Westerdijk Fungal Biodiversity Institute: Fungal identification and strain typing

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Identification and Strain Typing Facility

Accurate identification of unknown microbial isolates is essential, as assigning a correct name unlocks a wide range of biological, ecological, and applied information. The Westerdijk Institute offers a dedicated facility for the identification and strain typing of filamentous fungi, yeasts, and bacteria, building on its long-standing expertise in fungal biodiversity and systematics.

The identification service is based primarily on DNA sequence data and is often complemented by phenotypic and morphological characterization. The Institute hosts experts covering all major fungal groups, ensuring state-of-the-art identification supported by extensive reference collections and taxonomic knowledge.

Strain typing is used to gain insight into the genetic diversity within species and is particularly valuable for tracking and comparing isolates. This approach is widely applied for root cause analysis of fungal contaminations or investigating nosocomial outbreaks, allowing discrimination between closely related strains and supporting source tracking.

  • Sequence-based identification using barcoding genes, supplemented with phenotypic and morphological characterization where relevant
  • Strain typing to distinguish between different strains within the same species

The facility supports a broad range of users, for example:

  • Academic researchers
  • Quality control laboratories
  • Pharmaceutical, biotechnological, food, and healthcare industries

By combining molecular, phenotypic, and taxonomic expertise, the Westerdijk Institute provides reliable identification and strain typing services that support research, quality assurance, and applied microbiology.

Westerdijk Fungal Genomics

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Our expertise in fungal genome sequencing and genome analyses provides support for:

  • Fungal genomic DNA extraction and Oxford Nanopore Technology de novo sequencing and genome assembly (including quality control).
  • Gene prediction and functional annotation of fungal genomes.
  • Tailored-made (comparative) genomic analyses (e.g. evaluation of the mycotoxigenic potential of fungal strains, phylogenomics, identification of genes of interest).
    For the analyses of fungal genomes, tell us your specific need as we can employ diverse tools to address different questions.

ICAT (Innovation Center for Advanced Therapies)

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1 Shared Innovation Lab:

Fully equipped lab space for spin-outs and startups developing therapeutics, diagnostics, advanced in-vitro models and medical devices. Located in the brand-new Plus Ultra building at Utrecht Science Park, the shared innovation lab is at the heart of Utrecht’s life sciences and health ecosystem.

Services:

A. Flexible monthly memberships

  • Tier 1: General Lab (Vortex, Centrifuges, Balances, Ovens, Fume-hoods, Syringe pumps, 3D-printers, Histology bundle, PCR, BF microscopes, magnetic stirrers, warm plates, waterbaths, pH meters, vacuum ovens, plate reader, fridges, freezers etc)
  • Tier 2: ML-1 Mammalian Cell Culture (Biosafety Cabinets, Incubators, Cell counters, Centrifuges, Balances, BF & Fluorescence microscope, waterbaths, dPCR etc)
  • Tier 3: ML-2 Mammalian Cell Culture (Biosafety Cabinets, Incubators, Cell counters, Centrifuges, Balances, BF & Fluorescence microscope, waterbaths)

B. Hourly rentals & daily rentals of high-end and specialized equipment:

  • BD FACs Lyric Flow Cytometer
  • Rheometer – TA Instruments
  • DMA 850 – TA Instruments
  • R-GEN 200 bioprinter – REGENHU
  • ExplorerOne bioprinter – Biomotion
  • Xell bioprinter – Xolo
  • Zeiss™ AxioImager M2 Microscope
  • Leica Stereo M205 Microscope
  • Freeze-dryer – Salm & Kipp
  • Histology Bundle – Adamas Slee
  • 3D printer – Bambu Lab FDM printer
  • Form 4B DLP 3D printer
  • LifeTec Bi-axial osteochondral platform
  • Biostat WAVE Bioreactor (Sartorius)
  • Scinus Cell Expansion System
  • Miltenyi Clinimacs Prodigy

