title: Dental pulp as a source of low-contaminated DNA.
abstract: 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.
authors.affiliation: Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
authors.forename: Michel
authors.initials: M
authors.lastname: Drancourt
authors.affiliation: Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
authors.forename: Gérard
authors.initials: G
authors.lastname: Aboudharam
authors.affiliation: Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
authors.forename: Olivier
authors.initials: O
authors.lastname: Croce
authors.affiliation: Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
authors.forename: Fabrice
authors.initials: F
authors.lastname: Armougom
authors.affiliation: Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France.
authors.forename: Catherine
authors.initials: C
authors.lastname: Robert
authors.affiliation: Aix Marseille Université, IHU Méditerranée Infection, URMITE, UM 63, UMR_S 1095, UMR 7278, France. Electronic address: didier.raoult@gmail.com.
authors.forename: Didier
authors.initials: D
authors.lastname: Raoult
mesh_terms: D000818:Animals; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification*; D003782:Dental Pulp / Q000737:chemistry*; D004285:Dogs; D005580:Fossils; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008967:Molecular Biology / Q000379:methods*; D010163:Paleontology / Q000379:methods*; D017422:Sequence Analysis, DNA
chemical_list: D004247:DNA
keywords: Contamination; Dental pulp; Forensic sciences; Metagenomics; Paleogenetics; Paleomicrobiology