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Supply of microbial resources
Supply of microbial resources
Supply of microbial resources in different delivery forms or physiological conditions. You can consult the catalogue of MIRRI microbial resources here
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Deposit
Deposit
The microbiological material to be deposited is cultivated and preserved following the depositor’s instructions or using optimised conditions when necessary.
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Identification
Identification from microbial pure cultures
Identification of microbial isolates up to the genus or species level. The service includes consultancy to define the most suitable method considering the taxonomic group of the strain of interest.
Virus detection and identification
Multiphasic approach to identify and diagnose viruses
Human cell line authentication
Short Tandem Repeat (STR) profiling to verify human cell line's identity and presence of cross-contamination from other cell lines
Molecular typing and phylogenetic analysis
Gene sequencing and analysis
Characterisation based on the DNA/RNA sequence of molecular markers (housekeeping, rRNA, virulence, drug-resistance genes, etc.). Analysis of several markers (Multi-Locus Sequence Analysis/Typing, MLSA/MLST) allowing strain typing
Genotyping
Strain typing based on differences in the DNA sequence of the isolates or environmental samples. Used, for example, for strain typing/differentiation, for phylogenetic analysis or to study the microbial diversity of environmental samples. The service includes consultancy to define the most suitable method considering the type of sample or the taxonomic group of the strain of interest
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Clustering of isolates by MALDI-TOF MS protein profiles
High-throughput dereplication screening using MALDI-TOF MS to group isolates that represent the same taxon. Used to reduce a large number of isolates to a smaller, non-redundant set for further characterisation
Karyotyping
Separation of intact chromosomal DNAs by pulsed field gel electrophoresis (PFGE) to type at inter- and intra-specific level
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Determination of ploidy
Estimation of the number of copies of single chromosomes using flow cytometry and specific fluorescent dyes targeting DNA
Plasmid profile analysis
Characterisation of a strain based on presence, size and copy number of its plasmids. Used to type bacterial isolates
Phenotypic characterisation
Structural analysis
Analysis of structural components of the cells (fatty-acids, cell wall sugars, polar lipids, mycolic acids, antigens)
Metabolic and physiologic analyses
Analysis of the strain metabolism (e.g. degradation/production of metabolites, detection of enzymatic activities, capability to grow under certain conditions)
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NGS related services
Draft/complete genome sequencing of a pure culture
High-throughput genomic sequencing of a strain including quality assessment, scaffolding and assembly to obtain the draft/complete genome sequence
Taxon-specific gene amplification and sequencing of environmental samples or mixed communities
Analysis of the biodiversity of a sample by amplifying and sequencing taxon-specific genes (e.g. 16S rRNA, ITS, etc.)
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Details
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Whole Metagenome Shotgun (WMS) sequencing
High-throughput genomic sequencing of environmental samples or mixed communities
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Details
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Advanced genome and metagenome analyses
Analysis of the genomic sequences to make a deep characterisation of the strain/sample (strain typing, genome mining, overall genome relatedness indexes, taxonomic composition, etc.)
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Microorganism isolation, preservation and cultivation
Isolation and purification of strains
Isolation of strains from environmental samples or mixed cultures to obtain pure cultures
Freeze-drying
Freeze-drying of microbial strains cultures or biological samples for long-term preservation or preparation of samples for further analysis
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Optimisation of preservation conditions
Customised optimisation of preservation conditions of microbial cultures maximizing genetic stability and efficient recovery
Optimisation of cultivation/fermentation
Customised optimisation of cultivation and fermentation conditions of microbial cultures to enhance growth rates and productivity
Microbial counting/titer
Estimation of the number of cells/virus (total, viable, spores, mycorrhizal infective propagules, etc.) present in a culture or sample
Screening, tests and bioassays
Growth promoting / antimicrobial / antiviral bioassays
Test the effect of different types of agents (e.g. compounds, extracts, soil, etc.) on the growth, replication or yield of a particular microbial strain, virus or plant
High-throughput screening
Variety of automated platforms to select strains that produce specific bioactive substances, metabolites or enzymes or to test the production of these compounds or the growth of a strain under different conditions
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Details
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Characterisation of technological abilities of microbial strains
A variety of tests to assess the capacity of microbial strains to be used in different industrial applications
Detection of contaminants in raw materials and products
Detection of the presence or absence of viable microorganisms in raw materials and products
Material resistance testing
Analysis of the capacity of microbial strains to grow on certain materials
Other services
Other characterisation analyses
Miscellaneous characterisation analyses, such as Mycovirus detection, assessment of the metabolic status of a culture, Plasmid copy number quantification, safety assessment of strains for food and feed and high-throughput and high-resolution visualization
Purification of cells/metabolites
Miscellaneous purification services such as separation of cell populations by flow cytometry or purification of metabolites from cultures
Complementary services
Miscellaneous complementary services such as DNA extraction or construction and characterisation of intraspecific hybrids
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Taxonomic database tools
Taxonomic database tools
Access to a series of database tools for Taxonomic information or analysis.
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Consultancy, training and contract research
Consultancy, training and contract research
Consultancy, training and contracted research on topics related with the expertise of MIRRI, such as isolation, cultivation, preservation, identification, characterisation and valorisation of microbiological material, including regulatory issues and quality standards
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Supply of microbial resources
Supply of microbial resources
Supply of microbial resources in different delivery forms or physiological conditions. You can consult the catalogue of MIRRI microbial resources here
Compare
Inquire
Details

