Supply of freeze-dried biological material.

You can consult the catalogue of MIRRI microbial resources here.

Supply of actively growing cultures (agar plates or slopes or liquid media).

You can consult the catalogue of MIRRI microbial resources here.

Supply of frozen material.

You can consult the catalogue of MIRRI microbial resources here.

Supply of genomic DNA or plasmid DNA.

You can consult the catalogue of MIRRI microbial resources here.

Other delivery forms for the supply biological material (e.g., oil, water, etc.).

You can consult the catalogue of MIRRI microbial resources here.

Ready-to-use E.coli competent cell for bacterial transformation via heat shock or electroporation with a high transformation efficiency.

You can consult the catalogue of MIRRI microbial resources here.

Supply of inactivated and quantified cultures of microbial strains.

You can consult the catalogue of MIRRI microbial resources here,

Deposit of microbiological material that will be publicly available. Used, for example, for new species description

Deposit of microbiological material for patent purposes under the Budapest Treaty

Confidential and private deposit. Access to the microbiological material and associated data has to be authorized by the depositor

Identification based on the DNA sequence of molecular markers and comparison with curated sequence databases

Identification based on micro- and macroscopic examination combined with the study of different phenotypic and biochemical traits

Identification based on comparison of protein mass spectra generated from unknowns with mass spectra generated from well-characterised reference strains comprised in curated databases

Bioassays on test plants for visual evaluation of symptoms; analysis of morphological and molecular characteristics

Quantitative (qRT-PCR or IFA) or qualitative (PCR) detection and identification of viruses in biological products. Isolation of viruses using cell cultures. Viral genome characterisation (NGS)

The generated STR profile is compared to an appropriate reference sample. If available, DNA from the donor of the tested cell line is the best comparison. If donor DNA can no longer be accessed, the STR profile obtained for the sample is compared to all STR profiles available using an online database.

DNA amplification by PCR of the gene(s) of interest, followed by sequencing of the amplified fragments

DNA amplification by PCR with a single oligonucleotide that hybridizes randomly to the DNA under study, which generates a unique fingerprint of each isolate

DNA amplification by PCR of a fragment from a region of interest (fixed size), followed by separation of the fragments in a gel electrophoresis with an increasing denaturing gradient. This method can detect single base changes/mutations in environmental samples

DNA amplification by PCR of a conserved molecular marker followed by separation of the fragments in a denaturing acrylamide gel electrophoresis under a gradient of temperature. Used to study the microbial diversity of an environmental sample

Digestion of the genomic DNA with specific restriction enzymes followed by amplification by PCR, which generates a unique fingerprint of each isolate

DNA amplification by PCR of microsatellite regions, which generates a unique fingerprint of each isolate

DNA amplification by PCR of extragenic repetitive palindromic elements, which generates a unique fingerprint of each isolate

DNA amplification by PCR of sequences separating Long Terminal Repeats retrotransposons, which generates a unique fingerprint of each isolate

Digestion of the genomic DNA with specific restriction enzymes, which generates a unique fingerprint of each isolate

Digestion of the mitochondrial DNA with specific restriction enzymes, which generates a unique fingerprint of each isolate

DNA amplification by PCR of the 16S rDNA gene, followed by digestion with specific restriction enzymes, which generates a unique fingerprint of each isolate. Can be used to make phylogenetic studies of environmental samples by cloning the 16S rDNA genes of the sample

Digestion of the genomic DNA with specific restriction enzymes and hybridization with a ribosomal (rRNA) probe, to analyse the number and sequence diversity of the rRNA operons

Comparison of protein mass spectra generated from different isolates to cluster them

Separation of intact chromosomal DNAs

Quantification of the DNA content in single cells and histogram analysis to estimate the level of ploidy

Determination of the presence, size and copy number of plasmids

Detection of fatty acid methyl esters (FAME) by gas chromatography and analysis with specific software (e.g. Sherlock™ Microbial Identification System). Used to differentiate and to characterise isolates

