Chapter title |
Analysis of Ancient DNA in Microbial Ecology.
|
---|---|
Chapter number | 17 |
Book title |
Microbial Environmental Genomics (MEG)
|
Published in |
Methods in molecular biology, January 2016
|
DOI | 10.1007/978-1-4939-3369-3_17 |
Pubmed ID | |
Book ISBNs |
978-1-4939-3367-9, 978-1-4939-3369-3
|
Authors |
Gorgé, Olivier, Bennett, E Andrew, Massilani, Diyendo, Daligault, Julien, Pruvost, Melanie, Geigl, Eva-Maria, Grange, Thierry, Olivier Gorgé, E. Andrew Bennett, Diyendo Massilani, Julien Daligault, Melanie Pruvost, Eva-Maria Geigl, Thierry Grange |
Editors |
Francis Martin, Stephane Uroz |
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. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
Japan | 1 | 20% |
Unknown | 4 | 80% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 4 | 80% |
Scientists | 1 | 20% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Unknown | 24 | 100% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Student > Doctoral Student | 5 | 21% |
Student > Ph. D. Student | 4 | 17% |
Student > Bachelor | 3 | 13% |
Student > Master | 3 | 13% |
Researcher | 2 | 8% |
Other | 3 | 13% |
Unknown | 4 | 17% |
Readers by discipline | Count | As % |
---|---|---|
Agricultural and Biological Sciences | 7 | 29% |
Biochemistry, Genetics and Molecular Biology | 4 | 17% |
Arts and Humanities | 2 | 8% |
Immunology and Microbiology | 2 | 8% |
Nursing and Health Professions | 1 | 4% |
Other | 1 | 4% |
Unknown | 7 | 29% |