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Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding

Sujal Phadke¹, Andreia Filipa Salvador², Joana Isabel Alves²

¹J. Craig Venter Institute, 4120 Capricorn Lane, La Jolla, CA, 92037, USA.

Methods in Molecular Biology (Clifton, N.J.)

|May 26, 2017

Abstract:

Polymerase chain reaction (PCR) is central to methods in molecular ecology. Here, we describe PCR-dependent approaches useful for investigating microbial diversity and its function in various natural, human-associated, and built environment ecosystems. Protocols routinely used for DNA extraction, purification, cloning, and sequencing are included along with various resources for the statistical analysis following gel electrophoresis-based methods (DGGE) and sequencing. We also provide insights into eukaryotic microbiome analysis, sample preservation techniques, PCR troubleshooting, DNA quantification methods, and commonly used ordination techniques.

Keywords:

Canonical correspondence analysis (CCA)Denaturing gradient gel electrophoresis (DGGE)Microbiome Next generation sequencing (NGS)Polymerase chain reaction (PCR)Restriction fragment length polymorphism (T-RFLP)

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