Detection of cell wall polysaccharides using different chromatographic techniques

Structural analysis of peptidoglycan by hydrolysis and/or enzymatic digestion of whole-cell extracts coupled with separation of constituents by chromatography and detection by mass spectrometry

Extraction of the polar lipids (phospholipids, glycolipids, aminolipids) of the cell membrane, followed by chromatographic separation and detection, which provides a pattern of different lipidic compounds

Extraction of the mycolic acids, followed by HPLC separation and mass spectrometry detection. Can be used, for example, to rapidly differentiate Mycobacterium species from Nocardia or Rhodococcus species

Extraction and purification of the respiratory quinones, followed by HPLC analysis and quantification. Can be coupled with mass spectrometry to analyse complex mixtures. Provides an indication of the type of energy metabolism (aerobic vs anaerobic)

Immunoassays (e.g. ELISA, CL-IA, FIA, LF-IA) used to detect different antigens, including proteins, lipids, sugars, pesticides and other compounds in different types of samples even at low concentrations

High-resolution images of total microbial cells and their ultrathin sections by conventional electron microscopy. Elemental composition of individual cell

Characterisation of the strain based on a variety of assays targeting the metabolic and physiologic profile. The miniaturized systems (e.g. API, Biolog) can be used to tentatively identify the most relevant clinical and industrial microbial species

Cultivation of the strain to induce the production of the enzyme(s), followed by purification/concentration of the intra- or extra-cellular fraction and analysis using substrate-specific probes and/or proteomic approaches

Headspace sampling or metabolite extraction followed by gas chromatography coupled with mass spectrometry analysis/quantification of the volatile fraction

Detection of antioxidant activities on extracts using different reagents

Extraction and purification of the respiratory quinones, followed by HPLC analysis and quantification. Can be coupled with mass spectrometry to analyse complex mixtures. Provides an indication of the type of energy metabolism (aerobic vs anaerobic)

Optimisation of cultures for metabolite production (antimicrobials, pigments, b-glucans, fatty-acids, heterologous proteins expressed in fungi, organic acids, mycotoxins, etc.) and detection/analysis of the metabolite of interest

DNA extraction and next-Generation Sequencing to obtain the raw sequences of the isolate

Quality assessment, reads processing and scaffolding to obtain the draft/complete genome sequence

DNA extraction, PCR-amplification and next-Generation Sequencing

Quality assessment and reads processing

Obtention of the raw genomic sequences of the sample

Quality assessment and reads processing

Protein-coding gene prediction

Strain typing based on the raw sequences or the draft/complete genome sequence (e.g. single-nucleotide polymorphism (SNP) mapping, core genome multilocus sequence typing (cgMLST), G+C content, etc.)

Analysis of the presence of genes to predict phenotypic traits (serotype, antibiotic resistances, virulence factors, production of metabolites, enzymatic activities, etc.)

Pairwise comparison of the genomic sequence of a strain of interest with those of related type strain(s) for identification/classification at the genus/species level

Construction of phylogenetic trees based on reads or assembled sequences

Analysis of the taxonomic composition of an environmental sample or mixed community

Different computational analyses of the genomes on demand, e.g., co-assembly, gene calling, functional taxonomic profiling, recovering metagenome-assembled genomes (MAGs), phylogenomic comparison and profiling, pangenomics

Cultivation in specific media and conditions to separate isolates from mixed samples

Freeze-drying of microbial strains cultures or biological samples for long-term preservation or preparation of samples for further analysis

Customised optimisation of preservation conditions of microbial cultures maximising genetic stability and efficient recovery

Customised optimisation of cultivation and fermentation conditions of microbial cultures to enhance growth rates and productivity

Estimation of the number of cells/virus (total, viable, spores, mycorrhizal infective propagules etc.) present in a culture or sample

Qualitative or quantitative measurements of microbial growth in the presence of compounds or extracts

Test the resistance of a particular strain to different antibiotics

Test the effect of microorganisms, microbial extracts or other agents on the plant fitness infected with a particular pest

