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Molecular Identification of Bacteria by Total Sequence Screening: Determining the Cause of Death in Ancient Human Subjects

Adler, Ben, Thèves, Catherine, Senescau, Alice, Vanin, Stefano, Keyser, Christine, Ricaut, François Xavier, Alekseev, Anatoly N., Dabernat, Henri, Ludes, Bertrand, Fabre, Richard and Crubézy, Eric (2011) Molecular Identification of Bacteria by Total Sequence Screening: Determining the Cause of Death in Ancient Human Subjects. PLoS ONE, 6 (7). e21733. ISSN 1932-6203

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    Abstract

    Research of ancient pathogens in ancient human skeletons has been mainly carried out on the basis of one essential historical or archaeological observation, permitting specific pathogens to be targeted. Detection of ancient human pathogens without such evidence is more difficult, since the quantity and quality of ancient DNA, as well as the environmental bacteria potentially present in the sample, limit the analyses possible. Using human lung tissue and/or teeth samples from burials in eastern Siberia, dating from the end of 17th to the 19th century, we propose a methodology that includes the: 1) amplification of all 16S rDNA gene sequences present in each sample; 2) identification of all bacterial DNA sequences with a degree of identity $95%, according to quality criteria; 3) identification and confirmation of bacterial pathogens by the amplification of the rpoB gene; and 4) establishment of authenticity criteria for ancient DNA. This study demonstrates that from teeth samples originating from ancient human subjects, we can realise: 1) the correct identification of bacterial molecular sequence signatures by quality criteria; 2) the separation of environmental and pathogenic bacterial 16S rDNA sequences; 3) the distribution of bacterial species for each subject and for each burial; and 4) the characterisation of bacteria specific to the permafrost. Moreover, we identified three pathogens in different teeth samples by 16S rDNA sequence amplification: Bordetella sp., Streptococcus pneumoniae and Shigella dysenteriae. We tested for the presence of these pathogens by amplifying the rpoB gene. For the first time, we confirmed sequences from Bordetella pertussis in the lungs of an ancient male Siberian subject, whose grave dated from the end of the 17th century to the early 18th century.

    Item Type: Article
    Subjects: G Geography. Anthropology. Recreation > GE Environmental Sciences
    Q Science > QL Zoology
    R Medicine > RA Public aspects of medicine > RA1001 Forensic Medicine. Medical jurisprudence. Legal medicine
    Schools: School of Applied Sciences
    School of Applied Sciences > Forensic Biology Research Group
    Related URLs:
    Depositing User: Sara Taylor
    Date Deposited: 06 Oct 2011 13:24
    Last Modified: 05 Jul 2013 15:39
    URI: http://eprints.hud.ac.uk/id/eprint/11615

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