LabCom - V2 - Laboratoires communs organismes de recherche publics – PME/ETI - Vague 2

MICRObial Single Cell AnaLysEs Laboratory – MICROSCALE Lab

Submission summary

The ECOBIO laboratory and the company Cellenion propose to create the Joint MICROSCALE-lab Laboratory, in the fields of microbiology and molecular biology, for the analysis of single prokaryotic cells. MICROSCALE-lab is divided into three R&D axes: (i) IsoCell which targets the isolation of single microbial cells from a complex community using the cellenONE systems, (ii) IsoGenes and (iii) IsoTrans, focusing on the analysis of genomes and transcriptomes, respectively, of single microbial cells. The overall objective of these three axes is to offer a complete system (isolation, preparation of sequencing libraries and bioinformatic analysis) for the analysis of single microbial cells, creating a conceptual and technological breakthrough for the study of microbial communities. Indeed, while leading to significant advances in the field of microbiology during the last decades, the widely used 'meta-omics' approaches are currently showing their limits. A need for new tools to better understand microbial communities (i.e. microbiota), and especially to link microbial diversity and functions, is emerging. MICROSCALE-lab intends to fulfil this need by transferring single-cell sorting systems previously used on eukaryotic cells to prokaryotes, and by combining them with molecular analysis and bioinformatics tools. This will bring new insights in various fields of research, both fundamental and applied, targeting the microbiota. MICROSCALE-lab will benefit from the partnership between the ECOBIO laboratory, expert in microbial ecology and environmental genomics, and the company Cellenion, specialized in the design of tools for the isolation and study of single cells, and in molecular biology. The two LabCom’s partners will move forward in close collaboration on the three R&D axes, making the best use of their respective infrastructures, skills and expertise.
For 20 years, the ECOBIO laboratory has been developing research activities in the fields of microbial ecology and environmental microbiology that are internationally recognized and associated with the publication of numerous international peer-reviewed articles in high impact factor journals. The research team mobilized for MICROSCALE-lab is thus made up of microbiologists with complementary specialties, crossing different scientific disciplines centred on microbial ecology. In addition, MICROSCALE-lab will rely on the technical and human resources of the Environmental and Human Genomics (GEH) platform hosted by the ECOBIO laboratory. For its part, Cellenion, a fast-growing SASU, develops products and solutions for the isolation of single cells, including the cellenONE technology, which is internationally marketed. Cellenion's multidisciplinary research team combines robust expertise in molecular and cellular biology and microbiology, with strong skills in (bio)informatics and automation and optics engineering. Based on the strength of this partnership between ECOBIO and Cellenion, MICROSCALE-lab will target the industrial market devoted to the analysis of single cells which is currently in full expansion. It will position itself in microbiota study in the field of health, environment, bioproduction, agrifood, cosmetics, etc, and will open up new possibilities for generating new data on microbiota and their functioning, increasing major fundamental knowledge in microbiology and microbial ecology.

Project coordination

Philippe VANDENKOORNHUYSE (UMR6553 Ecosystèmes Biodiversité Evolution)

The author of this summary is the project coordinator, who is responsible for the content of this summary. The ANR declines any responsibility as for its contents.


ECOBIO UMR6553 Ecosystèmes Biodiversité Evolution
Cellenion SASU

Help of the ANR 362,962 euros
Beginning and duration of the scientific project: May 2021 - 54 Months

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