Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.
International audience 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 difficu...
Published in: | PLoS ONE |
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Main Authors: | , , , , , , , , , |
Other Authors: | , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
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HAL CCSD
2011
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Online Access: | https://hal.archives-ouvertes.fr/hal-00967582 https://hal.archives-ouvertes.fr/hal-00967582/document https://hal.archives-ouvertes.fr/hal-00967582/file/2011_ThA_ves_et_al_PlosOne.pdf https://doi.org/10.1371/journal.pone.0021733 |
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English |
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[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology [SDE]Environmental Sciences |
spellingShingle |
[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology [SDE]Environmental Sciences Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François-Xavier Alekseev, Anatoly N Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
topic_facet |
[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology [SDE]Environmental Sciences |
description |
International audience 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. |
author2 |
Anthropologie Moléculaire et Imagerie de Synthèse (AMIS) Université Toulouse III - Paul Sabatier (UT3) Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS) Laboratoire Bio Pole Department of Chemical and Biological Sciences University of Huddersfield Laboratoire d'Anthropobiologie (LA) École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3) Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML) Université Louis Pasteur - Strasbourg I laboratoire d'archéologie Université de Yakutsk |
format |
Article in Journal/Newspaper |
author |
Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François-Xavier Alekseev, Anatoly N Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric |
author_facet |
Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François-Xavier Alekseev, Anatoly N Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric |
author_sort |
Thèves, Catherine |
title |
Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
title_short |
Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
title_full |
Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
title_fullStr |
Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
title_full_unstemmed |
Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
title_sort |
molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
publisher |
HAL CCSD |
publishDate |
2011 |
url |
https://hal.archives-ouvertes.fr/hal-00967582 https://hal.archives-ouvertes.fr/hal-00967582/document https://hal.archives-ouvertes.fr/hal-00967582/file/2011_ThA_ves_et_al_PlosOne.pdf https://doi.org/10.1371/journal.pone.0021733 |
genre |
permafrost Siberia |
genre_facet |
permafrost Siberia |
op_source |
ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.archives-ouvertes.fr/hal-00967582 PLoS ONE, Public Library of Science, 2011, 6 (7), pp.e21733. ⟨10.1371/journal.pone.0021733⟩ |
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info:eu-repo/semantics/OpenAccess |
op_doi |
https://doi.org/10.1371/journal.pone.0021733 |
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PLoS ONE |
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ftccsdartic:oai:HAL:hal-00967582v1 2023-05-15T17:58:07+02:00 Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François-Xavier Alekseev, Anatoly N Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric Anthropologie Moléculaire et Imagerie de Synthèse (AMIS) Université Toulouse III - Paul Sabatier (UT3) Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS) Laboratoire Bio Pole Department of Chemical and Biological Sciences University of Huddersfield Laboratoire d'Anthropobiologie (LA) École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J)-Université Toulouse III - Paul Sabatier (UT3) Laboratoire d'Anthropologie Moléculaire, Institut de Médecine Légale, Strasbourg, France (IML) Université Louis Pasteur - Strasbourg I laboratoire d'archéologie Université de Yakutsk 2011-07-01 https://hal.archives-ouvertes.fr/hal-00967582 https://hal.archives-ouvertes.fr/hal-00967582/document https://hal.archives-ouvertes.fr/hal-00967582/file/2011_ThA_ves_et_al_PlosOne.pdf https://doi.org/10.1371/journal.pone.0021733 en eng HAL CCSD Public Library of Science info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0021733 info:eu-repo/semantics/altIdentifier/pmid/21765907 hal-00967582 https://hal.archives-ouvertes.fr/hal-00967582 https://hal.archives-ouvertes.fr/hal-00967582/document https://hal.archives-ouvertes.fr/hal-00967582/file/2011_ThA_ves_et_al_PlosOne.pdf doi:10.1371/journal.pone.0021733 PUBMED: 21765907 info:eu-repo/semantics/OpenAccess ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.archives-ouvertes.fr/hal-00967582 PLoS ONE, Public Library of Science, 2011, 6 (7), pp.e21733. ⟨10.1371/journal.pone.0021733⟩ [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology [SDE]Environmental Sciences info:eu-repo/semantics/article Journal articles 2011 ftccsdartic https://doi.org/10.1371/journal.pone.0021733 2021-01-24T00:12:56Z International audience 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. Article in Journal/Newspaper permafrost Siberia Archive ouverte HAL (Hyper Article en Ligne, CCSD - Centre pour la Communication Scientifique Directe) PLoS ONE 6 7 e21733 |