title: Analysis of Ancient DNA in Microbial Ecology.
abstract: The development of next-generation sequencing has led to a breakthrough in the analysis of ancient genomes, and the subsequent genomic analyses of the skeletal remains of ancient humans have revolutionized the knowledge of the evolution of our species, including the discovery of a new hominin, and demonstrated admixtures with more distantly related archaic populations such as Neandertals and Denisovans. Moreover, it has also yielded novel insights into the evolution of ancient pathogens. The analysis of ancient microbial genomes allows the study of their recent evolution, presently over the last several millennia. These spectacular results have been attained despite the degradation of DNA after the death of the host, which results in very short DNA molecules that become increasingly damaged, only low quantities of which remain. The low quantity of ancient DNA molecules renders their analysis difficult and prone to contamination with modern DNA molecules, in particular via contamination from the reagents used in DNA purification and downstream analysis steps. Finally, the rare ancient molecules are diluted in environmental DNA originating from the soil microorganisms that colonize bones and teeth. Thus, ancient skeletal remains can share DNA profiles with environmental samples and identifying ancient microbial genomes among the more recent, presently poorly characterized, environmental microbiome is particularly challenging. Here, we describe the methods developed and/or in use in our laboratory to produce reliable and reproducible paleogenomic results from ancient skeletal remains that can be used to identify the presence of ancient microbiota.
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France. gorge@ijm.univ-paris-diderot.fr.
authors.forename: Olivier
authors.initials: O
authors.lastname: Gorgé
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
authors.forename: E Andrew
authors.initials: EA
authors.lastname: Bennett
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
authors.forename: Diyendo
authors.initials: D
authors.lastname: Massilani
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
authors.forename: Julien
authors.initials: J
authors.lastname: Daligault
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
authors.forename: Melanie
authors.initials: M
authors.lastname: Pruvost
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
authors.forename: Eva-Maria
authors.initials: EM
authors.lastname: Geigl
authors.affiliation: Institut Jacques Monod, UMR 7592, CNRS, Université Paris Diderot, Batiment Buffon, 15 Rue Helene Brion, Paris, 75013, France.
authors.forename: Thierry
authors.initials: T
authors.lastname: Grange
mesh_terms: D000818:Animals; D004269:DNA, Bacterial / Q000235:genetics* / Q000302:isolation & purification; D005580:Fossils; D064349:Genome, Microbial / Q000235:genetics*; D023281:Genomics / Q000379:methods; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D010163:Paleontology / Q000379:methods*; D012988:Soil Microbiology
chemical_list: D004269:DNA, Bacterial
keywords: Ancient DNA; Contamination; Double-stranded library; Illumina; IonTorrent; NGS; Single-stranded library