A genomics approach to improve the analysis and design of strain selections.

Journal Article (Journal Article)

Strain engineering has been traditionally centered on the use of mutation, selection, and screening to develop improved strains. Although mutational and screening methods are well-characterized, selection remains poorly understood. We hypothesized that we could use a genome-wide method for assessing laboratory selections to design selections with enhanced sensitivity (true positives) and specificity (true negatives) towards a single desired phenotype. To test this hypothesis, we first applied multi-SCale Analysis of Library Enrichments (SCALEs) to identify genes conferring increased fitness in continuous flow selections with increasing levels of 3-hydroxypropionic acid (3-HP). We found that this selection not only enriched for 3-HP tolerance phenotypes but also for wall adherence phenotypes (41% false positives). Using this genome-wide data, we designed a serial-batch selection with a decreasing 3-HP gradient. Further examination by ROC analysis confirmed that the serial-batch approach resulted in significantly increased sensitivity (46%) and specificity (10%) for our desired phenotype (3-HP tolerance).

Full Text

Duke Authors

Cited Authors

  • Warnecke, TE; Lynch, MD; Karimpour-Fard, A; Sandoval, N; Gill, RT

Published Date

  • May 2008

Published In

Volume / Issue

  • 10 / 3-4

Start / End Page

  • 154 - 165

PubMed ID

  • 18514004

Electronic International Standard Serial Number (EISSN)

  • 1096-7184

International Standard Serial Number (ISSN)

  • 1096-7176

Digital Object Identifier (DOI)

  • 10.1016/j.ymben.2008.04.004


  • eng