2. GMP Simulation – Bridging the gap between preclinical research and GMP production of ATMPs

A. Consultation Services:

  • Specialist support in cell, viral vector and tissue engineering
  • Regulatory affairs for ATMPs
  • Health Economics
  • GMP compliance

B Contract Research on process & assay development and validation and stability studies

  • Process scale-up
  • Process & analytical assay development and validation
  • Stability studies

3. Cell Therapy Facility – State-of-the-art class B cleanrooms for GMP manufacturing of ATMPs in an academic setting

Centre for Sustainable Animal Stewardship

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At many levels, discussions evolve when it comes to living with animals. For example, management of wolves in the Netherlands, breeding on physical traits in dogs and the use of animals in laboratories for research. As many different interests and perspectives are involved, these discussions often reach an impasse. CenSAS provides a platform where stakeholders can discuss the underlying ethical and animal welfare questions, aiming to provide a base for finding solutions for the future.

Reaching coexistence requires a broad approach in which different parties and perspectives are essential. CenSAS addresses this through the following activities, explicitly taking the interests of animals into account.

Dialogue

CenSAS facilitates dialogue between citizens, people with lived experience, scientists, and professionals. By connecting local and scientific knowledge and encouraging conversation between people, CenSAS broadens and deepens discussions surrounding animal-related issues.

Research

CenSAS investigates issues related to animal welfare, human-animal relationships, and ethics. Greater knowledge and insight into underlying questions and problems help improve understanding of positions within public debates and support the search for responsible and sustainable ways of living together with animals.

Education

We work to link our projects to education and current research. Within our projects, we take advantage of the expertise available at Wageningen University and Research and Utrecht University, and we commission extra research in the fields of animal welfare, ethics, the relationship between humans and animals, and social aspects of these issues as necessary.

Consultation

Our objectives and methods place us at the centre of the interaction between parties and organisations that work with animals in the broadest sense. These include livestock farmers, animals protection organisations, animal-related commerce, and policy. CenSAS is open to provide substantive contributions in the fields of animal ethics, animal welfare, and human-animal relationships.

Single domain antibody services – QVQ

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QVQ is specialized in the discovery of tailor-made sdAbs. Our lead-discovery projects can be customized for affinity, epitope specificity, cross-species recognition, or functional activity. Although sdAbs are conventionally based on animals, QVQ is actively pursuing animal-free and computational approaches as well.

Services

Our services can be divided into four areas:

1. Single domain antibody discovery

  • Immunization of camelids including phage display library construction
  • Use of synthetic libraries to avoid immunization
  • Panning and screening using phage display of sdAb panels
  • Production and initial characterization of lead candidates
  • Upscaled production and custom labeling

All fee-for-service, no IP retained

2. Computational structural biology

  • Computer guided affinity maturation
  • VHH humanization using in house developed LLM
  • Optimization of VHH for developability and derisking
  • De novo design of VHH and minibinders

Performed on in house GPU workstation

3. Pharmacology services

  • Epitope binning services
  • Target engagement to verify target specificity
  • Cellular signalling assays
  • Off target screening

4. Off-the-shelf products

  • Single domain antibodies of QVQ or in-licensed from UU
  • C-direct tagged with free cysteine for directional coupling
  • Custom labeling services with dyes, biotin or chelators
  • Custom large scale production possible in e.coli, yeast or mammalian cells

UMC Utrecht Core Flow Facility

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The Core Flow Facility have several analyzers and sorters available for use. The main role of the CFF is to provide training and technical support to users. We also provide advice on designing multicolor experiments and analyzing data, and we can operate sorters on behalf of users. We are open to providing support from start to finish for research, clinical, and third-party applications.

Flow cytometry is a technology that rapidly analyzes single cells or particles as they flow past single or multiple lasers while suspended in a solution. Each particle is analyzed for visible light scatter and one or multiple fluorescence parameters.

