Single Microbial Cell Isolation
Exploring the Microbial World, One Cell at a Time
Microorganisms shape our world, from environmental ecosystems to human health and industrial biotechnology. Yet, the vast majority of microbial species remain poorly characterized. Single-cell isolation technologies open new possibilities to study individual microbes, enabling discoveries in microbiome research, infectious disease, and beyond.
In synthetic biology and biomanufacturing, microbial strains are engineered to produce high-value biomolecules such as DNA, proteins, or metabolites. Here, single-cell isolation plays a critical role: ensuring monoclonality and establishing pure, stable cultures that can be scaled for reliable, reproducible mass production.
With cellenONE®, microbiologists gain unmatched precision in isolating individual microbial cells, whether to explore microbial dark matter, validate engineered strains, or secure robust production lines for synthetic biology.
You're in good company
These leading institutions use our single cell and 3D cell model technologies:
Single microbial cell applications
Synthetic Biology and Biomanufacturing
Accelerate microbial strain engineering by securing monoclonality for robust, large-scale biomolecule production.
Host–Microbe Interaction Studies
Study both host and microbial cells from the same sample, with equal precision. cellenONE enables the simultaneous isolation of host cells and their associated microbes, preserving the complexity of interactions.
Single Microbial Cell Omics
Unlock hidden diversity with genomics, transcriptomics, and proteomics at the single-microbe level.
Making Single-Microbial Cell Studies Accessible
Typical synthetic biology workflow
Featured resources
PUBLICATION
Review on Single Microbe Omics Trends in Ecology & Evolution (2021)
Published by the University of Rennes (Philippe Vandenkoornhuyse lab), this review highlights the transformative potential of single microbial cell approaches. It outlines how technologies like cellenONE help overcome cultivation bottlenecks, enabling deeper exploration of microbial dark matter, host–microbe ecology, and the hidden players driving ecosystem function.
Application note
High-Throughput Generation of Bacterial Libraries
This study demonstrates how cellenONE’s image-based isolation and direct liquid cultivation streamline the creation of extensive microbial isolate libraries. By ensuring pure monoclonal cultures at scale, it unlocks new opportunities for culturomics, microbial diversity studies, and synthetic biology applications such as large-scale DNA or metabolite production.
Poster
Culturomics Proof of Concept on Vaginal Swabs
This proof-of-concept shows how cellenONE can sort both microbial and host cells from complex biological samples in a single workflow. The approach accelerates high-throughput culturomics while supporting downstream applications like microbiome research, infection biology, and microbial engineering, all with unmatched precision and throughput.