Isolate and investigate yet unknown microbes


The high-throughput cultivation and Biodiscovery Platform allows for isolation and investigation of yet unknown microorganisms. Subsequently, these can be used as building blocks for synthetic communities. 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, anaerobic cultivation


The Biodiscovery Platform is a single cell-based high-throughput cultivation and biodiscovery platform specifically adapted to the recovery of yet-uncultured strictly anaerobic microorganisms. In brief, it allows the design, construction and testing of defined synthetic or minimal microbial communities.

Defined synthetic or minimal microbial communities represent more complex natural microbial communities. In the future, they could 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 is often based on genome-predicted functionalities of individual microbial species. It depends on the availability of individual microorganisms either as pure cultures or – in case of strains not previously obtained in culture – physically isolated cells. 

The platform is specifically tuned to the discovery, characterization and utilization of strict anaerobes. It can, however, also be used for aerobic, microaerophilic and facultatively anaerobic microorganisms.

The 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. For additional info, read the technical details below.


Other platform benefits

The infrastructure of the Biodiscovery Platform enables 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. This can be done in physically separated compartments that share the same medium, i.e. in suspended beads or emulsion droplets. This will allow for the exchange of metabolites and/or signalling compounds between the compartments, which will further increase 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).

Microfluidic cell sorting and microbioreactors

The combination of single-cell cultivation systems with state-of-the-art microfluidic cell sorting equipment allows to distribute single cells in a random fashion to downstream single-cell cultivation devices. In this way, it can selectively retrieve and accumulate cells of a specific target population of interest for downstream cultivation. The single-cell recovery and cultivation units will, moreover, be complemented with microfluidic microbioreactor equipment for initial screening of (synthetic) mixed communities. Here, the response of microbial communities to specific process conditions can be screened. This includes, for instance, the stability of the community and its functionality, i.e. the metabolic output.

Sample processing

Complementing the single-cell recovery and cultivation units, the Sample Processing platform will comprise all necessary solid- and liquid handling equipment. This allows for efficient, automated extraction of biological materials, such as 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.

Integration with other platforms

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. These platforms allow for more detailed experiments to investigate intercellular interactions and to understand as well as control spatiotemporal coordination, robustness, and stability of the novel synthetic consortia.