Effect of DNA Extraction Methods on the Apparent Structure
of Yak Rumen Microbial Communities as Revealed by 16S rDNA Sequencing
Yabing Chen, Daoliang Lan, Cheng Tang, Xiaonong Yang , Jian Li Pol J Microbiol 2015; 64 (1): ICID: 1148772 Article type: Original article IC™ Value: 10.00
Abstract provided by Publisher
To better identify the microbial community of yak rumen, the standardization of DNA extraction is key to ensuring fidelity while studying environmental microbial communities. In this study, we systematically compared the efficiency of several extraction methods based on DNA yield, purity, and 16S rRNA high-throughput sequencing to gain optimal DNA extraction methods, whose DNA products can reflect complete bacterial communities by 16S rRNA sequencing technique. Results showed that method 6 (hexadyltrimethyl ammomum bromide–lysozyme–physical lysis by bead beating) is recommended for the DNA isolation of rumen microbial community because of its high yield, operational taxonomic unit, bacteria diversity, and excellent cell-breaking capability. Results also indicated that the bead-beating step is necessary to effectively break the cell walls of all microbes, especially for Gram-positive bacteria. Another aim of the work was to preliminarily analyze the bacterial community by 16S rRNA sequencing technique. The community spanned approximately 21 phyla, 35 classes, 75 families, and 112 genera. Comparative analysis showed some variations in microbial community between yaks and cattle, which may be attributed to diet and environmental differences. More intriguingly, numerous uncultured or unclassified bacteria were found in yak rumen, suggesting that further research is needed to determine their specific function and ecological roles in yak rumen. In summary, the investigation of optimal DNA extraction methods and preliminary evaluation of bacterial community composition of yak rumen provide evidence for further identifying the specificity of rumen microbial community in yak and discovering distinct gene resources.