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<p>Phenotype-based screening remains a major bottleneck in the development of microbial cell factories. Here, we present a Digital Colony Picker (DCP), an AI-powered platform for automated, high-throughput screening and export of microbial clones based on growth and metabolic phenotypes at single-cell resolution, without agar or physical contact. Using a microfluidic chip comprising 16,000 addressable picoliter-scale microchambers, individual cells are compartmentalized, dynamically monitored by AI-driven image analysis, and selectively exported via laser-induced bubble technique. Applied to <i>Zymomonas mobilis</i>, DCP enabled <i>en masse</i> screening and identified a mutant with 19.7% increased lactate production and 77.0% enhanced growth under 30 g/L lactate stress. This phenotype was linked to overexpression of ZMOp39x027, a canonical outer membrane autotransporter that promotes lactate transport and cell proliferation under stress. DCP provides a multi-modal phenotyping solution with spatiotemporal precision and scalable throughput, offering a generalizable strategy for accelerated strain engineering and functional gene discovery.</p>

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AI-powered high-throughput digital colony picker platform for sorting microbial strains by multi-modal phenotypes

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2025年10月10日

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  • Zhidian Diao,
  • Qiqun Peng,
  • Sijun Luo,
  • Lingyan Kan,
  • Anle Ge,
  • Wei Gao,
  • Runxia Li,
  • Weiwei Bao,
  • Xixian Wang,
  • Yuetong Ji,
  • Jian Xu,
  • Shihui Yang,
  • Bo Ma

摘要

Phenotype-based screening remains a major bottleneck in the development of microbial cell factories. Here, we present a Digital Colony Picker (DCP), an AI-powered platform for automated, high-throughput screening and export of microbial clones based on growth and metabolic phenotypes at single-cell resolution, without agar or physical contact. Using a microfluidic chip comprising 16,000 addressable picoliter-scale microchambers, individual cells are compartmentalized, dynamically monitored by AI-driven image analysis, and selectively exported via laser-induced bubble technique. Applied to Zymomonas mobilis, DCP enabled en masse screening and identified a mutant with 19.7% increased lactate production and 77.0% enhanced growth under 30 g/L lactate stress. This phenotype was linked to overexpression of ZMOp39x027, a canonical outer membrane autotransporter that promotes lactate transport and cell proliferation under stress. DCP provides a multi-modal phenotyping solution with spatiotemporal precision and scalable throughput, offering a generalizable strategy for accelerated strain engineering and functional gene discovery.