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Microwell Array Platform for High-throughput Screening and Discovery of Potential Probiotics

Microbe-microbe interactions influence microbial community dynamics, composition, and impact the host. In agriculture, research has shown that microorganisms can efficiently colonize the root of a plant and modulate root system architecture, thereby affecting plant growth. Researchers at Kansas State have developed a high-throughput screening approach for identifying pairs or higher-order networks of bacterial species that can potentially be used as soil amendments or as probiotic candidates. 

The screening platform uses a microwell array to create thousands of unique combinations between a fluorescently labeled focal species and different bacterial isolates from an environmental microbiome. Cells are trapped and cultured within their respective wells and monitored with fluorescent microscopy. Wells showing desired behavior are extracted and the antagonizing or promoting species are sequenced for identification. Screens can be used to identify bacteria that antagonize or promote the growth of plant pathogens or plant growth promoting bacteria.


  • High throughput screening - Allows testing multiple consortia in one assay

  • Easy microbe recovery – removable trap to recover microbes from wells with high precision and high recovery

  • Low-cost – minimum cost to build and operate

  • Operation – Operationally simple and efficient

  • Applicability and customization - adaptable to discovery in any microbiome


  • Discovery of soil amendment candidates

  • Discovery of probiotic candidates

  • High throughput screening of mutant libraries to identify the genetic basis of microbial interactions.

  • Comparing interactions across microbiomes of varied origin (different host species, different geographic origin, or between diseased and healthy hosts)

  • Screening for microbial phenotypes associated with specific physical features (e.g. diffusive environment) or chemical environments (e.g. plant host metabolites). 

Additional Details


Kansas State University

Intellectual Property Protection

Pending Patent

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