A Knöppel

A Porse

C Munck

C Pál

C Ritz

CJ Gregg

E Toprak

EA Rettedal

G Giaever

HH Lee

J Barroso-Batista

JE Sulston

JM Andrews

JR Blundell

JT Pronk

K Kretzschmar

KM Wetmore

L Imamovic

LC Thomason

M Hegreness

M Imhof

M Jaffe

M Knopp

ME Buckingham

MJ Obersriebnig

MM Mwangi

R Lutz

S Cardinale

S Datta

S Hansen

S Meylan

SF Levy

SIJ Ellenbroek

T Oz

TJ Kawecki

U Deppe

V Lazar

W Szybalski

Scientific Reports

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

Jahn, Leonie Johanna

Porse, Andreas

Munck, Christian

Simon, Daniel

Volkova, Svetlana

Sommer, Morten Otto Alexander

Online Research Database In Technology

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

AbstractAdaptive 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.</jats:p

Leonie Johanna Jahn

Andreas Porse

Christian Munck

Daniel Simon

Svetlana Volkova

Morten Otto Alexander Sommer

Crossref

http://orbit.dtu.dk/ws/files/148213460/Chromosomal_barcoding_as_a.pdf

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

Abstract

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