A droplet-to-data workflow for antimicrobial screening of complex matrices

EF2-enabled droplet assays for Escherichia coli found MIC at lower extract concentrations than 96-well microdilution for Taraxacum officinale, Rhodiola rosea, and Lonicera caerulea, using 27,059 segmented droplets.

• Why it matters: Conventional bulk screening of complex natural matrices is hindered by optical interference and averaging across bacterial subpopulations, making it hard to quantify antimicrobial potency and phenotype-specific effects.
• What they did: The workflow combines a polydisperse droplet-based assay with EasyFlow 2.0, using CellProfiler segmentation and a CellProfiler Analyst random forest to classify four growth phenotypes, plus automated thresholding and MIC estimation.
• The result: L. caerulea reduced E. coli aggregation while T. officinale did not, and R. rosea showed reduced growth in 96-well assays but droplet gelation at high concentrations blocked droplet-based analysis.

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