Chapter 16: Connecting Microbial Genotype with Phenotype in the Omics Era

Yongfu Yang, Mengyu Qiu, Qing Yang, Yu Wang, Hui Wei, Shihui Yang

Research output: Chapter in Book/Report/Conference proceedingChapterpeer-review


Although rational design-based metabolic engineering has been applied widely to obtain promising microbial biocatalysts, conventional strategies such as adaptive laboratory evolution (ALE) and mutagenesis are still efficient approaches to improve microorganisms for exceptional features such as a broad spectrum of substrate utilization, robustness of cell growth, as well as high titer, yield, and productivity of the target products. In this chapter, we describe the procedure to generate mutant strains with desired phenotypes using ALE and a new mutagenesis approach of Atmosphere and Room Temperature Plasma (ARTP). In addition, we discuss the methodology to combine next-generation sequencing (NGS)-based genome-resequencing and RNA-Seq transcriptomics approaches to characterize the mutant strains and connect the phenotypes with their corresponding genotypic changes.

Original languageAmerican English
Title of host publicationMethods in Molecular Biology
Subtitle of host publicationMethods in Molecular Biology, Volume 2096
EditorsM. E. Himmel, Y. J. Bomble
PublisherHumana Press Inc.
Number of pages17
StatePublished - 2020

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Bibliographical note

Publisher Copyright:
© Springer Science+Business Media, LLC, part of Springer Nature 2020.

NREL Publication Number

  • NREL/CH-2700-77591


  • Adaptive laboratory evolution (ALE)
  • Atmosphere and Room Temperature Plasma (ARTP) mutagenesis
  • CLC Genomics Workbench, JMP Genomics
  • Next-generation sequencing (NGS)
  • RNA-Seq


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