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Changing the scope in microbiology, from satellite view to macro lens, with cellenONE®


The most significant discoveries in microbiology were made thanks to culture-based methods and metagenomics and metatranscriptomics studies, but while the former give a truncated and artificial vision of natural reality, the latter give an averaged information, rarely disentangled. Daily, microbiology theories and hypotheses are rising, creating the need for breakthrough innovations, allowing to access the microbial individual level, i.e. single individual microbial cells, genomes, and transcriptomes. Single microbial cell studies, using cellenONE®, will open unprecedented perspectives in all fields of microbiology.

The automated cell sorter cellenONE® is the most appropriate tool for single microbial cell studies prokaryote because:

  • it uses picoliter-scale liquid dispensing technology: single microbes are isolated in cellenONE® in picoliter-scale drops and the very same robot can be used to dispense a great range of buffers and reagents, reducing contamination probability and hands-on time, and allowing the miniaturisation of virtually all downstream applications, including NGS library preparation, that drastically reduces reagent costs,
  • it is unbiased: all cells in a solution can be sorted by cellenONE®, independently of their relative abundance, making possible the discovery of rare microbes and gene repertoires that would be hidden by the most abundant ones using other techniques,  
  • it is based on (fluorescence) imaging so can theoretically be combined by all possible techniques of microbial fluorescent labelling,
  • it is very gentle and does not kill cells when sorting them,
  • it is highly versatile: cellenONE® is the most polyvalent single-cell isolation on the market allowing to work on the greatest variety of biological and physical objects, of different size and shape.


So far, it allowed to successfully isolate a variety:

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…

Microbial Metabolism


Microbial metabolism reactions are daily used for a variety of industrial applications (food and beverage, paper, agricultural tools, cosmetics, pharmaceutical products and probiotics). Microbial metabolism also has daily tremendous financial and sanitary consequences (e.g. food and crop decay and pathogenesis).

Single microbial cell studies made possible by cellenONE®, will allow to:

  • Screen microbial strains at high throughput for target metabolisms (culturomics),
  • Discover new microbial metabolisms,
  • Identify metabolically relevant gene assemblages and gene expression regulations

Microbial Evolution


Microbes are capable of extraordinary fast evolution. This is due to their extremely high multiplication and mutation rates, but also to their ability to acquire genetic material from other organisms by horizontal gene transfer.

Accessing the single individual genome level, which cellenONE® could allow, will for instance allow to:

  • Anticipate host-pathogen co-evolution events, 
  • Decipher mechanisms of gene loss and gain,
  • Trace horizontal gene transfer events