Scinus Cell Expansion

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Scinus Cell Expansion provides access to expertise, technology and practical support for automated and scalable cell culture in the Osilaris bioreactor system. The facility is intended to help academic, clinical and industry partners develop, test and optimise cell expansion workflows in a controlled, single-use bioprocessing environment.

Core capabilities include:

  • Cell culture process development and feasibility studies in the Osilaris system
  • Support for adherent cell culture on microcarriers and suspension culture workflows
  • Practical guidance on culture bag selection, bioreactor operation and workflow setup
  • Support for iPSC and other advanced therapy / regenerative medicine-related cell culture applications
  • Training, demonstrations and protocol transfer support for users who want to evaluate or implement automated cell expansion using the Osilaris bioreactor.

Typical users include researchers and development teams working on stem cell biology, regenerative medicine, ATMP development, translational research and scalable in vitro cell culture models. The facility can support early feasibility work, process optimisation, training and collaborative development activities.

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i-HUB – Plus Ultra Utrecht

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Our 2,500 m² start-up floor is designed to fuel innovation. At Kadans, we understand that start-ups evolve rapidly. Designed to support the realisation of ideas, our concept Innovation HUB, or i-HUB for short, features fully-furnished labs and offices tailored to your needs. Whether you need a small, medium or large office, the i-HUB offers different sizes for both lab and office space.

Laboratory modules range from 40 m² up to 104 m². Office space in the i-HUB can be a single desk in the Co-Working Space, or a private office.

Designed to support the realisation of ideas, our concept of the Co-Working space features a fully-furnished office space tailored to your needs. Here, you have the opportunity to rent a single desk in a collaborative and cross-disciplinary environment.

Single desk in a shared, open office environment.

Explore the possibilities, join a thriving community of pioneers, and take your ideas to the next level.

Ask us about availability!

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Exposome-Maps

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Exposome Maps — Geospatial Environmental Exposure Platform

Exposome Maps is an open geospatial data platform developed by Utrecht University’s Institute for Risk Assessment Sciences (IRAS) through the Exposome-NL and EXPANSE programmes (Horizon 2020). It provides over 200 harmonised, geospatially resolved environmental exposure surfaces — collectively covering the full external exposome — that researchers can link directly to health data in epidemiological studies.

The platform organises exposures across four dimensions. The Physico-Chemical Environment (99 surfaces) includes air pollution (PM2.5, PM10, NO₂, ozone, black carbon), noise, pesticides, weather, night-time light, biodiversity, and electromagnetic fields. The Social Environment (70 surfaces) covers neighbourhood socioeconomic position, social capital, safety, mental health indicators, labour market conditions, and proximity to services. The Built Environment (28 surfaces) captures green, blue, and grey space — parks, waterways, and urban land use. The Food Environment (4 surfaces) characterises food access and a healthy food index.

Surfaces can be explored interactively through the Exposome Data Platform in map or catalogue view, with European and Netherlands coverage, selectable time periods, and full metadata for each surface. Surfaces not directly available through the platform can be requested via a structured data access procedure

Core Capabilities

  • 200+ harmonised geospatial exposure surfaces (Exposome Surfaces) ready for epidemiological linkage
  • Coverage across four exposome dimensions: Physico-Chemical (99 surfaces), Social (70), Built Environment (28), and Food Environment (4)
  • Interactive map and catalogue view via the Exposome Data Platform, with European and Netherlands-level visualisation
  • Data available at varying temporal and spatial resolutions with full provenance and source attribution

Unique Assets

  • Single harmonised inventory spanning air pollution, noise, pesticides, electromagnetic fields, biodiversity, night-time light, neighbourhood socioeconomic position, social capital, and more
  • Developed and validated within large-scale European cohort studies (EXPANSE, Exposome-NL)
  • Open data policy with structured access request procedure for surfaces not directly available on the platform
  • Interoperable with cohort and biobank data for multi-exposure mixture analyses

