Microbiology
The Microbiology Facility provides state-of-the-art microbiological infrastructure, advanced technologies, and scientific expertise to support high-quality and reproducible research in microbiology and microbiome science.
The Facility has developed specialized expertise in high-throughput culturomics, integrating automated microbial isolation, advanced cultivation strategies, MALDI-TOF mass spectrometry, and sequencing-based approaches to enable comprehensive characterization of complex microbial communities.
By combining cultivation-dependent and cultivation-independent methodologies, the Facility provides a unique hybrid workflow that allows researchers to move beyond microbiome profiling and access viable microbial isolates for downstream functional characterization, including strain identification, antimicrobial susceptibility testing, host–microbe interaction studies, and mechanistic validation.
The Facility supports research projects focused on host–microbe interactions, cancer microbiome research, microbial ecology, antimicrobial resistance, microbial phenotyping, and translational microbiome studies. Standardized workflows, quality control procedures, and institutional biosafety standards ensure robust and reproducible experimental outcomes.
Access to the Facility is also available to external academic and industrial collaborators upon request. Researchers receive support throughout the experimental workflow, including experimental design, protocol optimization, microbial isolation and characterization, and interpretation of results.For information about available services or to discuss your project, please contact Alessandra De Giani.
Staff
Alessandra De Giani
Head of Microbiology Facility
Services
The Facility provides specialized microbiological infrastructure, technical expertise, and scientific support for a broad range of experimental applications, including:
- Cultivation of aerobic and anaerobic bacteria under standardized aseptic conditions
- High-throughput culturomics for the isolation and characterization of microorganisms from complex biological and environmental samples
- Isolation, purification, and maintenance of bacterial strains
- Antibiotic susceptibility testing
- Microbial growth and kinetic analyses
- Quantification of bacterial load by colony-forming unit (CFU) counting and integration with molecular approaches
- Cryopreservation and long-term biobanking of bacterial isolates
- Bacterial identification by MALDI-TOF mass spectrometry
- Integration of culture-based microbiology with 16S rRNA gene and shotgun metagenomic sequencing workflows
- Experimental design, protocol optimization, troubleshooting, and user training
High-Throughput Culturomics
The Facility has established dedicated expertise in high-throughput culturomics, enabling the large-scale recovery, identification, and preservation of microorganisms from complex microbial communities.
Our culturomics workflow integrates:
- Standardized cultivation under multiple growth conditions to maximize microbial recovery
- Rapid bacterial identification by MALDI-TOF mass spectrometry
- Molecular confirmation by targeted sequencing when required
- Cryopreservation and biobanking of bacterial isolates
- Integration with microbiome datasets generated by 16S rRNA gene sequencing and shotgun metagenomics
This hybrid workflow combines the strengths of classical microbiology with modern sequencing technologies, allowing researchers not only to profile microbial communities but also to recover viable isolates for downstream functional studies, host–microbe interaction experiments, antimicrobial susceptibility testing, and mechanistic validation.
MALDI-TOF Mass Spectrometry for Bacterial Identification
The Facility offers rapid, accurate, and cost-effective bacterial identification using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-TOF) mass spectrometry.
The platform provides:
- Rapid identification at the genus and species level of the bacterial isolates
- Direct analysis from isolated colonies with minimal sample preparation
- High-throughput processing using 96-spot target arrays, allowing the analysis of up to 48 bacterial isolates per run in duplicate for increased identification confidence
- Database matching through the Mabritec reference database (The world’s largest online MALDI-TOF MS database for bacterial species identification)
- Expert support for spectral interpretation and customized analytical workflows
Typical applications include:
- Identification of clinical, environmental, and research isolates
- Verification of strain identity and culture purity
- Quality control of bacterial collections
- Validation of culturomics workflows and microbiome projects
Equipment
The Facility provides access to dedicated microbiological instrumentation and advanced platforms supporting microbial isolation, cultivation, identification, and biobanking, including:
- Class II biological safety cabinets
- Aerobic and anaerobic incubators
- Personalized cryopreservation systems for long-term strain storage
- Isolation Bio Prospector® automated microbial isolation and cultivation platform for high-throughput recovery of bacterial isolates from complex microbial communities
- Shimadzu AXIMA MALDI-TOF mass spectrometer connected to the Mabritec reference database for rapid bacterial identification and strain characterization
Acknowledgement
Users are kindly requested to acknowledge the IOR Microbiology Facility in publications, presentations, and grant applications arising from work performed using the Facility's infrastructure, instrumentation, services, or scientific expertise. Co-authorship should be considered whenever Facility staff provide.