Supply of freeze-dried biological material.

You can consult the catalogue of MIRRI microbial resources here.

Inquire
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Details

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

You can consult the catalogue of MIRRI microbial resources here.

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Details

Supply of frozen material.

You can consult the catalogue of MIRRI microbial resources here.

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Supply of genomic DNA or plasmid DNA.

You can consult the catalogue of MIRRI microbial resources here.

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

You can consult the catalogue of MIRRI microbial resources here.

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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.

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Supply of inactivated and quantified cultures of microbial strains.

You can consult the catalogue of MIRRI microbial resources here,

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Deposit
Deposit
The microbiological material to be deposited is cultivated and preserved following the depositor’s instructions or using optimised conditions when necessary.
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Details

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

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Deposit of microbiological material for patent purposes under the Budapest Treaty

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

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Identification
Identification from microbial pure cultures
Identification of microbial isolates up to the genus or species level. The service includes consultancy to define the most suitable method considering the taxonomic group of the strain of interest.
Compare
Inquire
Details

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

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Details

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

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

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Virus detection and identification
Multiphasic approach to identify and diagnose viruses
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Details

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

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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)

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Human cell line authentication
Short Tandem Repeat (STR) profiling to verify human cell line's identity and presence of cross-contamination from other cell lines
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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.

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Molecular typing and phylogenetic analysis
Gene sequencing and analysis
Characterisation based on the DNA/RNA sequence of molecular markers (housekeeping, rRNA, virulence, drug-resistance genes, etc.). Analysis of several markers (Multi-Locus Sequence Analysis/Typing, MLSA/MLST) allowing strain typing
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DNA amplification by PCR of the gene(s) of interest, followed by sequencing of the amplified fragments

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Genotyping
Strain typing based on differences in the DNA sequence of the isolates or environmental samples. Used, for example, for strain typing/differentiation, for phylogenetic analysis or to study the microbial diversity of environmental samples. The service includes consultancy to define the most suitable method considering the type of sample or the taxonomic group of the strain of interest
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DNA amplification by PCR with a single oligonucleotide that hybridizes randomly to the DNA under study, which generates a unique fingerprint of each isolate

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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

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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

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

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

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

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

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

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

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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

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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

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Clustering of isolates by MALDI-TOF MS protein profiles
High-throughput dereplication screening using MALDI-TOF MS to group isolates that represent the same taxon. Used to reduce a large number of isolates to a smaller, non-redundant set for further characterisation
Compare
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Details

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

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Karyotyping
Separation of intact chromosomal DNAs by pulsed field gel electrophoresis (PFGE) to type at inter- and intra-specific level
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Details

Separation of intact chromosomal DNAs

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Determination of ploidy
Estimation of the number of copies of single chromosomes using flow cytometry and specific fluorescent dyes targeting DNA
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Details

