Molecular identification of bacteria by total sequence screening

Determining the cause of death in ancient human subjects

Catherine Thèves, Alice Senescau, Stefano Vanin, Christine Keyser, François Xavier Ricaut, Anatoly N. Alekseev, Henri Dabernat, Bertrand Ludes, Richard Fabre, Eric Crubézy

Research output: Contribution to journalArticle

14 Citations (Scopus)

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.

Original languageEnglish
Article numbere21733
JournalPLoS One
Volume6
Issue number7
DOIs
Publication statusPublished - 2011

Fingerprint

Pathogens
Cause of Death
Bacteria
Screening
Ribosomal DNA
death
screening
Burial
Tooth
pathogens
bacteria
Amplification
teeth
Genes
Bordetella
Shigella dysenteriae
Siberia
Bacterial DNA
Bordetella pertussis
Lung

Cite this

Thèves, C., Senescau, A., Vanin, S., Keyser, C., Ricaut, F. X., Alekseev, A. N., ... Crubézy, E. (2011). Molecular identification of bacteria by total sequence screening: Determining the cause of death in ancient human subjects. PLoS One, 6(7), [e21733]. https://doi.org/10.1371/journal.pone.0021733
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. In: PLoS One. 2011 ; Vol. 6, No. 7.
@article{7da24ca73b7b4c79b16fd19ef4d37977,
title = "Molecular identification of bacteria by total sequence screening: Determining the cause of death in ancient human subjects",
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.",
author = "Catherine Th{\`e}ves and Alice Senescau and Stefano Vanin and Christine Keyser and Ricaut, {Fran{\cc}ois Xavier} and Alekseev, {Anatoly N.} and Henri Dabernat and Bertrand Ludes and Richard Fabre and Eric Crub{\'e}zy",
year = "2011",
doi = "10.1371/journal.pone.0021733",
language = "English",
volume = "6",
journal = "PLoS One",
issn = "1932-6203",
publisher = "Public Library of Science",
number = "7",

}

Thèves, C, Senescau, A, Vanin, S, Keyser, C, Ricaut, FX, Alekseev, AN, Dabernat, H, Ludes, B, Fabre, R & Crubézy, E 2011, 'Molecular identification of bacteria by total sequence screening: Determining the cause of death in ancient human subjects', PLoS One, vol. 6, no. 7, e21733. https://doi.org/10.1371/journal.pone.0021733

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.

In: PLoS One, Vol. 6, No. 7, e21733, 2011.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Molecular identification of bacteria by total sequence screening

T2 - Determining the cause of death in ancient human subjects

AU - Thèves, Catherine

AU - Senescau, Alice

AU - Vanin, Stefano

AU - Keyser, Christine

AU - Ricaut, François Xavier

AU - Alekseev, Anatoly N.

AU - Dabernat, Henri

AU - Ludes, Bertrand

AU - Fabre, Richard

AU - Crubézy, Eric

PY - 2011

Y1 - 2011

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84855258227&partnerID=8YFLogxK

U2 - 10.1371/journal.pone.0021733

DO - 10.1371/journal.pone.0021733

M3 - Article

VL - 6

JO - PLoS One

JF - PLoS One

SN - 1932-6203

IS - 7

M1 - e21733

ER -