Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages

Abstract Adaptive laboratory evolution is an important tool to evolve organisms to increased tolerance towards different physical and chemical stress. It is applied to study the evolution of antibiotic resistance as well as genetic mechanisms underlying improvements in production strains. Adaptive e...

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Autores principales:	Leonie Johanna Jahn, Andreas Porse, Christian Munck, Daniel Simon, Svetlana Volkova, Morten Otto Alexander Sommer
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2018
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6cace45641bd4f5ba04d935ec69d73e0
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spelling	oai:doaj.org-article:6cace45641bd4f5ba04d935ec69d73e02021-12-02T11:40:47ZChromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages10.1038/s41598-018-25201-52045-2322https://doaj.org/article/6cace45641bd4f5ba04d935ec69d73e02018-05-01T00:00:00Zhttps://doi.org/10.1038/s41598-018-25201-5https://doaj.org/toc/2045-2322Abstract Adaptive laboratory evolution is an important tool to evolve organisms to increased tolerance towards different physical and chemical stress. It is applied to study the evolution of antibiotic resistance as well as genetic mechanisms underlying improvements in production strains. Adaptive evolution experiments can be automated in a high-throughput fashion. However, the characterization of the resulting lineages can become a time consuming task, when the performance of each lineage is evaluated individually. Here, we present a novel method for the markerless insertion of randomized genetic barcodes into the genome of Escherichia coli using a novel dual-auxotrophic selection approach. The barcoded E. coli library allows multiplexed phenotyping of evolved strains in pooled competition experiments. We use the barcoded library in an adaptive evolution experiment; evolving resistance towards three common antibiotics. Comparing this multiplexed phenotyping with conventional susceptibility testing and growth-rate measurements we can show a significant positive correlation between the two approaches. Use of barcoded bacterial strain libraries for individual adaptive evolution experiments drastically reduces the workload of characterizing the resulting phenotypes and enables prioritization of lineages for in-depth characterization. In addition, barcoded clones open up new ways to profile community dynamics or to track lineages in vivo or situ.Leonie Johanna JahnAndreas PorseChristian MunckDaniel SimonSvetlana VolkovaMorten Otto Alexander SommerNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 8, Iss 1, Pp 1-12 (2018)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Leonie Johanna Jahn Andreas Porse Christian Munck Daniel Simon Svetlana Volkova Morten Otto Alexander Sommer Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
description	Abstract Adaptive laboratory evolution is an important tool to evolve organisms to increased tolerance towards different physical and chemical stress. It is applied to study the evolution of antibiotic resistance as well as genetic mechanisms underlying improvements in production strains. Adaptive evolution experiments can be automated in a high-throughput fashion. However, the characterization of the resulting lineages can become a time consuming task, when the performance of each lineage is evaluated individually. Here, we present a novel method for the markerless insertion of randomized genetic barcodes into the genome of Escherichia coli using a novel dual-auxotrophic selection approach. The barcoded E. coli library allows multiplexed phenotyping of evolved strains in pooled competition experiments. We use the barcoded library in an adaptive evolution experiment; evolving resistance towards three common antibiotics. Comparing this multiplexed phenotyping with conventional susceptibility testing and growth-rate measurements we can show a significant positive correlation between the two approaches. Use of barcoded bacterial strain libraries for individual adaptive evolution experiments drastically reduces the workload of characterizing the resulting phenotypes and enables prioritization of lineages for in-depth characterization. In addition, barcoded clones open up new ways to profile community dynamics or to track lineages in vivo or situ.
format	article
author	Leonie Johanna Jahn Andreas Porse Christian Munck Daniel Simon Svetlana Volkova Morten Otto Alexander Sommer
author_facet	Leonie Johanna Jahn Andreas Porse Christian Munck Daniel Simon Svetlana Volkova Morten Otto Alexander Sommer
author_sort	Leonie Johanna Jahn
title	Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
title_short	Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
title_full	Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
title_fullStr	Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
title_full_unstemmed	Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
title_sort	chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages
publisher	Nature Portfolio
publishDate	2018
url	https://doaj.org/article/6cace45641bd4f5ba04d935ec69d73e0
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_version_	1718395521206321152

Chromosomal barcoding as a tool for multiplexed phenotypic characterization of laboratory evolved lineages

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