MF1 Joint Microbiome Facility

State-of-the-art DNA/RNA sequencing

The JMF, coordinated by David Berry and Petra Pjevac, offers individualized consulting and services in study design, sample processing, sequencing, bioinformatic analyses, and data interpretation to both clinical and environmental microbiome researchers.

The JMF offers DNA/RNA extraction from diverse sample types, amplicon sequencing, full-length primer-free rRNA profiling, and metagenomic and metatranscriptomic sequencing using Illumina and Oxford Nanopore technologies.

The JMF is also developing and implementing amplicon approaches that allow for absolute, fully integrated ultra-high throughput long-read sequencing and activity-based sequencing approaches based on the incorporation of bioorthogonal or isotope-labeled nucleotides.

MF3&4 Fluorescence In Situ Hybridization and Single-Cell Transcriptomics facility

Spatially resolved single-cell transcriptomics through parallel sequential FISH

Fluorescence in situ hybridization (FISH) with rRNA-targeted probes is a gold standard technique for the identification and visualization of microorganisms in environmental and clinical samples. This facility will make FISH, advanced confocal and super-resolution fluorescence microscopy, and digital image analysis techniques available to all CoE members. For selected projects, highly multiplexed FISH and multicolor imaging techniques for the parallel identification of multiple microbial species in complex samples will be adopted. For spatially structured microbiomes, 2D and 3D image analysis will extract important information, such as the spatial arrangement patterns of microbial populations.

Analyzing single-cell gene expression patterns within natural environments offers exciting opportunities to better understand microbial interactions and responses to perturbation. This facility will leverage signal amplification and multicolor imaging techniques to establish an mRNA-targeted FISH approach for spatially-resolved single-cell transcriptomics, which will be applied to detect selected gene transcripts directly in complex microbial communities.

MF6 Chemical Imaging Facility

Super-fast functional analyses of microbiomes

The CoE projects will benefit from a well-established NanoSIMS facility (unique in Austria), several spontaneous Raman micro spectrometry instruments coupled to fluorescence microscopes, and cutting-edge nano-infrared spectroscopy.

Furthermore, the projects will have access to a unique microfluidic-based Raman sorting device that enables us to sort thousands of microbial cells based on their isotopic composition or other chemical features. In addition, high-throughput single-cell isotope imaging in microbiome samples will be possible using our custom-made Stimulated Raman Spectroscopy (SRS) instrument, which is unique in Europe. It combines SRS with two-photon microscopy and enables, for example, quantification of the deuterium content (after heavy water incubation) of FISH-identified microbial cells at unprecedented speed.

The facility will push the limits of nano-IR spectroscopy by developing a dual-frequency comb spectroscopy approach for high-throughput chemical imaging.

MF8 Protein Characterization Facility

Joint forces for structural biology of proteins

Genes of particular interest revealed by the CoE microbiome projects will be heterologously expressed (or native proteins and complexes purified directly from bacterial cultures), and their structures will be analyzed using integrative structural biology approaches.

The Djinovic lab at the University of Vienna has access to a blend of complementary molecular biophysics and structural biology techniques and is equipped for protein expression and purification.

The Sazanov lab at ISTA has access to state-of-the-art cryo-EM facilities, including a high-end 300 kV TEM Titan Krios for collecting high-resolution datasets, a 200 kV TEM Glacios for optimizing cryo-EM grids and preliminary data collection, and cryo-FIB/SEM Aquilos for preparing samples for cryogenic electron tomography.

Selected projects will be supported with enzyme discovery, profiling, and in-silico predictions, e.g., on secreted proteins by microbiome members using deep learning models trained on the sequence and structural features.

MF10 Life Science Compute Cluster

High-performance computing infrastructure for computational life science

The Life Science Compute Cluster (LiSC) consists of data storage and high-performance computing facilities, and a user helpdesk. Parallel file systems with a total capacity of 1 PB are used for high-performance storage of original and derived data. Backups are performed on separate storage in a different location. The high-performance computing nodes provide >3,000 CPU cores and 30 GPUs and are used via a job scheduling system.

To facilitate easy and reproducible access to all relevant state-of-the-art scientific software, the LiSC provides a helpdesk to its users. The helpdesk not only supports users in case of problems with scientific computing, statistics, and data analysis but also takes installation requests for software versions.

The LiSC is connected to other high-performance computing facilities, namely the Vienna Scientific Cluster, allowing users straightforward access to additional computing power if needed.