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  Comparison of extraction methods for recovering ancient microbial DNA from paleofeces

Hagan, R., Hofman, C. A., Hübner, A., Reinhard, K., Schnorr, S., Lewis Jr, C. M., et al. (2020). Comparison of extraction methods for recovering ancient microbial DNA from paleofeces. American Journal of Physical Anthropology, 171(2): ajpa.23978, pp. 275-284. doi:10.1002/ajpa.23978.

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 Urheber:
Hagan, Richard1, Autor           
Hofman, Courtney A., Autor
Hübner, Alexander1, Autor           
Reinhard, Karl, Autor
Schnorr, Stephanie, Autor
Lewis Jr, Cecil M., Autor
Sankaranarayanan, Krithivasan, Autor
Warinner, Christina G.1, Autor           
Affiliations:
1Archaeogenetics, Max Planck Institute for the Science of Human History, Max Planck Society, ou_2074310              

Inhalt

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Schlagwörter: ancient DNA, coprolite, gut microbiome, paleogenomics
 Zusammenfassung: Objectives
Paleofeces are valuable to archeologists and evolutionary biologists for their potential to yield health, dietary, and host information. As a rich source of preserved biomolecules from host-associated microorganisms, they can also provide insights into the recent evolution and changing ecology of the gut microbiome. However, there is currently no standard method for DNA extraction from paleofeces, which combine the dual challenges of complex biological composition and degraded DNA. Due to the scarcity and relatively poor preservation of paleofeces when compared with other archeological remains, it is important to use efficient methods that maximize ancient DNA (aDNA) recovery while also minimizing downstream taxonomic biases.

Methods
In this study, we use shotgun metagenomics to systematically compare the performance of five DNA extraction methods on a set of well-preserved human and dog paleofeces from Mexico (~1,300 BP).

Results
Our results show that all tested DNA extraction methods yield a consistent microbial taxonomic profile, but that methods optimized for ancient samples recover significantly more DNA.

Conclusions
These results show promise for future studies that seek to explore the evolution of the human gut microbiome by comparing aDNA data with those generated in modern studies.

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Sprache(n): eng - English
 Datum: 2019-08-132019-11-092019-11-302020-02
 Publikationsstatus: Erschienen
 Seiten: 10
 Ort, Verlag, Ausgabe: -
 Inhaltsverzeichnis: 1 Introduction
2 Material and methods
2.1 Samples and study design
2.2 DNA extraction
2.2.1 Extraction Method A: Human Microbiome Project protocol with PowerSoil kit
2.2.2 Extraction Method B: Modified MinElute protocol
2.2.3 Extraction Method C: Phenol-chloroform + modified MinElute protocol
2.2.4 Extraction Method D: Split modified MinElute protocol
2.2.5 Extraction Method E: HMP protocol + modified MinElute protocol
2.3 Library construction and sequencing
2.4 Data analysis
2.4.1 Data filtering and quality control
2.4.2 Assessment of method impact on DNA yield
2.4.3 Microbial community profiling
2.4.4 Assessment of paleofeces microbial preservation
2.4.5 Host determination of paleofeces
3 Results and discussion
3.1 DNA recovery by extraction method
3.2 Effect of DNA extraction protocol on microbial community reconstruction
3.3 Gut microbiome preservation
3.4 Host confirmation of paleofeces
4 Conclusions
 Art der Begutachtung: Expertenbegutachtung
 Identifikatoren: DOI: 10.1002/ajpa.23978
Anderer: shh2475
 Art des Abschluß: -

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Titel: American Journal of Physical Anthropology
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: New York, NY : Wiley-Liss, Inc.
Seiten: - Band / Heft: 171 (2) Artikelnummer: ajpa.23978 Start- / Endseite: 275 - 284 Identifikator: ISSN: 0002-9483
CoNE: https://pure.mpg.de/cone/journals/resource/954926960915