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 |
---|---|
Main Authors: | , , , , , , , , , , |
Other Authors: | , , , , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
HAL CCSD
2011
|
Subjects: | |
Online Access: | https://hal.science/hal-02112810 https://doi.org/10.1371/journal.pone.0021733 |
id |
ftunivtoulouse2:oai:HAL:hal-02112810v1 |
---|---|
record_format |
openpolar |
spelling |
ftunivtoulouse2:oai:HAL:hal-02112810v1 2024-04-21T08:10:21+00:00 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 Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric Adler, Ben Anthropologie Moléculaire et Imagerie de Synthèse (AMIS) Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) Laboratoire Bio Pole Department of Chemical and Biological Sciences University of Huddersfield Centre National de la Recherche Scientifique (CNRS) Laboratoire d'Anthropobiologie (LA) École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J) Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) Institut de Médecine Légale - IML (Paris, France) Monash University Clayton 2011-07-13 https://hal.science/hal-02112810 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-02112810 https://hal.science/hal-02112810 doi:10.1371/journal.pone.0021733 PUBMED: 21765907 PUBMEDCENTRAL: PMC3135582 ISSN: 1932-6203 EISSN: 1932-6203 PLoS ONE https://hal.science/hal-02112810 PLoS ONE, 2011, 6 (7), pp.e21733. ⟨10.1371/journal.pone.0021733⟩ [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology info:eu-repo/semantics/article Journal articles 2011 ftunivtoulouse2 https://doi.org/10.1371/journal.pone.0021733 2024-03-25T18:14:52Z 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 17(th) to the 19(th) 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 17(th) century to the early 18(th) century. Article in Journal/Newspaper permafrost Siberia Université Toulouse 2 - Jean Jaurès: HAL PLoS ONE 6 7 e21733 |
institution |
Open Polar |
collection |
Université Toulouse 2 - Jean Jaurès: HAL |
op_collection_id |
ftunivtoulouse2 |
language |
English |
topic |
[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology |
spellingShingle |
[SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François Xavier Alekseev, Anatoly Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric Adler, Ben 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 |
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 17(th) to the 19(th) 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 17(th) century to the early 18(th) century. |
author2 |
Anthropologie Moléculaire et Imagerie de Synthèse (AMIS) Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) Laboratoire Bio Pole Department of Chemical and Biological Sciences University of Huddersfield Centre National de la Recherche Scientifique (CNRS) Laboratoire d'Anthropobiologie (LA) École des hautes études en sciences sociales (EHESS)-Université Toulouse - Jean Jaurès (UT2J) Université de Toulouse (UT)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3) Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) Institut de Médecine Légale - IML (Paris, France) Monash University Clayton |
format |
Article in Journal/Newspaper |
author |
Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François Xavier Alekseev, Anatoly Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric Adler, Ben |
author_facet |
Thèves, Catherine Senescau, Alice Vanin, Stefano Keyser, Christine Ricaut, François Xavier Alekseev, Anatoly Dabernat, Henri Ludes, Bertrand Fabre, Richard Crubézy, Eric Adler, Ben |
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.science/hal-02112810 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.science/hal-02112810 PLoS ONE, 2011, 6 (7), pp.e21733. ⟨10.1371/journal.pone.0021733⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1371/journal.pone.0021733 info:eu-repo/semantics/altIdentifier/pmid/21765907 hal-02112810 https://hal.science/hal-02112810 doi:10.1371/journal.pone.0021733 PUBMED: 21765907 PUBMEDCENTRAL: PMC3135582 |
op_doi |
https://doi.org/10.1371/journal.pone.0021733 |
container_title |
PLoS ONE |
container_volume |
6 |
container_issue |
7 |
container_start_page |
e21733 |
_version_ |
1796951779136503808 |