Test the effect of microorganisms, microbial extracts, soils or other agents on the plant growth/yield

Test the effect of microorganisms, microbial extracts or other agents on the viral fitness

Metabolomic analysis on multiwell plates using a UV/VIS fluorescence microplate reader

Viability estimation under different conditions measuring the absorbance of cultures stained with iodonitrotetrazolium violet on multiwell plates

Analysis of adhesive activities of strains stained with crystal violet on multiwell plates

Assessment of the productivity, robustness, harvesting characteristics and/or production of metabolites (bioproducts, bioactive substances, enzymes, etc.) of a strain culture

Analysis of the capacity of microbial strains to adhere to different surfaces

Analysis of the capacity of microbial strains to produce molecules with biosurfactant and emulsion activity

Cultivation protocols adapted to the test materials and products are used to evidence contaminating microorganisms

The resistance of diverse materials against microbial damage is analysed using growth tests and control strains

Assessment of the metabolic status of a microbial strain analysing the O2 consumption / CO2 production ratio

Quantification of absolute count of DNA or RNA using Droplet digital PCR

Phenotypic and genome mining based assessment of key traits recommended by the European Food Safety Agency (EFSA) (e.g., presence of virulence, bacteriocin and antimicrobial resistance genes; presence of elements involved in horizontal gene transfer; antimicrobial resistance assays)

Combination of microscopy and flow cytometry providing bright-field, dark-field (SSC), and several fluorescent images of each cell in flow, at high speed. It can be used for spatial localisation of biomolecules and cellular components, reporting signal intensity with very high sensitivity.

Separation of cell populations based on different features such as size and granularity (via light scattering) or fluorescence characteristics (fluorescence detector). Separated cells remain viable and can be cultured after the process

Extraction and purification of metabolites of interest

Genomic DNA extraction from a pure culture of the microorganism suited for subsequent analysis (e.g. PCR, WGS)

Conjugation of cells/spores by micromanipulation and analysis of the resulting zygotes (flow cytometry, electrophoretic karyotyping, marker analysis, stability, etc.)

Online database documenting new mycological names and combinations, eventually combined with descriptions and illustrations. MycoBank is one of three nomenclatural repositories recognized by the Nomenclature Committee for Fungi. You can access the database here.

Online tool for yeasts identification based on the analysis of the sequence of multiple marked genes (D1/D2 region, ITS, RPB2). You can access here.

Online database of fungal species hold in worldwide culture collections (mostly those registered in the World Data Center of Microorganisms, WDCM). You can access the database here.

Online tool for yeasts identification based on Restriction Fragments Length Polymorphism (RFLP) of the Intergenic Transcribed Region (includes the 5.8S rRNA gene and the ITS region). You can access here.

Web platform that hosts a collection of curated, open or private databases of genome sequences and genotypes based on multilocus sequence  typing (MLST), whole genome based typing and supplementary schemes. You can access here.

Identification of Klebsiella pneumoniae and K. oxytoca strains based on the raw data obtained from a MALDI-TOF mass spectrometer. You can access here.

Online tool for Cell Lines Molecular Authentication based on STR profiles from cell lines available at different collections (e.g. ATCC, JCRB, DSMZ, COG, ICLC). It allows to identify user's cell lines and to search known profiles by locus value or by cell line name. You can access here.

Variety of training courses related to several topics (isolation, cultivation, preservation, identification, characterisation and valorisation of microbiological material, plasmid DNA handling techniques, quality management and operation of culture collections, etc) and also tailored training courses adapted to the specific needs of the user. See more details here.

Research contracts with companies related to the use of microorganisms. Topics aligned with the MIRRI’s Strategic Research & Innovation Agenda. See more details here.

Clusters of expertise open forum or private consultancy about Legal/Regulatory issues & Standards; Applications in Biotechnology & Bioindustries; High-end technologies & platforms; Bioprospection, Cultivation & Preservation; Taxonomy; mBRC Quality Management. See more details here.