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

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Plasmid profile analysis
Characterisation of a strain based on presence, size and copy number of its plasmids. Used to type bacterial isolates
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Determination of the presence, size and copy number of plasmids

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Phenotypic characterisation
Structural analysis
Analysis of structural components of the cells (fatty-acids, cell wall sugars, polar lipids, mycolic acids, antigens)
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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

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Detection of cell wall polysaccharides using different chromatographic techniques

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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

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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

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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

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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)

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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

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

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Metabolic and physiologic analyses
Analysis of the strain metabolism (e.g. degradation/production of metabolites, detection of enzymatic activities, capability to grow under certain conditions)
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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

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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

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

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Detection of antioxidant activities on extracts using different reagents

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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)

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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

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NGS related services
Draft/complete genome sequencing of a pure culture
High-throughput genomic sequencing of a strain including quality assessment, scaffolding and assembly to obtain the draft/complete genome sequence
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DNA extraction and next-Generation Sequencing to obtain the raw sequences of the isolate

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

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Taxon-specific gene amplification and sequencing of environmental samples or mixed communities
Analysis of the biodiversity of a sample by amplifying and sequencing taxon-specific genes (e.g. 16S rRNA, ITS, etc.)
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DNA extraction, PCR-amplification and next-Generation Sequencing

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Quality assessment and reads processing

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Whole Metagenome Shotgun (WMS) sequencing
High-throughput genomic sequencing of environmental samples or mixed communities
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Obtention of the raw genomic sequences of the sample

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Quality assessment and reads processing

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Advanced genome and metagenome analyses
Analysis of the genomic sequences to make a deep characterisation of the strain/sample (strain typing, genome mining, overall genome relatedness indexes, taxonomic composition, etc.)
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Protein-coding gene prediction

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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.)

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

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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

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Construction of phylogenetic trees based on reads or assembled sequences

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

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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

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Microorganism isolation, preservation and cultivation
Isolation and purification of strains
Isolation of strains from environmental samples or mixed cultures to obtain pure cultures
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Cultivation in specific media and conditions to separate isolates from mixed samples

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

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

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

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

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

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

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Screening, tests and bioassays
Growth promoting / antimicrobial / antiviral bioassays
Test the effect of different types of agents (e.g. compounds, extracts, soil, etc.) on the growth, replication or yield of a particular microbial strain, virus or plant
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Qualitative or quantitative measurements of microbial growth in the presence of compounds or extracts

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Test the resistance of a particular strain to different antibiotics

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

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

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

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High-throughput screening
Variety of automated platforms to select strains that produce specific bioactive substances, metabolites or enzymes or to test the production of these compounds or the growth of a strain under different conditions
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Metabolomic analysis on multiwell plates using a UV/VIS fluorescence microplate reader

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

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

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Characterisation of technological abilities of microbial strains
A variety of tests to assess the capacity of microbial strains to be used in different industrial applications
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Assessment of the productivity, robustness, harvesting characteristics and/or production of metabolites (bioproducts, bioactive substances, enzymes, etc.) of a strain culture

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

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

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Detection of contaminants in raw materials and products
Detection of the presence or absence of viable microorganisms in raw materials and products
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Cultivation protocols adapted to the test materials and products are used to evidence contaminating microorganisms

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Material resistance testing
Analysis of the capacity of microbial strains to grow on certain materials
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The resistance of diverse materials against microbial damage is analysed using growth tests and control strains

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Other services
Other characterisation analyses
Miscellaneous characterisation analyses, such as Mycovirus detection, assessment of the metabolic status of a culture, Plasmid copy number quantification, safety assessment of strains for food and feed and high-throughput and high-resolution visualization
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Assessment of the metabolic status of a microbial strain analysing the O2 consumption / CO2 production ratio

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

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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)

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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.

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Purification of cells/metabolites
Miscellaneous purification services such as separation of cell populations by flow cytometry or purification of metabolites from cultures
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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

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Extraction and purification of metabolites of interest

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Complementary services
Miscellaneous complementary services such as DNA extraction or construction and characterisation of intraspecific hybrids
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Genomic DNA extraction from a pure culture of the microorganism suited for subsequent analysis (e.g. PCR, WGS)

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

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Taxonomic database tools
Taxonomic database tools
Access to a series of database tools for Taxonomic information or analysis.
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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.