Typical Users

  • Epidemiologists linking external environmental exposures to health outcomes in population cohorts
  • Urban planners and policymakers assessing the health impact of the built and social environment
  • Data managers building or harmonising exposure datasets across European study sites
  • Researchers designing new cohort studies who need baseline exposure characterisation

Access

  • Freely accessible via exposome.uu.nl for visualisation
  • Data access for research use via structured request form; governed by Data Access and Publication Policy

Air View Mobile Platform

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The Air View Car — Mobile Urban Air Quality Monitoring

Utrecht University’s Institute for Risk Assessment Sciences (IRAS) operates two Air View Cars that map street-level air quality across European cities with laboratory-grade precision. Unlike fixed monitoring stations, which capture the temporal variation of air pollution, the cars can measure on many streets and generate millions of data points per campaign. This mobile approach produces high-resolution, street-by-street pollution maps that would be impossible to achieve with stationary infrastructure alone.

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Instrumentation

Each car carries a suite of complementary instruments covering the major dimensions of urban air pollution:

  • CAPS NO2 Monitor (Aerodyne)— uses Cavity Attenuated Phase Shift spectroscopy to measure nitrogen dioxide (NO₂) every second. Its fast response time is essential for mobile monitoring, where concentrations can change sharply within metres as the car passes junctions, loading bays, or heavily trafficked corridors.
  • EPC 3783 (TSI) — counts individual ultrafine particles down to approximately 3 nm in diameter. This instrument is central to the project’s focus on ultrafine dust, for which no European regulatory limits currently exist despite growing evidence of health impacts. The water-based design avoids the use of organic solvents, making it well suited to continuous field operation.
  • AE33 Aethalometer (Magee Scientific)— measures black carbon (soot) concentrations every second using optical light absorption across seven wavelengths. This multi-wavelength capability allows the instrument to distinguish between soot from fossil fuel combustion (predominantly traffic) and biomass burning, providing source attribution alongside concentration data.
  • DustTrak DRX (TSI)— measures fine particulate matter (PM2.5), the size fraction regulated under European air quality standards and most strongly associated with cardiovascular and respiratory disease in the epidemiological literature.
  • Partector Pro 2 (Naneos) — measures lung-deposited surface area (LDSA) and particle number size distribution, capturing how particles of different sizes are likely to deposit in the respiratory tract. This goes beyond simple particle counts to provide a health-relevant characterization of the aerosol.

From Data to Impact

Together, these instruments capture the full spectrum of urban air pollution. The data are processed by IRAS into actionable hyperlocal maps that municipalities, urban planners, public health services, and researchers use to design healthier cities: routing cycling and walking infrastructure away from pollution hotspots, positioning green buffers such as hedgerows near schools and playgrounds, and providing the exposure data needed for epidemiological studies linking air quality to mortality, cardiovascular disease, and neurodegenerative outcomes.

Core Capabilities

  • Street-level mapping of NO₂, black carbon, PM2.5, ultrafine particles, and lung-deposited surface area
  • Continuous street-by-street measurements, millions of data points per campaign
  • Source attribution: distinguishes traffic vs. biomass burning emissions

Unique Assets

  • Two fully equipped laboratory-grade mobile monitoring cars
  • Only mobile platform in the Netherlands measuring ultrafine particles (currently unregulated in Europe)
  • Integrated data pipeline from raw sensor output to validated hyperlocal city maps
  • Track record across 10+ European cities since 2019

Typical Users

  • Municipal health services and urban planners designing low-emission zones or green buffers
  • Epidemiologists linking hyperlocal exposure to health outcomes (mortality, cardiovascular, neurological)
  • Architects and area developers optimising building placement and public space
  • Researchers needing high-resolution exposure data for cohort studies

Access

  • Available for collaborative research projects across European cities
  • Data outputs include georeferenced pollution maps suitable for GIS integration and epidemiological linkage