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Bacteria isolation


cellenONE offers a great alternative to tedious clone picking approaches for single bacteria cloning.

A range of bacteria have been successfully isolated on cellenONE systems using both IBSCI and FIBSCI technologies.

For smaller bacteria, the use of fluorescent labels in conjunction with FIBSCI is recommended.

List of bacterial genus successfully isolated so far:

  • Bacillus
  • Escherichia
  • Lactobacillus
  • Microccocus



Example of colonies grown from single bacteria (E. coli and S. epidermidis) dispensed on agar as a checkerboard pattern. Image courtesy of the Zengler lab, UCSD.

Due to their very small size, bacteria are too small to be seen by IBSCITM only. Fluorescent labels helped successful isolation of various bacteria using FIBSCITM.


Micrococcus labelled with CellTracker Deep Red
E. coli labelled with CellTracker Deep Red

Microbial Ecology


Microbes react fast to ecosystem changes and their response can have severe consequences. For instance, soil and ocean microbiota are stimulated by global warming, inducing a feedback increase of greenhouse gas emission by microbes. Similarly, our gut microbiota is influenced by our diet and way of life and, in turn, influences all aspects of our health, including immune response, mental status and behaviour.

Microbial ecology, studying microbiota assembly and responses, now needs single microbial cell methods, and cellenONE®, to:

  • Discover rare microbial species and functions, 
  • Evaluate microbial intra-populational heterogeneity,
  • Elucidate networks and co-occurrences of genes and functions,
  • Investigate species co-existence patterns
  • Post-Metagenomics and -Metatranscriptomics Microbiota Analyses

     Post-Metagenomics and -Metatranscriptomics Microbiota Analyses using cellenONE® Technology

    Mechanisms of microbial community assembly and microbial evolution are poorly understood, despite their prominent role of in essential ecosystem processes. While less than 1% of prokaryotic species can be cultivated in the lab, metagenome and metatranscriptome studies have been the top microbiology methods over the past 2 decades: they allowed a significant number of high-impact discoveries but also raised an even more significant number of questions that can only be answered by accessing the bacterial population and individual level.

    A recent theory of evolution, the Black Queen Hypothesis (BQH), suggests that organisms could adapt to their environment by loss of trait or function, and not only by complexification. These theories and hypotheses cannot be demonstrated in natural environments, because the respective attribution of functional traits to the different populations and individuals remains impossible by the currently used methods.

    This thesis project aims to explore the influence of BQH on the assembly of the microbiota by developing single microbial cell isolation and single microbial genome and transcriptome sequencing techniques, going beyond the limits of meta-omics.
    This PhD project is carried out between Cellenion, ECOBIO, UMR academic partner and the OSUR Environmental and Human Genomics platform.

    The cellenONE® device recently acquired within the GEH platform is used to isolate bacterial cells from environmental samples (plant microbiota, soil). cellenONE® beforehand visualisation and automated imaging, gentle cell manipulation, pico-liter scale volumes, and relative high-throughput will altogether help decreasing the sample contamination and library prep cost. Bacterial cell-wide genome and transcriptome amplification tools will be used, and a pipeline for high throughput analysis of bacterial genomes and transcriptomes will be developed.

    Duration: January 2020 - January 2023

    Program Type: Bourse CIFRE

    Involved Partners:


    Thanks for the support: