Improved extraction of PCR-quality community DNA from digesta and fecal samples.
By Zhongtang Yu, M. Morrison. BioTechniques, 2004
1,566 citations recorded by the source corpus.
Several DNA extraction methods have been reported for use with digesta or fecal samples, but problems are often encountered in terms of relatively low DNA yields and/or recovering DNA free of inhibitory substances. Here we report a modified method to extract PCR-quality microbial community DNA from these types of samples, which employs bead beating in the presence of high concentrations of sodium dodecyl sulfate (SDS), salt, and EDTA, and with subsequent DNA purification by QIAamp columns [referred to as repeated bead beating plus column (RBB + C) method]. The RBB + C method resulted in a 1.5- to 6-fold increase in DNA yield when compared to three other widely used methods. The community DNA prepared with the RBB + C method was also free of inhibitory substances and resulted in improved denaturing gradient gel electrophoresis (DGGE) profiles, which is indicative of a more complete lysis and representation of microbial diversity present in such samples.
Subfields: Ecology, Water Science and Technology
View Paper: https://www.semanticscholar.org/paper/8de41f1907d69011b2aa94ab03ff64e81407a72c
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Citations in the corpus
- Effect of coconut oil and garlic powder on in vitro fermentation using gas production technique (2010, methodology): “The final portion was stored at −20 °C for DNA extraction (Yu and Morrison, 2004).”
- Gene-centric metagenomics of the fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases (2009, methodology): “Samples were then partitioned into FA fractions and liquid fractions before DNA extraction (14, 51).”
- Composition, Diversity, and Origin of the Bacterial Community in Grass Carp Intestine (2012, background): “Prior to sequencing, the DNA concentration of each PCR product was determined using a Quant-iT PicoGreen doublestranded DNA assay (Invitrogen, Germany) and was quality controlled on an Agilent 2100 bioanalyzer (Agilent, USA).”
- Effects of dietary Saccharomyces cerevisiae fermentation product (DVAQUA®) on growth performance, intestinal autochthonous bacterial community and non-specific immunity of hybrid tilapia (Oreochromis niloticus ♀×O. aureus ♂) cultured in cages (2009, methodology): “The total genomic DNAwas extracted using the bead mill method (Yu and Morrison, 2005; Zhou et al., 2007b).”