Method of growing and analyzing single cells within microfluidic droplets

Unmet Need

The importance and influence of the microbiome on human health is becoming increasingly recognized, with the human microbiome linked to processes varying widely across the body. Accumulating data suggests that the microbiome plays an important role in human health and function across the body – from immune system development like autoimmunity and homeostasis, to behavioral influences on mood and cognition, and even neurological processes like autism and depression. Understanding the genetic makeup of microbial communities and how they change over time is a powerful investigative approach that is rapidly gaining popularity, with the global market for microbiome sequencing projected to increase from $885M in 2018 to over $2B in 2023 (CAGR 18.2%). However, culturing these varied microbial communities and untangling the genetic sequences still poses challenges. There is a need for high-throughput methods of isolating, growing, and analyzing individual bacterial strains from complex mixtures such as human microbiome samples.


Duke inventors have developed high-throughput methods of isolating, growing, and analyzing individual cells from complex mixtures such as human microbiome samples. This technology is intended to be combined into a single device to consolidate cell isolation, culturing, and high-throughput analysis. These methods combine microfluidics and genetic sequencing, loading up single cells into individual microdroplets to create millions of distinct culture volumes in minutes with fewer time, resource, and volume restraints as compared to traditional plate-based culturing methods. Bacterial isolates grown in these individual microdroplets can then be analyzed by a variety of methods, such as high throughput 16S rRNA sequencing, which was successfully demonstrated by the inventors. Furthermore, the colonies encapsulated in these microdroplets can be continually experimented upon as they grow, for example to assay the response of individual bacterial strains to a new antibiotic. These methods have been used to measure strain growth rates and compare prebiotic utilization potential between individuals' microbiome samples, demonstrating proof of principle.

Other Applications

This approach to individually encapsulate microbes and cells for further analysis can be widely applicable beyond human microbiome studies, from drug screening to environmental microbiology.


  • Can create millions of workable culture volumes in an hour
  • Effectively separates and cultures individual microbial strains, with fraction of cultivatable strains comparable to traditional plate-based culturing
  • Single-emulsion microfluidics simpler than other current droplet-based techniques
  • Easy-to-use methods using affordable, off-the-shelf components that can fit in compact work environments
  • Adding more strains does not appreciably increase effort or time
  • Highly flexible workflow for further analysis and experimentation
Bacteria encapsulated in droplets. (Source: inventor internal presentation)

Duke File (IDF) Number



  • David, Lawrence
  • Bloom, Rachael "Rachael"


    • Patent Number: 11,313,000
    • Country: United States of America

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School of Medicine (SOM)