Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization
Name
Anahtar-2016-Efficient Nucleic Ac.pdf
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859.39 KB
Format
Adobe PDF
Checksum (MD5)
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Author(s)
Anahtar, Melis N.
Bowman, Brittany A.
Kwon, Douglas
Date Issued
April 2016
Journal
Journal of Visualized Experiments
Publisher
MyJoVE Corporation
Citation
Anahtar, Melis N., Brittany A. Bowman, and Douglas S. Kwon. “Efficient Nucleic Acid Extraction and 16S rRNA Gene Sequencing for Bacterial Community Characterization.” JoVE no. 110 (April 14, 2016).
Version
Final published version
Abstract
There is a growing appreciation for the role of microbial communities as critical modulators of human health and disease. High throughput sequencing technologies have allowed for the rapid and efficient characterization of bacterial communities using 16S rRNA gene sequencing from a variety of sources. Although readily available tools for 16S rRNA sequence analysis have standardized computational workflows, sample processing for DNA extraction remains a continued source of variability across studies. Here we describe an efficient, robust, and cost effective method for extracting nucleic acid from swabs. We also delineate downstream methods for 16S rRNA gene sequencing, including generation of sequencing libraries, data quality control, and sequence analysis. The workflow can accommodate multiple samples types, including stool and swabs collected from a variety of anatomical locations and host species. Additionally, recovered DNA and RNA can be separated and used for other applications, including whole genome sequencing or RNA-seq. The method described allows for a common processing approach for multiple sample types and accommodates downstream analysis of genomic, metagenomic and transcriptional information.
MIT Department
Ragon Institute of MGH, MIT and Harvard
Koch Institute for Integrative Cancer Research at MIT
Terms of Use
Creative Commons Attribution-NonCommercial-NoDerivs License
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.3791/53939
