Dental pulp as a source of low-contaminated DNA

• Published in: Microbial Pathogenesis
• Main Authors: Drancourt, Michel, Aboudharam, Gerard, Croce, Olivier, Armougom, Fabrice, Robert, Catherine, Raoult, Didier
• Other Authors: 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
• Language: English
• Published: HAL CCSD 2017
• Subjects: [SDV.MHEP.MI]Life Sciences [q-bio]/Human health and pathology/Infectious diseases; Canis lupus
• Online Access: https://hal.archives-ouvertes.fr/hal-01521247; https://doi.org/10.1016/j.micpath.2017.02.007

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.