Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community

Lu, Yang, Hugenholtz, Phillip and Batstone, Damien John (2015) Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community. PLoS One, 10 11: e0142720.1-e0142720.10. doi:10.1371/journal.pone.0142720


Author Lu, Yang
Hugenholtz, Phillip
Batstone, Damien John
Title Evaluating DNA Extraction Methods for Community Profiling of Pig Hindgut Microbial Community
Journal name PLoS One   Check publisher's open access policy
ISSN 1932-6203
Publication date 2015-11-11
Year available 2015
Sub-type Article (original research)
DOI 10.1371/journal.pone.0142720
Open Access Status DOI
Volume 10
Issue 11
Start page e0142720.1
End page e0142720.10
Total pages 10
Place of publication San Francisco, CA United States
Publisher Public Library of Science
Collection year 2016
Language eng
Formatted abstract
Recovery of high quality PCR-amplifiable DNA has been the general minimal requirement for DNA extraction methods for bulk molecular analysis. However, modern high through-put community profiling technologies are more sensitive to representativeness and reproducibility of DNA extraction method. Here, we assess the impact of three DNA extraction methods (with different levels of extraction harshness) for assessing hindgut microbiomes from pigs fed with different diets (with different physical properties). DNA extraction from each sample was performed in three technical replicates for each extraction method and sequenced by 16S rRNA amplicon sequencing. Host was the primary driver of molecular sequencing outcomes, particularly on samples analysed by wheat based diets, but higher variability, with one failed extraction occurred on samples from a barley fed pig. Based on these results, an effective method will enable reproducible and quality outcomes on a range of samples, whereas an ineffective method will fail to generate extract, but host (rather than extraction method) remains the primary factor.
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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Created: Fri, 20 Nov 2015, 13:01:46 EST by Mrs Louise Nimwegen on behalf of School of Chemistry & Molecular Biosciences