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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.

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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.

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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.

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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.

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

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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.

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Consultancy, training and contract research
Consultancy, training and contract research
Consultancy, training and contracted research on topics related with the expertise of MIRRI, such as isolation, cultivation, preservation, identification, characterisation and valorisation of microbiological material, including regulatory issues and quality standards
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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.

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

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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.

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Supply of microbial resources
Supply of microbial resources
Supply of microbial resources in different delivery forms or physiological conditions. You can consult the catalogue of MIRRI microbial resources here
Compare
Inquire
Details
Supply of freeze-dried biological material. You can consult the catalogue of MIRRI microbial resources here.
Inquire
Compare
Inquire
Details
Supply of actively growing cultures (agar plates or slopes or liquid media). You can consult the catalogue of MIRRI microbial resources here.
Inquire
Compare
Inquire
Details
Supply of frozen material. You can consult the catalogue of MIRRI microbial resources here.
Inquire
Compare
Inquire
Details
Supply of genomic DNA or plasmid DNA. You can consult the catalogue of MIRRI microbial resources here.
Inquire
Compare
Inquire
Details
Other delivery forms for the supply biological material (e.g., oil, water, etc.). You can consult the catalogue of MIRRI microbial resources (Read More)
Inquire
Compare
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Details
Ready-to-use E.coli competent cell for bacterial transformation via heat shock or electroporation with a high transformation efficiency. You can (Read More)
Inquire
Compare
Inquire
Details
Supply of inactivated and quantified cultures of microbial strains. You can consult the catalogue of MIRRI microbial resources here,
Inquire
Deposit
Deposit
The microbiological material to be deposited is cultivated and preserved following the depositor’s instructions or using optimised conditions when necessary.
Compare
Inquire
Details
Deposit of microbiological material that will be publicly available. Used, for example, for new species description
Inquire
Compare
Inquire
Details
Deposit of microbiological material for patent purposes under the Budapest Treaty
Inquire
Compare
Inquire
Details
Confidential and private deposit. Access to the microbiological material and associated data has to be authorized by the depositor
Inquire
Identification
Identification from microbial pure cultures
Identification of microbial isolates up to the genus or species level. The service includes consultancy to define the most suitable method considering the taxonomic group of the strain of interest.
Compare
Inquire
Details
Identification based on the DNA sequence of molecular markers and comparison with curated sequence databases
Inquire
Compare
Inquire
Details
Identification based on micro- and macroscopic examination combined with the study of different phenotypic and biochemical traits
Inquire
Compare
Inquire
Details
Identification based on comparison of protein mass spectra generated from unknowns with mass spectra generated from well-characterised reference (Read More)
Inquire
Virus detection and identification
Multiphasic approach to identify and diagnose viruses
Compare
Inquire
Details
Bioassays on test plants for visual evaluation of symptoms; analysis of morphological and molecular characteristics
Inquire
Compare
Inquire
Details
Quantitative (qRT-PCR or IFA) or qualitative (PCR) detection and identification of viruses in biological products. Isolation of viruses using cell (Read More)
Inquire
Human cell line authentication
Short Tandem Repeat (STR) profiling to verify human cell line's identity and presence of cross-contamination from other cell lines
Compare
Inquire
Details
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 (Read More)
Inquire
Molecular typing and phylogenetic analysis
Gene sequencing and analysis
Characterisation based on the DNA/RNA sequence of molecular markers (housekeeping, rRNA, virulence, drug-resistance genes, etc.). Analysis of several markers (Multi-Locus Sequence Analysis/Typing, MLSA/MLST) allowing strain typing
Compare
Inquire
Details
DNA amplification by PCR of the gene(s) of interest, followed by sequencing of the amplified fragments
Inquire
Genotyping
Strain typing based on differences in the DNA sequence of the isolates or environmental samples. Used, for example, for strain typing/differentiation, for phylogenetic analysis or to study the microbial diversity of environmental samples. The service includes consultancy to define the most suitable method considering the type of sample or the taxonomic group of the strain of interest
Compare
Inquire
Details
DNA amplification by PCR with a single oligonucleotide that hybridizes randomly to the DNA under study, which generates a unique fingerprint of each (Read More)
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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 (Read More)
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DNA amplification by PCR of a conserved molecular marker followed by separation of the fragments in a denaturing acrylamide gel electrophoresis (Read More)
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Digestion of the genomic DNA with specific restriction enzymes followed by amplification by PCR, which generates a unique fingerprint of each (Read More)
