus_cab_mito.bam
116.44 KB
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TuRE.Equus_cab_nucl.bam
547.64 MB
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TuRE.Homo_sapiens_nucl.bam
10.25 MB
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Ty_metaphlan.txt
7.43 KB
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Ty.Equus_cab_mito.bam
2.20 KB
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Ty.Equus_cab_nucl.bam
7.40 MB
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Ty.Homo_sapiens_nucl.bam
848.37 KB
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TyRE_metaphlan.txt
7.68 KB
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TyRE.Equus_cab_mito.bam
12.64 KB
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TyRE.Equus_cab_nucl.bam
23.41 MB
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TyRE.Homo_sapiens_nucl.bam
2.61 MB
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Ya_metaphlan.txt
5.90 KB
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Ya.Equus_cab_mito.bam
3.21 KB
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Ya.Homo_sapiens_nucl.bam
253.43 KB
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YaRE_metaphlan.txt
7.67 KB
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YaRE.Equus_cab_mito.bam
49.96 KB
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YaRE.Homo_sapiens_nucl.bam
873.28 KB
Abstract
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.