Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects.
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...
Published in: | PLoS ONE |
---|---|
Main Authors: | , , , , , , , , , |
Format: | Article in Journal/Newspaper |
Language: | English |
Published: |
Public Library of Science (PLoS)
2011
|
Subjects: | |
Online Access: | https://doi.org/10.1371/journal.pone.0021733 https://doaj.org/article/48c9563553d14427a803b0fc43497dd5 |
id |
ftdoajarticles:oai:doaj.org/article:48c9563553d14427a803b0fc43497dd5 |
---|---|
record_format |
openpolar |
spelling |
ftdoajarticles:oai:doaj.org/article:48c9563553d14427a803b0fc43497dd5 2023-05-15T17:58:08+02:00 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 2011-01-01T00:00:00Z https://doi.org/10.1371/journal.pone.0021733 https://doaj.org/article/48c9563553d14427a803b0fc43497dd5 EN eng Public Library of Science (PLoS) https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21765907/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0021733 https://doaj.org/article/48c9563553d14427a803b0fc43497dd5 PLoS ONE, Vol 6, Iss 7, p e21733 (2011) Medicine R Science Q article 2011 ftdoajarticles https://doi.org/10.1371/journal.pone.0021733 2022-12-31T09:00:12Z 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 Directory of Open Access Journals: DOAJ Articles PLoS ONE 6 7 e21733 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
Medicine R Science Q |
spellingShingle |
Medicine R Science Q Catherine Thèves Alice Senescau Stefano Vanin Christine Keyser François Xavier Ricaut Anatoly N Alekseev Henri Dabernat Bertrand Ludes Richard Fabre Eric Crubézy Molecular identification of bacteria by total sequence screening: determining the cause of death in ancient human subjects. |
topic_facet |
Medicine R Science Q |
description |
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. |
format |
Article in Journal/Newspaper |
author |
Catherine Thèves Alice Senescau Stefano Vanin Christine Keyser François Xavier Ricaut Anatoly N Alekseev Henri Dabernat Bertrand Ludes Richard Fabre Eric Crubézy |
author_facet |
Catherine Thèves Alice Senescau Stefano Vanin Christine Keyser François Xavier Ricaut Anatoly N Alekseev Henri Dabernat Bertrand Ludes Richard Fabre Eric Crubézy |
author_sort |
Catherine Thèves |
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 |
Public Library of Science (PLoS) |
publishDate |
2011 |
url |
https://doi.org/10.1371/journal.pone.0021733 https://doaj.org/article/48c9563553d14427a803b0fc43497dd5 |
genre |
permafrost Siberia |
genre_facet |
permafrost Siberia |
op_source |
PLoS ONE, Vol 6, Iss 7, p e21733 (2011) |
op_relation |
https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21765907/?tool=EBI https://doaj.org/toc/1932-6203 1932-6203 doi:10.1371/journal.pone.0021733 https://doaj.org/article/48c9563553d14427a803b0fc43497dd5 |
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_ |
1766166675667812352 |