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DNA amplification by PCR of microsatellite regions, which generates a unique fingerprint of each isolate
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DNA amplification by PCR of extragenic repetitive palindromic elements, which generates a unique fingerprint of each isolate
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DNA amplification by PCR of sequences separating Long Terminal Repeats retrotransposons, which generates a unique fingerprint of each isolate
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Digestion of the genomic DNA with specific restriction enzymes, which generates a unique fingerprint of each isolate
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Digestion of the mitochondrial DNA with specific restriction enzymes, which generates a unique fingerprint of each isolate
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DNA amplification by PCR of the 16S rDNA gene, followed by digestion with specific restriction enzymes, which generates a unique fingerprint of each (Read More)
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Digestion of the genomic DNA with specific restriction enzymes and hybridization with a ribosomal (rRNA) probe, to analyse the number and sequence (Read More)
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Clustering of isolates by MALDI-TOF MS protein profiles
High-throughput dereplication screening using MALDI-TOF MS to group isolates that represent the same taxon. Used to reduce a large number of isolates to a smaller, non-redundant set for further characterisation
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Comparison of protein mass spectra generated from different isolates to cluster them
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Karyotyping
Separation of intact chromosomal DNAs by pulsed field gel electrophoresis (PFGE) to type at inter- and intra-specific level
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Separation of intact chromosomal DNAs
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Determination of ploidy
Estimation of the number of copies of single chromosomes using flow cytometry and specific fluorescent dyes targeting DNA
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Quantification of the DNA content in single cells and histogram analysis to estimate the level of ploidy
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Plasmid profile analysis
Characterisation of a strain based on presence, size and copy number of its plasmids. Used to type bacterial isolates
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Determination of the presence, size and copy number of plasmids
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Phenotypic characterisation
Structural analysis
Analysis of structural components of the cells (fatty-acids, cell wall sugars, polar lipids, mycolic acids, antigens)
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Detection of fatty acid methyl esters (FAME) by gas chromatography and analysis with specific software (e.g. Sherlock™ Microbial Identification (Read More)
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Detection of cell wall polysaccharides using different chromatographic techniques
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Structural analysis of peptidoglycan by hydrolysis and/or enzymatic digestion of whole-cell extracts coupled with separation of constituents by (Read More)
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Extraction of the polar lipids (phospholipids, glycolipids, aminolipids) of the cell membrane, followed by chromatographic separation and detection, (Read More)
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Extraction of the mycolic acids, followed by HPLC separation and mass spectrometry detection. Can be used, for example, to rapidly differentiate (Read More)
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Extraction and purification of the respiratory quinones, followed by HPLC analysis and quantification. Can be coupled with mass spectrometry to (Read More)
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Immunoassays (e.g. ELISA, CL-IA, FIA, LF-IA) used to detect different antigens, including proteins, lipids, sugars, pesticides and other compounds (Read More)
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High-resolution images of total microbial cells and their ultrathin sections by conventional electron microscopy. Elemental composition of (Read More)
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Metabolic and physiologic analyses
Analysis of the strain metabolism (e.g. degradation/production of metabolites, detection of enzymatic activities, capability to grow under certain conditions)
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Characterisation of the strain based on a variety of assays targeting the metabolic and physiologic profile. The miniaturized systems (e.g. API, (Read More)
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Cultivation of the strain to induce the production of the enzyme(s), followed by purification/concentration of the intra- or extra-cellular fraction (Read More)
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Headspace sampling or metabolite extraction followed by gas chromatography coupled with mass spectrometry analysis/quantification of the volatile (Read More)
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Detection of antioxidant activities on extracts using different reagents
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Extraction and purification of the respiratory quinones, followed by HPLC analysis and quantification. Can be coupled with mass spectrometry to (Read More)
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Optimisation of cultures for metabolite production (antimicrobials, pigments, b-glucans, fatty-acids, heterologous proteins expressed in fungi, (Read More)
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NGS related services
Draft/complete genome sequencing of a pure culture
High-throughput genomic sequencing of a strain including quality assessment, scaffolding and assembly to obtain the draft/complete genome sequence
