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Author |
Der Sarkissian C, Ermini L, Jónsson H, Alekseev A N, Crubezy E, Shapiro B, Orlando L, |
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Title |
Shotgun microbial profiling of fossil remains
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Journal Article |
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Year |
2014 |
Publication |
Molecular Ecology |
Abbreviated Journal  |
Mol. Ecol. |
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Volume |
23 |
Issue |
7 |
Pages |
1780-1798 |
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Keywords |
ancient DNA, metagenomics, microbial profiling, next-generation sequencing, |
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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 c. 200- to 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 abundance. 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 postmortem DNA damage with the presence and/or abundance of particular microbes.
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1038 |
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1365-294X |
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yes |
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4901 |
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Author |
Wynen L.P., Goldsworthy S.D., Guinet C., Bester M.N., Boyd I.L., Gjertz I., Hofmeyr G.J.G., White R.W.G. & Slade R. |
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Title |
Postsealing genetic variation and population structure of two species of fur seal(Arctocephalus gazella and A. tropicalis). |
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Journal Article |
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Year |
2000 |
Publication |
Molecular biology |
Abbreviated Journal |
Mol. Biol. (N.Y.) |
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Volume |
9 |
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299-314 |
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109 |
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0026-8933 |
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1011 |
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Barnes P.R.F., Wolff E.W., Mallard D.C. & Mader H.M. |
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Title |
SEM studies of the morphology and chemistry of polar ice. |
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Journal Article |
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Year |
2003 |
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Microscopy research and technique |
Abbreviated Journal |
Microsc. Res. Tech. |
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62 |
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1 |
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62-69 |
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960 |
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1059-910X |
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2429 |
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Author |
Dominé F., Lauzier T., Cabanes A., Egagneux L., Kuhs W.F., Techmer K. & Heinrichs T. |
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Title |
Snow metamorphism as revealed by scanning electron microscopy. |
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Journal Article |
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Year |
2003 |
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Microscopy research and technique |
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Microsc. Res. Tech. |
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62 |
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33-48 |
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437 |
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1059-910X |
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yes |
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2746 |
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Author |
Delille D., Basseres A. & Dessommes A. |
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Title |
Seasonal Variation of Bacteria in Sea Ice Contaminated by Diesel Fuel and Dispersed Crude Oil. |
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Journal Article |
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Year |
1997 |
Publication |
Microbial ecology |
Abbreviated Journal |
Microb. Ecol. |
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33 |
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97-105 |
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193 |
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0095-3628 |
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yes |
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Serial |
360 |
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Author |
Delille D. & Siron R. |
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Title |
Effect of Dispersed Oil Heterotrophic Bacterial Communities in Cold Marine Waters. |
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Journal Article |
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Year |
1993 |
Publication |
Microbial ecology |
Abbreviated Journal |
Microb. Ecol. |
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Volume |
25 |
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263-273 |
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193 |
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0095-3628 |
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yes |
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424 |
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Author |
Delille D. |
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Title |
Response of Antarctic soil bacteria assemblages to contamination by diesel fuel and crude oil. |
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Journal Article |
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Year |
2000 |
Publication |
Microbial ecology |
Abbreviated Journal |
Microb. Ecol. |
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40 |
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159-168 |
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193 |
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0095-3628 |
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967 |
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Author |
Delille D., Delille B. & Pelletier E. |
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Title |
Effectiveness of bioremediation of crude oil contaminated subAntarctic intertidal sediment: the bacterial response. |
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Journal Article |
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Year |
2002 |
Publication |
Microbial ecology |
Abbreviated Journal |
Microb. Ecol. |
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Volume |
14 |
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118-126 |
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193 |
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yes |
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2365 |
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Author |
Delille D., Coulon F. & Pelletier E. |
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Title |
Biostimulation of natural microbial assemblages in oil-amended vegetated and desert sub-Antarctic soils. |
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Journal Article |
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Year |
2004 |
Publication |
Microbial ecology |
Abbreviated Journal |
Microb. Ecol. |
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Volume |
47 |
Issue |
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Pages |
407-415 |
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193 |
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0095-3628 |
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yes |
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2911 |
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Author |
Engrand C. & Maurette M. |
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Title |
Carbonaceous micrometeorites from Antarctica. |
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Journal Article |
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Year |
1998 |
Publication |
Meteoritics & planetary science |
Abbreviated Journal |
Meteorit Planet Sci |
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33 |
Issue |
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565-580 |
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226 |
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1086-9379 |
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yes |
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286 |
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