Isolate and investigate yet unknown microbes


The high-throughput cultivation and Biodiscovery Platform allows for isolation and investigation of yet unknown microorganisms (and consortia) that can be used as building blocks for synthetic mixed cultures. The platform is geared towards strictly anaerobic microorganisms, but is universally applicable.

Wageningen University & Research
high-throughput cultivation, single-cell based, microfluidic cell sorting, microbioreactor unit, high throughput sample processing unit for biomolecular analyses
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The emerging field of synthetic ecology aims at the design of defined synthetic microbial consortia predicted to represent more complex natural microbial communities, followed by experimental testing of their functioning under specific process conditions. Synthetic microbial communities are expected to provide important contributions to food safety and production, human and animal health, bioresource utilization and sustainable production of biobased chemicals. The ability to assemble synthetic communities based on genome-predicted functionalities depends on the availability of individual microorganisms either as pure cultures or physically isolated cells in case of strains not previously obtained in culture.

Platform benefits

A single cell-based high-throughput cultivation and biodiscovery platform specifically adapted to the recovery of yet-uncultured strictly anaerobic microorganisms allows the design, construction and testing of defined ‘synthetic’ or ‘minimal’ microbial communities. While the Biodiscovery Platform will be specifically tuned to the discovery, characterization and utilization of strict anaerobes, it can also be used for aerobic, microaerophilic and facultatively anaerobic microorganisms.

Finally, the Biodiscovery Platform comprises a central sample processing platform that provides high throughput capacity for largely automated sample processing and storage for downstream biomolecular and metabolome analyses.

Experimental units

The Biodiscovery Platform will employ infrastructure for the cultivation at microcolony and single cell level. More specifically, these systems will allow the propagation of single cells as well as (random) combinations of a limited number of cells from environmental samples, in physically separated compartments that share the same medium. This will allow for the exchange of metabolites and/or signalling compounds between the physically separated microcompartments (i.e. suspended beads or emulsion droplets), further increasing the odds of growth of otherwise unculturable microorganisms. Furthermore, medium composition and other process conditions can be adjusted to fit eco-physiological properties of specific organisms of interest, predicted from (meta)genomic data (Gutleben et al., 2017).

Single-cell cultivation systems will be combined with state-of-the-art microfluidic cell sorting equipment that allows to 1) distribute single cells in a random fashion to downstream single-cell cultivation devices, or 2) selectively retrieve and accumulate cells of a specific target population of interest for downstream cultivation.

The single cell recovery and cultivation units will be complemented with microfluidic microbioreactor equipment for initial screening of (synthetic) mixed communities. In this microbioreactor unit, natural as well as synthetic communities can be screened with respect to their response to specific process conditions with respect to microbial community stability and functionality in terms of metabolic output. Most promising synthetic microbial communities can then be further studied in the larger and more advanced reactors of the Parallel Cultivation and/or Modular Bioreactor platforms, allowing for more detailed experiments to investigate intercellular interactions and to understand and control spatiotemporal coordination, robustness, and stability of the novel synthetic consortia.

Complementing the single cell recovery and cultivation units, the Sample Processing platform will comprise all necessary solid- and liquid handling equipment for efficient, automated extraction of DNA, RNA, proteins and polar and non-polar metabolites from undivided samples of mixed microbial communities. Furthermore, sample aliquots will be snap-frozen during handling and stored at dedicated sample storage units. Viable aliquots of mixed microbial communities and individual strains will be stored as cryo-stocks and/or lyophilized stocks.