Dental pulp as a source of low-contaminated DNA. (April 2017)

• Record Type: Journal Article
• Authors: Drancourt, Michel; Aboudharam, Gérard; Croce, Olivier; Armougom, Fabrice; Robert, Catherine; Raoult, Didier
• Is Part Of: Microbial pathogenesis. Volume 105(2017)
• Page Start: 63
• Page End: 67
• Publication Date: 2017-04
• Subjects: Dental pulp -- Contamination -- Metagenomics -- Forensic sciences -- Paleomicrobiology -- Paleogenetics; Pathogenic microorganisms -- Periodicals; Pathology, Molecular -- Periodicals; Communicable Diseases -- microbiology -- Periodicals; Communicable Diseases -- parasitology -- Periodicals; Micro-organismes pathogènes -- Périodiques; Pathologie moléculaire -- Périodiques; Electronic journals; 616.9041
• DOI: 10.1016/j.micpath.2017.02.007
• Languages: English
• ISSNs: 0882-4010

Abstract

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. Highlights: The dental pulp is almost free of in-laboratory contamination by modern DNA. Applying good laboratory practice to the dental pulp experiments limits the in-lab contamination of the samples. The dental pulp is a useful sample for detection of the significant nucleic sequences in both modern and ancient samples.