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Extraction of DNA from murine fecal pellets for downstream phylogenetic microbiota analysis by next-generation sequencing

Elien Eeckhout (UGent) and Andy Wullaert (UGent)
(2018) BIO-PROTOCOL. 8(3).
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Abstract
Mouse models are widely used to evaluate the potential impact of the gut microbial composition on health and disease. Standardized protocols for sampling and storing murine feces, as well as for extracting DNA from these fecal pellets are needed to limit experimental variation between different studies. Both efficient lysis of the microbiota and the quality of the obtained fecal DNA are important for allowing the downstream next-generation sequencing to cover the phylogenetic diversity of both Gram-negative and Gram-positive bacteria living in the mouse gut. Here we present a detailed protocol for fecal sample collection and DNA extraction that we validated in a study on the impact of inflammasomes on the murine gut microbiota. This protocol for DNA extraction from murine fecal pellets utilizes a combination of mechanical and chemical lysis, which aligns with the procedure that was recently recommended as a benchmark protocol for DNA extraction from human feces.
Keywords
Gut microbiota, Fecal DNA, Mouse feces, DNA extraction, 16S phylogenetic analysis, Next-generation sequencing

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Citation

Please use this url to cite or link to this publication:

Chicago
Eeckhout, Elien, and Andy Wullaert. 2018. “Extraction of DNA from Murine Fecal Pellets for Downstream Phylogenetic Microbiota Analysis by Next-generation Sequencing.” Bio-protocol 8 (3).
APA
Eeckhout, Elien, & Wullaert, A. (2018). Extraction of DNA from murine fecal pellets for downstream phylogenetic microbiota analysis by next-generation sequencing. BIO-PROTOCOL, 8(3).
Vancouver
1.
Eeckhout E, Wullaert A. Extraction of DNA from murine fecal pellets for downstream phylogenetic microbiota analysis by next-generation sequencing. BIO-PROTOCOL. 2018;8(3).
MLA
Eeckhout, Elien, and Andy Wullaert. “Extraction of DNA from Murine Fecal Pellets for Downstream Phylogenetic Microbiota Analysis by Next-generation Sequencing.” BIO-PROTOCOL 8.3 (2018): n. pag. Print.
@article{8550572,
  abstract     = {Mouse models are widely used to evaluate the potential impact of the gut microbial composition on health and disease. Standardized protocols for sampling and storing murine feces, as well as for extracting DNA from these fecal pellets are needed to limit experimental variation between different studies. Both efficient lysis of the microbiota and the quality of the obtained fecal DNA are important for allowing the downstream next-generation sequencing to cover the phylogenetic diversity of both Gram-negative and Gram-positive bacteria living in the mouse gut. Here we present a detailed protocol for fecal sample collection and DNA extraction that we validated in a study on the impact of inflammasomes on the murine gut microbiota. This protocol for DNA extraction from murine fecal pellets utilizes a combination of mechanical and chemical lysis, which aligns with the procedure that was recently recommended as a benchmark protocol for DNA extraction from human feces.},
  articleno    = {e2707},
  author       = {Eeckhout, Elien and Wullaert, Andy},
  issn         = {2331-8325},
  journal      = {BIO-PROTOCOL},
  keywords     = {Gut microbiota,Fecal DNA,Mouse feces,DNA extraction,16S phylogenetic analysis,Next-generation sequencing},
  language     = {eng},
  number       = {3},
  pages        = {6},
  title        = {Extraction of DNA from murine fecal pellets for downstream phylogenetic microbiota analysis by next-generation sequencing},
  url          = {http://dx.doi.org/10.21769/bioprotoc.2707},
  volume       = {8},
  year         = {2018},
}

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