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PCR pp 225-248 | Cite as

Harnessing the Power of PCR Molecular Fingerprinting Methods and Next Generation Sequencing for Understanding Structure and Function in Microbial Communities

  • Sujal Phadke
  • Andreia Filipa Salvador
  • Joana Isabel Alves
  • Orianna Bretschger
  • Maria Madalena Alves
  • Maria Alcina PereiraEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1620)

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.

Key words

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

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Copyright information

© Springer Science+Business Media LLC 2017

Authors and Affiliations

  • Sujal Phadke
    • 1
  • Andreia Filipa Salvador
    • 2
  • Joana Isabel Alves
    • 2
  • Orianna Bretschger
    • 1
  • Maria Madalena Alves
    • 2
  • Maria Alcina Pereira
    • 2
    Email author
  1. 1.J. Craig Venter InstituteLa JollaUSA
  2. 2.CEB–Centre of Biological EngineeringUniversity of MinhoBragaPortugal

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