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DNA extraction and next-Generation Sequencing to obtain the raw sequences of the isolate
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Quality assessment, reads processing and scaffolding to obtain the draft/complete genome sequence
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Taxon-specific gene amplification and sequencing of environmental samples or mixed communities
Analysis of the biodiversity of a sample by amplifying and sequencing taxon-specific genes (e.g. 16S rRNA, ITS, etc.)
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DNA extraction, PCR-amplification and next-Generation Sequencing
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Whole Metagenome Shotgun (WMS) sequencing
High-throughput genomic sequencing of environmental samples or mixed communities
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Obtention of the raw genomic sequences of the sample
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Advanced genome and metagenome analyses
Analysis of the genomic sequences to make a deep characterisation of the strain/sample (strain typing, genome mining, overall genome relatedness indexes, taxonomic composition, etc.)
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Protein-coding gene prediction
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Strain typing based on the raw sequences or the draft/complete genome sequence (e.g. single-nucleotide polymorphism (SNP) mapping, core genome (Read More)
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Analysis of the presence of genes to predict phenotypic traits (serotype, antibiotic resistances, virulence factors, production of metabolites, (Read More)
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Pairwise comparison of the genomic sequence of a strain of interest with those of related type strain(s) for identification/classification at the (Read More)
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Construction of phylogenetic trees based on reads or assembled sequences
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Analysis of the taxonomic composition of an environmental sample or mixed community
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Different computational analyses of the genomes on demand, e.g., co-assembly, gene calling, functional taxonomic profiling, recovering (Read More)
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Microorganism isolation, preservation and cultivation
Isolation and purification of strains
Isolation of strains from environmental samples or mixed cultures to obtain pure cultures
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Cultivation in specific media and conditions to separate isolates from mixed samples
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Freeze-drying
Freeze-drying of microbial strains cultures or biological samples for long-term preservation or preparation of samples for further analysis
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Freeze-drying of microbial strains cultures or biological samples for long-term preservation or preparation of samples for further analysis
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Optimisation of preservation conditions
Customised optimisation of preservation conditions of microbial cultures maximizing genetic stability and efficient recovery
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Customised optimisation of preservation conditions of microbial cultures maximising genetic stability and efficient recovery
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Optimisation of cultivation/fermentation
Customised optimisation of cultivation and fermentation conditions of microbial cultures to enhance growth rates and productivity
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Customised optimisation of cultivation and fermentation conditions of microbial cultures to enhance growth rates and productivity
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Microbial counting/titer
Estimation of the number of cells/virus (total, viable, spores, mycorrhizal infective propagules, etc.) present in a culture or sample
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Estimation of the number of cells/virus (total, viable, spores, mycorrhizal infective propagules etc.) present in a culture or sample
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Screening, tests and bioassays
Growth promoting / antimicrobial / antiviral bioassays
Test the effect of different types of agents (e.g. compounds, extracts, soil, etc.) on the growth, replication or yield of a particular microbial strain, virus or plant
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Qualitative or quantitative measurements of microbial growth in the presence of compounds or extracts
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Test the resistance of a particular strain to different antibiotics
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Test the effect of microorganisms, microbial extracts or other agents on the plant fitness infected with a particular pest
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Test the effect of microorganisms, microbial extracts, soils or other agents on the plant growth/yield
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Test the effect of microorganisms, microbial extracts or other agents on the viral fitness
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High-throughput screening
Variety of automated platforms to select strains that produce specific bioactive substances, metabolites or enzymes or to test the production of these compounds or the growth of a strain under different conditions
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Metabolomic analysis on multiwell plates using a UV/VIS fluorescence microplate reader
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Viability estimation under different conditions measuring the absorbance of cultures stained with iodonitrotetrazolium violet on multiwell plates
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Analysis of adhesive activities of strains stained with crystal violet on multiwell plates
