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Peer-reviewedCC BY 4.0PLOS One

Simple and multiplexed tracking of bacterial growth in double emulsion droplets

  • Sebastián Somolinos Cedeño1
  • Samuel Thompson2
  • Polly Fordyce2,3,4,5
  • Drew Endy2,6,7
7 affiliations
  1. 1Department of Microbiology and Immunology, Stanford University, Stanford, California, United States of America
  2. 2Department of Bioengineering, Stanford University, Stanford, California, United States of America
  3. 3Department of Genetics, Stanford University, Stanford, California, United States of America
  4. 4Sarafan ChEM-H Institute, Stanford University, Stanford, California, United States of America
  5. 5Chan Zuckerberg Biohub, San Francisco, California, United States of America
  6. 6Center for International Security and Cooperation, Freeman Spogli Institute, Stanford, California, United States of America
  7. 7Hoover Institution, Stanford, California, United States of America
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Abstract

Droplet-based microfluidics enable researchers to observe phenotypic heterogeneity within complex biological mixtures through parallel encapsulation of individual samples followed by imaging. Observing or quantifying dynamic heterogeneity remains challenging due to complexities associated with trapping and tracking many individual droplets. Current approaches for time-lapse imaging require specialized devices with droplet traps that limit accessibility and throughput. Here, using readily available materials and software, we demonstrate a simple method for stabilizing and monitoring many, individual droplets for up to 12 hours. We leveraged our method to track bacterial growth within droplets in a high-throughput manner for over 6 hours. Our method allows tracking the changes and variation in growth rate within and across droplets, revealing heterogeneity in growth patterns hidden in batch assays. Improving the affordability and throughput of time-dependent phenotyping assays helps to advance biological discovery and biotechnology innovation.

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Cite

BibTeXRIS
BibTeX
@article{cedeno2026simple,
  title = {{Simple and multiplexed tracking of bacterial growth in double emulsion droplets}},
  author = {Sebastián Somolinos Cedeño and Samuel Thompson and Polly Fordyce and Drew Endy},
  journal = {PLOS One},
  year = {2026},
  month = nov,
  doi = {10.1371/journal.pone.0362111},
  url = {https://doi.org/10.1371/journal.pone.0362111},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Simple and multiplexed tracking of bacterial growth in double emulsion droplets
AU  - Sebastián Somolinos Cedeño
AU  - Samuel Thompson
AU  - Polly Fordyce
AU  - Drew Endy
PY  - 2026
DA  - 2026/11/04
JO  - PLOS One
DO  - 10.1371/journal.pone.0362111
UR  - https://doi.org/10.1371/journal.pone.0362111
AB  - Droplet-based microfluidics enable researchers to observe phenotypic heterogeneity within complex biological mixtures through parallel encapsulation of individual samples followed by imaging. Observing or quantifying dynamic heterogeneity remains challenging due to complexities associated with trapping and tracking many individual droplets. Current approaches for time-lapse imaging require specialized devices with droplet traps that limit accessibility and throughput. Here, using readily available materials and software, we demonstrate a simple method for stabilizing and monitoring many, individual droplets for up to 12 hours. We leveraged our method to track bacterial growth within droplets in a high-throughput manner for over 6 hours. Our method allows tracking the changes and variation in growth rate within and across droplets, revealing heterogeneity in growth patterns hidden in batch assays. Improving the affordability and throughput of time-dependent phenotyping assays helps to advance biological discovery and biotechnology innovation.
SN  - 1932-6203
ER  -