Wenzel, T. | bioRxiv Science

bioRxiv2026

An open-source, 3D-printable droplet microfluidics platform with strobe-enhanced microscopy

Droplet microfluidics underpins many single-cell, precision biomedical, and nanomaterial techniques. However, implementing these methods reproducibly remains challenging outside specialised laboratories due to high equipment costs, operational inflexibility, mechanical impracticality at the microscope stage, as well as open-source pumping solutions that are inadequately validated for low-flow stability. We present an accessible, research-grade, open-source droplet microfluidics platform integrating a compact, microfluidics-optimised microscopy stage with networked syringe-pump control. Designed for local digital fabrication, primarily 3D printing, and widely available components, the platform supports reproducible builds across diverse settings. This setup enables stable droplet generation, observation of rapid droplet dynamics, and automation-ready networked workflows. The microscopy module uses a Raspberry Pi camera and microsecond stroboscopic illumination to capture sharp images of fast-moving droplets without the need for a high-speed camera. A modular hardware interface and extensible, web-accessible software stack provide a path to integrate additional modules and laboratory automation beyond the configuration evaluated here. For infusion, we introduce an open-source syringe pump optimised for low reliable flow rather than maximum rates, combining gearbox-assisted stepper mechanics with workflow-centric control that enables manual intervention (keypad control) and remote operation (web interface and automation hooks). We benchmark droplet regimes, size tuning, and time-stability under low-flow conditions (between 25 and 2500 uL/h) relevant to advanced assays and demonstrate biomedical readiness through the encapsulation and incubation of cells, beads, and bacteria in monodisperse droplets. The platform has been replicated across laboratories in Latin America and globally, including independent builds, supporting reproducibility. All design files, firmware/software, analysis notebooks, and benchmark datasets are openly released.

bioengineering↗

bioRxiv2023

Consistency across multi-omics layers in a drug-perturbed gut microbial community

Multi-omics analyses are increasingly employed in microbiome studies to obtain a holistic view of molecular changes occurring within microbial communities exposed to different conditions. However, it is not always clear to what extent each omics data type contributes to our understanding of the community dynamics and whether they are concordant with each other. Here we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers, namely 16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics, and metabolomics. Using this controlled setting, we find that all omics methods with species resolution in their readouts are highly consistent in estimating relative species abundances across conditions. Furthermore, different omics methods complement each other in their ability to capture functional changes in response to the drug perturbations. For example, while nearly all omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control and metabolomics revealed a decrease in polysaccharide uptake, likely caused by Bacteroidota depletion. Taken together, our study provides insights into how multi-omics datasets can be utilised to reveal complex molecular responses to external perturbations in microbial communities.

microbiology↗