Lineage tracking for probing heritable phenotypes at single-cell resolution
Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes-via growth-over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology.
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dig-wur-nl-wurpubs-5063542024-09-23 Cottinet, Denis Condamine, Florence Bremond, Nicolas Griffiths, Andrew D. Rainey, Paul B. de Visser, Arjan Baudry, Jean Bibette, Jérôme Article/Letter to editor PLoS ONE 11 (2016) 4 ISSN: 1932-6203 Lineage tracking for probing heritable phenotypes at single-cell resolution 2016 Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes-via growth-over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology. en application/pdf https://research.wur.nl/en/publications/lineage-tracking-for-probing-heritable-phenotypes-at-single-cell- 10.1371/journal.pone.0152395 https://edepot.wur.nl/387283 Life Science https://creativecommons.org/licenses/by/4.0/ Wageningen University & Research |
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Life Science Life Science Cottinet, Denis Condamine, Florence Bremond, Nicolas Griffiths, Andrew D. Rainey, Paul B. de Visser, Arjan Baudry, Jean Bibette, Jérôme Lineage tracking for probing heritable phenotypes at single-cell resolution |
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Determining the phenotype and genotype of single cells is central to understand microbial evolution. DNA sequencing technologies allow the detection of mutants at high resolution, but similar approaches for phenotypic analyses are still lacking. We show that a drop-based millifluidic system enables the detection of heritable phenotypic changes in evolving bacterial populations. At time intervals, cells were sampled and individually compartmentalized in 100 nL drops. Growth through 15 generations was monitored using a fluorescent protein reporter. Amplification of heritable changes-via growth-over multiple generations yields phenotypically distinct clusters reflecting variation relevant for evolution. To demonstrate the utility of this approach, we follow the evolution of Escherichia coli populations during 30 days of starvation. Phenotypic diversity was observed to rapidly increase upon starvation with the emergence of heritable phenotypes. Mutations corresponding to each phenotypic class were identified by DNA sequencing. This scalable lineage-tracking technology opens the door to large-scale phenotyping methods with special utility for microbiology and microbial population biology. |
format |
Article/Letter to editor |
topic_facet |
Life Science |
author |
Cottinet, Denis Condamine, Florence Bremond, Nicolas Griffiths, Andrew D. Rainey, Paul B. de Visser, Arjan Baudry, Jean Bibette, Jérôme |
author_facet |
Cottinet, Denis Condamine, Florence Bremond, Nicolas Griffiths, Andrew D. Rainey, Paul B. de Visser, Arjan Baudry, Jean Bibette, Jérôme |
author_sort |
Cottinet, Denis |
title |
Lineage tracking for probing heritable phenotypes at single-cell resolution |
title_short |
Lineage tracking for probing heritable phenotypes at single-cell resolution |
title_full |
Lineage tracking for probing heritable phenotypes at single-cell resolution |
title_fullStr |
Lineage tracking for probing heritable phenotypes at single-cell resolution |
title_full_unstemmed |
Lineage tracking for probing heritable phenotypes at single-cell resolution |
title_sort |
lineage tracking for probing heritable phenotypes at single-cell resolution |
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https://research.wur.nl/en/publications/lineage-tracking-for-probing-heritable-phenotypes-at-single-cell- |
work_keys_str_mv |
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1813200143198978048 |