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Related Concept Videos

Methods to Assess Microbial Populations01:30

Methods to Assess Microbial Populations

Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
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Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
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Related Experiment Video

Updated: May 11, 2026

High Throughput Yeast Strain Phenotyping with Droplet-Based RNA Sequencing
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AI-powered high-throughput digital colony picker platform for sorting microbial strains by multi-modal phenotypes.

Zhidian Diao1,2,3,4, Qiqun Peng5, Sijun Luo6

  • 1Key Laboratory of Photoelectric Conversion and Utilization of Solar Energy, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, China.

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|October 10, 2025
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Summary

We developed an AI-powered Digital Colony Picker (DCP) for high-throughput microbial screening. DCP identified a Zymomonas mobilis mutant with significantly enhanced lactate production and stress tolerance, accelerating strain engineering.

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Area of Science:

  • Synthetic Biology
  • Microbial Engineering
  • Biotechnology

Background:

  • Phenotype-based screening is a critical bottleneck in developing microbial cell factories.
  • Automated, high-throughput methods are needed to overcome these limitations.

Purpose of the Study:

  • To present a novel AI-powered platform, the Digital Colony Picker (DCP), for automated, high-throughput screening and export of microbial clones.
  • To demonstrate DCP's capability in identifying beneficial microbial mutants for industrial applications.

Main Methods:

  • Utilized a microfluidic chip with 16,000 picoliter-scale microchambers for single-cell compartmentalization.
  • Employed AI-driven image analysis for dynamic monitoring of microbial growth and metabolic phenotypes.
  • Implemented a laser-induced bubble technique for selective export of desired microbial clones without physical contact.

Main Results:

  • Screened Zymomonas mobilis using DCP, identifying a mutant with 19.7% increased lactate production.
  • The identified mutant exhibited 77.0% enhanced growth under high lactate stress (30 g/L).
  • Linked the improved phenotype to the overexpression of ZMOp39x027, an outer membrane autotransporter enhancing lactate transport and stress tolerance.

Conclusions:

  • DCP offers a multi-modal phenotyping solution with high spatiotemporal precision and scalable throughput.
  • This platform provides a generalizable strategy for accelerated microbial strain engineering and functional gene discovery.
  • DCP significantly advances the development of microbial cell factories by overcoming screening bottlenecks.