Soil-on-chip devices in the study of microbial communities: Active Matter
Author
Jesús Domínguez
Publication Date
September 14, 2019
Status
Keywords
microbial communities
Soil-on-chip
bioremediation
chemical gradients
heterogeneity in soil
microbiology
soil ecology
soil-microbe interactions
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Microfluidic soil-on-chip devices: introduction
Soil-on-chip devices will have many applications. Soil is a complex environment defined by a main characteristic: heterogeneity.
The conditions of this system, such as topography and composition, are highly irregular and often prone to changes, leading to the development of diverse and interlinked microbial communities with a broad set of requirements for their survival.
Many of these requirements can be challenging to control artificially, namely the communication and interactions between microbial species. For that reason, even to this day, very few of the soil-dwelling microorganisms can be cultured in a laboratory and be adequately studied.
Since direct monitoring of actual soil samples often implies a fundamental alteration of the medium to the extent where the natural properties and original behavior are lost, the need arises for a device to recreate such conditions while allowing analysis.
Microfluidic soil-on-chip devices: project description
What is more, given that most of the microbes in the soil behave as active matter (composed of large numbers of active “agents,” each of which consumes energy to move or to exert mechanical forces), information about its movement and expansion through the available space depending on the set conditions can also be extracted. This offers valuable insight into environmental science, microbiology, and physics.
This project aims to overcome many obstacles in microbial monitoring through microfluidics, where some general advantages like transparency, the tailored shape of microfluidic chips, and the possibility of establishing chemical gradients are exciting.
As a result, many valuable applications can be derived from a better understanding of the soil system, including bioremediation, enhanced crop growth, and the development of new antibiotics. This is what soil-on-chip devices aim to achieve.
Related content & results from this project
In the light of the Active Matter project, we developed a microbiology incubator.
We also published a review about soil-on-chip devices, and another one about microswimmers chemotaxis behavior.
Funding
This soil-on-chip project has received funding from the European Union’s Horizon research and innovation program under the Marie Sklodowska-Curie grant agreement No 812780 (ActiveMatter project).
Researcher
Jesús Domínguez
Marie-Curie PhD Candidate Elvesys/Gothenburg University
- Traineeship in Nanoparticle Characterisation (Joint Research Centre in Geel, Belgium)
- Double University Degree in Physics and Materials Engineering (Universidad de Sevilla, Spain)
Areas of expertise:
Physics, physical chemistry, materials science, rheology, chemical engineering, nanotechnology, particle characterisation, emulsions.
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FAQ – Soil-on-chip for the study of microbial communities: Active Matter
What is the issue that NAP4DIVE is attempting to address?
The most important barrier to CNS therapies is the blood-brain barrier (BBB). Although Europe has a massive disease burden, estimated to be 180 million affected by the diseases, including Alzheimer’s, Parkinson’s, schizophrenia, and brain cancers, less than 5% of drug candidates ever make it to the brain at therapeutic levels. NAP4DIVE directly fills that gap through nanoparticle design and testing informed by the biology of the human BBB.
What is this NAP4DIVE approach?
Two tools to be used together, complementary to each other:
A high-throughput BBB-on-chip platform (an in-vitro, microfluidic model of a human BBB), and an artificial intelligence-based machine-learning NP Design Simulator to determine the nanoparticle formulations with the highest probability of activation across the BBB without undue harm.
Experiments consist of predictions and experimental readouts. That iteration speeds up selection and scales up, and is de-risked.
What is the rationale for the in vitro use of the BBB-on-chip instead of animal models?
Since animal BBB responses are not typically aligned with human data, the time/cost footprint is substantial. The organ-on-chip pathway provides you with regulated shear stress and human cell interfaces together with readouts of reproducible barriers, and significantly reduces the use of animals. It iterates more quickly, organization space is cheaper, and it is closer to the target physiology.
Which are the families of nanoparticles that are scoped?
A number of nanoparticle classes to be screened in the project include lipid nanoparticles, polymer nanoparticles, and metal-core nanoparticles. The various levers that can be systematically probed by the simulator and the chip for each class are stability, surface chemistry, size/shape distributions, and targeting ligands.
What is the role played by the Microfluidics Innovation Center (MIC)? in comparison with biology on static gels?
MIC designs the fluidic system, which feeds the cells under control, imposes controlled flow and shear forces, and injects well-characterized nanoparticle formulations. Consider it the chip’s circulation system: strong perfusion, accurate dosing, and controls that make experiments reproducible. MIC also assists in setting the test conditions and throughput with the consortium.
What are the most important partners in the biological sphere?
The development of the BBB cell culture and barrier architecture on which the chip is fabricated was pioneered by Finnadvance, which is currently known as Akita. MIC and Akita are developed shoulder-to-shoulder, so that biological fidelity and fluidic realism develop together.
What are the outputs of the data and models generated?
Characterization information will be stored in a digital warehouse accessible to everyone. The nanoparticle designs that have the greatest potential are then tested on the BBB-on-chip and cross-validated against clinical and pre-clinical datasets provided by the pharma partner – the evidence chain is visible and above board.
Is NAP4DIVE financed, and by what date?
The European Union supports NAP4DIVE through Grant Agreement No. 101155875 under the HORIZON-HLTH-2024-TOOL-05 (two-stage) topic.
Start date: 1 January 2025
End date: 31 December 2028
EU contribution: EUR7,767,276.26
At the conclusion of the 4-year program, the team aims for market-readiness, demonstrating cost-efficiency analysis and a specific ethical evaluation that considers harm and cost reduction.
What is the shortening of the route of CNS drug candidates with this project?
By eliminating the trial-and-error approach to design. The simulator reduces the search area; the chip narrows down winning candidates based on human-significant flow and barrier conditions. Their joint efforts reduce experimental cycles and assist in the prioritization of the effective and manufacturable candidates, or in other words, what the pharma teams require prior to the costly IND-enabling research.
I am developing a Horizon Europe consortium- where should MIC be placed outside this project?
MIC is a microfluidics SME specializing in regularly participating in EU consortia to provide hardware, automation, and measurement components for complex bioassays. We prepare offers together, model work packages based on prototype deliverables, and risk-proof manufacturable designs. Consortia incorporating MIC prototype-first model usually claim success rates that are twice the official baseline at similar calls- a trend we put down to obvious technical way, believable milestones, and early demonstrators.
Does MIC assist in the delivery of non-BBB or nanoparticles?
Yes. Our products include organ-on-chip systems, bespoke flow/pressure/oxygenation systems, high throughput screening systems, sensorized microfluidic systems, and chem/bio. If your project requires microfabrication, controlled perfusion, or stable automation under realistic shear and mass-transfer conditions, that is our day-to-day business.