title: Lineage Tracking for Probing Heritable Phenotypes at Single-Cell Resolution.
abstract: 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.
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.
authors.forename: Denis
authors.initials: D
authors.lastname: Cottinet
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.
authors.forename: Florence
authors.initials: F
authors.lastname: Condamine
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Bremond
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Griffiths
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.|New Zealand Institute for Advanced Study, Massey University, Auckland, New Zealand.|Max Planck Institute for Evolutionary Biology, Plön, Germany.
authors.forename: Paul B
authors.initials: PB
authors.lastname: Rainey
authors.affiliation: Laboratory of Genetics, Wageningen University, Wageningen, The Netherlands.
authors.forename: J Arjan G M
authors.initials: JA
authors.lastname: de Visser
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.
authors.forename: Jean
authors.initials: J
authors.lastname: Baudry
authors.affiliation: Chemistry Biology Innovation (CNRS UMR 8231), École supérieure de physique et de chimie industrielles de la Ville de Paris (ESPCI ParisTech), PSL* Research University, Paris, France.
authors.forename: Jérôme
authors.initials: J
authors.lastname: Bibette
mesh_terms: D019070:Cell Lineage / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics* / Q000254:growth & development; D029968:Escherichia coli Proteins / Q000235:genetics*; D019143:Evolution, Molecular; D016680:Genome, Bacterial; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D059010:Single-Cell Analysis / Q000379:methods*
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins