Isolate and investigate yet unknown microbes
Isolate and investigate yet unknown microbes
About the Biodiscovery Platform
Key specifications
Location: Wageningen University & Research
Features: high-throughput cultivation, single-cell based, microfluidic cell sorting, microbioreactor unit, high throughput sample processing unit, anaerobic cultivation
The Biodiscovery Platform allows for investigation and isolation 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. The infrastructure of the Biodiscovery Platform enables cultivation at scales ranging from single-cell level to 2 ml bioreactors.
Equipment
Microbioreactor Unit
The Microbioreactor Unit is used for the initial screening of natural and defined mixed communities. It can also be used for culturing strict anaerobes. The unit can be operated in batch and feed-batch modes with constant, linear, exponential, and pulse feeding options under oxic and anoxic conditions. It supports temperature control between 10 and 50°C, shaking speeds ranging from 100 to 1500 rpm, and online regulation of feeding, gas flow, and pH within a range of 4 to 7.5. Depending on the plate type, the unit allows the simultaneous operation of 48 batch cultures and 32 fed-batch cultures with volumes ranging from 0.8 to 2.4 mL per well. Several parameters—such as biomass concentration, pH, dissolved oxygen, and temperature—can be monitored online.
High Throughput Sample Processing Unit
The High Throughput Sample Processing Unit enables the simultaneous extraction and analysis of relevant biomolecular fractions from single samples, including DNA, RNA, proteins, and both polar and non-polar metabolites. The unit supports a wide range of sample types, including fecal, soil, sediment, water, and bioreactor sludge. Its high level of automation and capability to process small volumes is critical for high-throughput sample processing of environmental and host-associated samples.
Raman Assisted Microfluidic Cell Sorting Unit
The Raman Assisted Microfluidic Cell Sorting Unit enables the sorting and characterization of cells from a targeted population of interest for downstream cultivation. The system is composed of four main units: a Raman microscope, optical tweezers, a microfluidic cell sorter, and a single-cell cultivation chamber. Single cells are trapped while flowing through a microfluidic device using integrated optical tweezers. Raman interference determines whether the cell has a characteristic of interest (e.g., isotopic labeling), which is then used to sort or discard the cell. Individual cells can be characterized and sorted based on functional characteristics and genetic identity within a complex microbial community. Using the Biodiscovery Platform, sorted single cells can be cultured for downstream analyses.
MicroWriter ML3 Pro
The MicroWriter ML3 Pro is an advanced benchtop photolithography system that allows precision patterning in applications such as microfluidics, MEMS, and advanced micro-optical systems. With this tool, we can generate microfluidic chips with minimum feature sizes of 0.6 μm, with an optional resolution of 0.4 μm, all at very high writing speeds. This makes it an ideal choice for rapid prototyping and for creating complex designs for downstream single-cell cultivation, phenotyping, and genotyping.
ONT Sequencing
The Biodiscovery Platform at UNLOCK enables microbial community analysis for downstream applications, including the extraction of relevant biomolecules, DNA and RNA sequencing, and comprehensive bioinformatics and downstream analysis.
We offer Oxford Nanopore Technology (ONT) long-read sequencing through two devices:
GridION
GridION is a compact, benchtop device that offers flexibility and scalability. It supports up to five independent MinION or Flongle Flow Cells. It delivers up to 240 GB of real-time sequence data, with 48 GB per MinION flow cell or 2.8 GB per Flongle Flow Cell. This robust platform is perfect for multiple users with varied applications, offering accessible ONT sequencing solutions. GridION is compatible with both MinION and Flongle Flow Cells, supporting diverse applications such as whole genome analysis, metagenomics, targeted sequencing, large transcriptomes (cDNA), and small transcriptomes (direct RNA sequencing). The Flow Cell enables direct, real-time DNA and cDNA sequencing on smaller, single-use flow cells, while the MinION Flow Cell supports real-time sequencing of DNA, cDNA, or native RNA.
PromethION 2 Solo
PromethION 2 Solo is a small benchtop device designed to run up to two PromethION flow cells. Each flow cell is independently addressable, meaning that experiments can be run concurrently or staggered over time. The current chemistry of the P2 Solo offers a high output of up to 290 GB data from a single PromethION flow cell. PromethION 2 Solo is compatible with the PromethION Flow Cell, enabling applications such as whole mammalian genome sequencing, complete metagenomes, large targeted sequencing, and small and large RNA sequencing applications.
Frequently asked questions
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.
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 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.
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 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.
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