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Paleomicrobiology Data: Authentification and Interpretation

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  • Author: Michel Drancourt1
  • Editors: Michel Drancourt2, Didier Raoult3
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    Affiliations: 1: Aix-Marseille Université, URMITE (Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes), UMR CNRS 7278, IRD 198, Inserm 1095, Institut Hospitalier Universitaire Méditerranée Infection, Marseille, France; 2: Aix Marseille Université Faculté de Médecine, Marseille, France; 3: Aix Marseille Université Faculté de Médecine, Marseille, France
  • Source: microbiolspec June 2016 vol. 4 no. 3 doi:10.1128/microbiolspec.PoH-0017-2015
  • Received 15 December 2015 Accepted 14 January 2016 Published 03 June 2016
  • Michel Drancourt, michel.drancourt@univ-amu.fr
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  • Abstract:

    The authenticity of some of the very first works in the field of paleopathology has been questioned, and standards have been progressively established for the experiments and the interpretation of data. Whereas most problems initially arose from the contamination of ancient specimens with modern human DNA, the situation is different in the field of paleomicrobiology, in which the risk for contamination is well-known and adequately managed by any laboratory team with expertise in the routine diagnosis of modern-day infections. Indeed, the exploration of ancient microbiota and pathogens is best done by such laboratory teams, with research directed toward the discovery and implementation of new techniques and the interpretation of data.

  • Citation: Drancourt M. 2016. Paleomicrobiology Data: Authentification and Interpretation. Microbiol Spectrum 4(3):PoH-0017-2015. doi:10.1128/microbiolspec.PoH-0017-2015.

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References

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32. Rasmussen S, Allentoft ME, Nielsen K, Orlando L, Sikora M, Sjögren KG, Pedersen AG, Schubert M, Van Dam A, Kapel CM, Nielsen HB, Brunak S, Avetisyan P, Epimakhov A, Khalyapin MV, Gnuni A, Kriiska A, Lasak I, Metspalu M, Moiseyev V, Gromov A, Pokutta D, Saag L, Varul L, Yepiskoposyan L, Sicheritz-Pontén T, Foley RA, Lahr MM, Nielsen R, Kristiansen K, Willerslev E. 2015. Early divergent strains of Yersinia pestis in Eurasia 5,000 years ago. Cell 163:571–582. [PubMed][CrossRef]
33. Willerslev E, Cooper A. 2005. Ancient DNA. Proc Biol Sci 272:3–16. [PubMed][CrossRef]
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2016-06-03
2017-09-20

Abstract:

The authenticity of some of the very first works in the field of paleopathology has been questioned, and standards have been progressively established for the experiments and the interpretation of data. Whereas most problems initially arose from the contamination of ancient specimens with modern human DNA, the situation is different in the field of paleomicrobiology, in which the risk for contamination is well-known and adequately managed by any laboratory team with expertise in the routine diagnosis of modern-day infections. Indeed, the exploration of ancient microbiota and pathogens is best done by such laboratory teams, with research directed toward the discovery and implementation of new techniques and the interpretation of data.

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Figures

Image of FIGURE 1
FIGURE 1

Sources and prevention of contamination of ancient specimens by microbes and microbial products in the common example of buried specimens. Red bars indicate a pathogen present in the specimen at the time of death; blue and green circles indicate environmental microbes naturally contaminating the specimen during taphonomic processes; blue stars and yellow triangles indicate microbial contamination from discoverers of the specimen and fomites.

Source: microbiolspec June 2016 vol. 4 no. 3 doi:10.1128/microbiolspec.PoH-0017-2015
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Image of FIGURE 2
FIGURE 2

Distribution of read length after throughput pyrosequencing of DNA extracted from a 14th century coprolite (blue curve) and from 1720 plague dental pulp specimens (red curve).

Source: microbiolspec June 2016 vol. 4 no. 3 doi:10.1128/microbiolspec.PoH-0017-2015
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Tables

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TABLE 1

A list of criteria for the authentication of microbes in ancient specimens appears below

Source: microbiolspec June 2016 vol. 4 no. 3 doi:10.1128/microbiolspec.PoH-0017-2015

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