CULTUROMIC

The Culturomic platform is attached to the Federation of Research "Microbial Systems" (SysMic) of the University of Clermont Auvergne. This federation is composed of 4 support units (LMGE, M2iSH, MEDIS, UMRF) and teams of 7 associated units (Institut Pascal, Institut de Chimie, GDEC, EPIA, UMRH, UREP, URNH).
It is a privileged partner in the realization of scientific projects related to microbiology.

The equipments are mainly used by members of the federation and by other laboratories, internal or external to the UCA.The equipments will be accessible independently to the users subject to having followed a preliminary training with the referents of each equipment of the platform.
The complementarity of these tools will make it possible to:

• Enumerate, characterize, isolate microorganisms from various ecosystems (aquatic, soil, atmosphere, plants, animals, humans, etc.).
• Cultivate microorganisms in planktonic, biofilm, anaerobic conditions.
• Directly quantify a genome element (DNA or RNA) in a biological or environmental sample.
• Study the interactions of microorganisms with eukaryotic cells.

The equipments are located at the CBRV site Dunant of the UCA and are under the responsibility of referents.

The anaerobic enclosure is equipped with 4 gloves (2 peoples), a thermostated incubator and a controlled anaerobic atmosphere (N₂/CO₂/H₂ 90/5/5). This equipment allows the preparation, culture and/or isolation of anaerobic microorganisms.
 

Sylvain DENIS (MEDiS) / Sylvie MIQUEL (LMGE) / Adeline SIVIGNON (M2iSH)

The CellZscope2 (nanoAnalytics) allows the study of the influence of substances, toxins, molecules or microorganisms on the permeability of the cell layer by impedance monitoring (TER + capacitance). This approach is real-time, direct (without marker), adaptable to different cellular models and requires little material (inserts of 6, 12 or 24 wells).

Adeline SIVIGNON (M2iSH) / Marjolaine DELABRE, Sylvie MIQUEL (LMGE)

The easySpiral Dilute® is designed to dilute a sample up to a dilution of 10^-5, then automatically seed round Petri dishes of 90 or 150 mm in different modes (exponential, constant, circle, mass) to standardize seeding and facilitate bacterial colony counting. It allows a seeding of several dilutions per box and therefore a significant saving of consumables.
 

Caroline CHEVARIN (M2iSH), Michaël RODRIGUES (M2iSH), Nicolas CHARBONNEL (LMGE)

This automatic counter allows the counting of bacterial colonies on round Petri dishes 55, 90, 100, 150 mm and square boxes 120 mm with manual or automatic seeding thanks to the easySpiral Dilute®. It can count colonies on chromogenic agars, filtration membranes and read susceptibility tests.
 

Caroline CHEVARIN (M2iSH), Michaël RODRIGUES (M2iSH), Nicolas CHARBONNEL (LMGE)

This automate has 1 arm with 8 independent channels allowing volume pipetting from 1 to 1000 μL and 1 displacement arm for SBS microplates and 90 mm Petri dishes. Its use allows the distribution of liquids, dilutions serial in microplates etc ... Pickolo is a colony picker coupled to Tecan liquid handlers, it allows colony picking from a 90 mm round Petri dish and seeded in a 96-well microplate. Colony selection can be done by size, colour and shape or fluorescent (GFP). Its use requires the creation and validation of the computer script corresponding to the desired applications. The consumables used must be standardized and of the same reference.

Frédéric FAURE (M2iSH), Laurent NAKUSI (LMGE)

The BioFlux® system allows cell-based tests to be performed under physiological flow conditions. Through the use of microplates with an integrated microfluidic component, a variable and controlled flow (0.1-200 dyne/cm2) is obtained in the microplate channel. This system allows the study of the formation of biofilm, adherent cells under a flow. An inverted epifluorescence microscope (thermostated chamber, CO2 controller, Apotome, motorized stage,...) allows automated imaging for the analysis of living cells under shear flow.
 

Damien BALESTRINO (LMGE)

Spark Cyto is a multi-mode plate reader with fluorescence imaging and cytometry capabilities, unlocking new possibilities for your cell-based research. By combining live cell imaging with industry-leading detection technologies, you now have the ability to unite qualitative and quantitative information into unique multi-parameter data sets. There are three reading modes: Absorbance: monochromator, UV/Visible from 200 nm to 1000 nm, end point or kinetic, Fluorescence: Double monochromator, Excitation 230-900 nm, Emission 280-900nm, reading from above and/or below, TR time-resolved fluorescent, Luminescence: 38 filters, luminescence scans from 390 nm to 660 nm, multiplex measurements. Spark Cyto includes three magnification levels (x2, x4, x10) combined with four channels for fluorescence and bright field imaging, enabling high quality cell analysis for a wide variety of applications.
 

Caroline CHEVARIN (M2iSH), Damien BALESTRINO (LMGE)

Based on water-emulsion droplet technology, Droplet Digital PCR fractionates a DNA sample in 20,000 droplets. PCR amplification of the template subsequently occurs in each individual droplet, and counting the positive droplets gives precise, absolute target quantification. It is highly effective for resolving low abundance targets, such as allelic or structural variants but also for genotyping, absolute quantification, and copy number variation. Quantifying the sample target does not require a calibration curve.
 

Damien BALESTRINO, Jérôme LESOBRE (LMGE), Pierre SAUVANET (M2iSH)