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Prescreening of Microbial Populations for the Assessment of Sequencing Potential

  • Irene B. HanningEmail author
  • Steven C. Ricke
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 733)

Abstract

Next-generation sequencing (NGS) is a powerful tool that can be utilized to profile and compare microbial populations. By amplifying a target gene present in all bacteria and subsequently sequencing amplicons, the bacteria genera present in the populations can be identified and compared. In some scenarios, little to no difference may exist among microbial populations being compared in which case a prescreening method would be practical to determine which microbial populations would be suitable for further analysis by NGS. Denaturing density-gradient electrophoresis (DGGE) is relatively cheaper than NGS and the data comparing microbial populations are ready to be viewed immediately after electrophoresis. DGGE follows essentially the same initial methodology as NGS by targeting and amplifying the 16S rRNA gene. However, as opposed to sequencing amplicons, DGGE amplicons are analyzed by electrophoresis. By prescreening microbial populations with DGGE, more efficient use of NGS methods can be accomplished. In this chapter, we outline the protocol for DGGE targeting the same gene (16S rRNA) that would be targeted for NGS to compare and determine differences in microbial populations from a wide range of ecosystems.

Key words

DGGE Microbial Populations Screening 16S rRNA Comparison 

Notes

Acknowledgments

This book chapter was funded by an Institute of Food Science and Engineering grant through the University of Arkansas.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  1. 1.Department of Food Science and TechnologyUniversity of TennesseeKnoxvilleUSA

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