Toward Best Practice in Livestock Microbiota Research: A Comprehensive Comparison of Sample Storage and DNA Extraction Strategies
| Autor: | Nikolaus Grabner, Mahdi Ghanbari, Viviana Klose, Gertrude Wegl, Andreas Köstelbauer |
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| Jazyk: | angličtina |
| Rok vydání: | 2021 |
| Předmět: |
Microbiology (medical)
Standardization Best practice lcsh:QR1-502 Sample (statistics) Biology Gut flora Microbiology lcsh:Microbiology 03 medical and health sciences sample storage Sample Type DNA extraction 030304 developmental biology Original Research next generation sequencing 0303 health sciences 030306 microbiology business.industry livestock microbiota biology.organism_classification Biotechnology Livestock Extraction methods 16S rRNA gene business |
| Zdroj: | Frontiers in Microbiology Frontiers in Microbiology, Vol 12 (2021) |
| ISSN: | 1664-302X |
| Popis: | Understanding the roles of microorganisms in the animal gastrointestinal microenvironment is highly important for the development of effective strategies to manage and manipulate these microbial communities. In order to guide future animal gut microbiota research projects and standardization efforts, we have conducted a systematic comparison of 10 currently used sample preservation and DNA extraction approaches for pig and chicken microbiota samples and quantified their effects on bacterial DNA yield, quality, integrity, and on the resulting sequence-based bacterial composition estimates. The results showed how key stages of conducting a microbiota study, including the sample storage and DNA extraction, can substantially affect DNA recovery from the microbial community, and therefore, biological interpretation in a matrix-dependent manner. Our results highlight the fact that the influence of storage and extraction methods on the resulting microbial community structure differed by sample type, even within the same species. As the effects of these technical steps are potentially large compared with the real biological variability to be explained, standardization is crucial for accelerating progress in the area of livestock microbiota research. This study provided a framework to assist future animal gut microbiota research projects and standardization efforts. |
| Databáze: | OpenAIRE |
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