Torres PJ, Kelley ST. Sampling, Extraction, and High-Throughput Sequencing Methods for Environmental Microbial and Viral Communities.
Methods Mol Biol 2017;
1712:163-173. [PMID:
29224074 DOI:
10.1007/978-1-4939-7514-3_11]
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Abstract
The emergence of high-throughput sequencing technologies has deepened our understanding of complex microbial communities and greatly facilitated the study of as-yet uncultured microbes and viruses. Studies of complex microbial communities require high-quality data to generate valid results. Here, we detail current methods of microbial and viral community sample acquisition, DNA extraction, sample preparation, and sequencing on Illumina high-throughput platforms. While using appropriate analytical tools is important, it must not overshadow the need for establishing a proper experimental design and obtaining sufficient numbers of samples for statistical purposes. Researchers must also take care to sample biologically relevant sites and control for potential confounding factors (e.g., contamination).
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