Dental pulp as a source of low-contaminated DNA
International audience The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this w...
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Online Access: | https://hal.archives-ouvertes.fr/hal-01521247 https://doi.org/10.1016/j.micpath.2017.02.007 |
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ftunivtoulon:oai:HAL:hal-01521247v1 2023-05-15T15:50:39+02:00 Dental pulp as a source of low-contaminated DNA Drancourt, Michel Aboudharam, Gerard Croce, Olivier Armougom, Fabrice Robert, Catherine Raoult, Didier Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48 Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut méditerranéen d'océanologie (MIO) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) 2017-04 https://hal.archives-ouvertes.fr/hal-01521247 https://doi.org/10.1016/j.micpath.2017.02.007 en eng HAL CCSD Elsevier info:eu-repo/semantics/altIdentifier/doi/10.1016/j.micpath.2017.02.007 hal-01521247 https://hal.archives-ouvertes.fr/hal-01521247 doi:10.1016/j.micpath.2017.02.007 ISSN: 0882-4010 EISSN: 1096-1208 Microbial Pathogenesis https://hal.archives-ouvertes.fr/hal-01521247 Microbial Pathogenesis, Elsevier, 2017, 105, pp.63-67. ⟨10.1016/j.micpath.2017.02.007⟩ [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases info:eu-repo/semantics/article Journal articles 2017 ftunivtoulon https://doi.org/10.1016/j.micpath.2017.02.007 2022-09-27T22:33:59Z International audience The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing. This yielded a total of 487,828 trimmed reads with a length of 227 +/- 35 bp. Sequence analysis of the final dataset using Blast algorithm search and stringent thresholds for sequence identity and coverage against a database including both Canis lupus familiaris and Homo sapiens complete genomes showed that 95% of reads were assigned to C familiaris whereas 0.03% was assigned to H. sapiens. In a second step, two teeth collected from two 12th century mammals were manipulated following the same protocol. A total of 13,890 trimmed reads with a 157 +/- 67 bp length yielded 0-0.35% reads assigned to H. sapiens. This study indicates that the dental pulp is a useful for detecting the significant nucleic sequences in both modern and ancient samples. (C) 2017 Elsevier Ltd. All rights reserved. Article in Journal/Newspaper Canis lupus Université de Toulon: HAL Microbial Pathogenesis 105 63 67 |
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Open Polar |
collection |
Université de Toulon: HAL |
op_collection_id |
ftunivtoulon |
language |
English |
topic |
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases |
spellingShingle |
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases Drancourt, Michel Aboudharam, Gerard Croce, Olivier Armougom, Fabrice Robert, Catherine Raoult, Didier Dental pulp as a source of low-contaminated DNA |
topic_facet |
[SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases |
description |
International audience The in-laboratory contamination of the ancient samples hinders the result interpretation of the investigations in the field of paleomicrobiology. We had promoted the dental pulp as a sample that limits the risks of in-laboratory contamination of the ancient material. In this work, we measured the contamination of the dental pulp manipulated according to paleomicrobiology protocol, used as a source of a total DNA for metagenomics. First, total DNA extracted from two dog canines was sequenced using next generation sequencing. This yielded a total of 487,828 trimmed reads with a length of 227 +/- 35 bp. Sequence analysis of the final dataset using Blast algorithm search and stringent thresholds for sequence identity and coverage against a database including both Canis lupus familiaris and Homo sapiens complete genomes showed that 95% of reads were assigned to C familiaris whereas 0.03% was assigned to H. sapiens. In a second step, two teeth collected from two 12th century mammals were manipulated following the same protocol. A total of 13,890 trimmed reads with a 157 +/- 67 bp length yielded 0-0.35% reads assigned to H. sapiens. This study indicates that the dental pulp is a useful for detecting the significant nucleic sequences in both modern and ancient samples. (C) 2017 Elsevier Ltd. All rights reserved. |
author2 |
Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes (URMITE) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut National de la Santé et de la Recherche Médicale (INSERM)-IFR48 Institut des sciences biologiques (INSB-CNRS)-Institut des sciences biologiques (INSB-CNRS)-Centre National de la Recherche Scientifique (CNRS) Institut méditerranéen d'océanologie (MIO) Institut de Recherche pour le Développement (IRD)-Aix Marseille Université (AMU)-Institut national des sciences de l'Univers (INSU - CNRS)-Université de Toulon (UTLN)-Centre National de la Recherche Scientifique (CNRS) |
format |
Article in Journal/Newspaper |
author |
Drancourt, Michel Aboudharam, Gerard Croce, Olivier Armougom, Fabrice Robert, Catherine Raoult, Didier |
author_facet |
Drancourt, Michel Aboudharam, Gerard Croce, Olivier Armougom, Fabrice Robert, Catherine Raoult, Didier |
author_sort |
Drancourt, Michel |
title |
Dental pulp as a source of low-contaminated DNA |
title_short |
Dental pulp as a source of low-contaminated DNA |
title_full |
Dental pulp as a source of low-contaminated DNA |
title_fullStr |
Dental pulp as a source of low-contaminated DNA |
title_full_unstemmed |
Dental pulp as a source of low-contaminated DNA |
title_sort |
dental pulp as a source of low-contaminated dna |
publisher |
HAL CCSD |
publishDate |
2017 |
url |
https://hal.archives-ouvertes.fr/hal-01521247 https://doi.org/10.1016/j.micpath.2017.02.007 |
genre |
Canis lupus |
genre_facet |
Canis lupus |
op_source |
ISSN: 0882-4010 EISSN: 1096-1208 Microbial Pathogenesis https://hal.archives-ouvertes.fr/hal-01521247 Microbial Pathogenesis, Elsevier, 2017, 105, pp.63-67. ⟨10.1016/j.micpath.2017.02.007⟩ |
op_relation |
info:eu-repo/semantics/altIdentifier/doi/10.1016/j.micpath.2017.02.007 hal-01521247 https://hal.archives-ouvertes.fr/hal-01521247 doi:10.1016/j.micpath.2017.02.007 |
op_doi |
https://doi.org/10.1016/j.micpath.2017.02.007 |
container_title |
Microbial Pathogenesis |
container_volume |
105 |
container_start_page |
63 |
op_container_end_page |
67 |
_version_ |
1766385639211663360 |