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Characterisation of technological abilities of microbial strains
A variety of tests to assess the capacity of microbial strains to be used in different industrial applications
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Assessment of the productivity, robustness, harvesting characteristics and/or production of metabolites (bioproducts, bioactive substances, enzymes, (Read More)
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Analysis of the capacity of microbial strains to adhere to different surfaces
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Analysis of the capacity of microbial strains to produce molecules with biosurfactant and emulsion activity
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Detection of contaminants in raw materials and products
Detection of the presence or absence of viable microorganisms in raw materials and products
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Cultivation protocols adapted to the test materials and products are used to evidence contaminating microorganisms
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Material resistance testing
Analysis of the capacity of microbial strains to grow on certain materials
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The resistance of diverse materials against microbial damage is analysed using growth tests and control strains
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Other services
Other characterisation analyses
Miscellaneous characterisation analyses, such as Mycovirus detection, assessment of the metabolic status of a culture, Plasmid copy number quantification, safety assessment of strains for food and feed and high-throughput and high-resolution visualization
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Assessment of the metabolic status of a microbial strain analysing the O2 consumption / CO2 production ratio
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Quantification of absolute count of DNA or RNA using Droplet digital PCR
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Phenotypic and genome mining based assessment of key traits recommended by the European Food Safety Agency (EFSA) (e.g., presence of virulence, (Read More)
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Combination of microscopy and flow cytometry providing bright-field, dark-field (SSC), and several fluorescent images of each cell in flow, at high (Read More)
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Purification of cells/metabolites
Miscellaneous purification services such as separation of cell populations by flow cytometry or purification of metabolites from cultures
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Separation of cell populations based on different features such as size and granularity (via light scattering) or fluorescence characteristics (Read More)
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Extraction and purification of metabolites of interest
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Complementary services
Miscellaneous complementary services such as DNA extraction or construction and characterisation of intraspecific hybrids
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Genomic DNA extraction from a pure culture of the microorganism suited for subsequent analysis (e.g. PCR, WGS)
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Conjugation of cells/spores by micromanipulation and analysis of the resulting zygotes (flow cytometry, electrophoretic karyotyping, marker (Read More)
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Taxonomic database tools
Taxonomic database tools
Access to a series of database tools for Taxonomic information or analysis.
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Online database documenting new mycological names and combinations, eventually combined with descriptions and illustrations. MycoBank is one of (Read More)
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Online tool for yeasts identification based on the analysis of the sequence of multiple marked genes (D1/D2 region, ITS, RPB2). You can access (Read More)
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Online database of fungal species hold in worldwide culture collections (mostly those registered in the World Data Center of Microorganisms, WDCM). (Read More)
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Online tool for yeasts identification based on Restriction Fragments Length Polymorphism (RFLP) of the Intergenic Transcribed Region (includes the (Read More)
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Web platform that hosts a collection of curated, open or private databases of genome sequences and genotypes based on multilocus sequence  (Read More)
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Identification of Klebsiella pneumoniae and K. oxytoca strains based on the raw data obtained from a MALDI-TOF mass spectrometer. You can access (Read More)
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Online tool for Cell Lines Molecular Authentication based on STR profiles from cell lines available at different collections (e.g. ATCC, JCRB, DSMZ, (Read More)
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Consultancy, training and contract research
Consultancy, training and contract research
Consultancy, training and contracted research on topics related with the expertise of MIRRI, such as isolation, cultivation, preservation, identification, characterisation and valorisation of microbiological material, including regulatory issues and quality standards
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Variety of training courses related to several topics (isolation, cultivation, preservation, identification, characterisation and valorisation of (Read More)
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Research contracts with companies related to the use of microorganisms. Topics aligned with the MIRRI’s Strategic Research & Innovation (Read More)
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Clusters of expertise open forum or private consultancy about Legal/Regulatory issues & Standards; Applications in Biotechnology & (Read More)
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