Reference: Roberto Gobetto, Angelo Gallo 

The NMR group of the Department of Chemistry of the University of Turin offers NMR analysis of biological fluids and cell culture with the aid of chemometric analysis [acquisition and analysis of 1D and 2D NMR spectra and chemometric tools]. Results are usually available in 6-8 weeks. Upon request, protein structure determination and its respective interaction sites with specific effectors [acquisition and analysis of multidimensional NMR spectra and computational tools for structure determination] are provided. See also  https://www.nmr.unito.it/

Reference: Marco Vincenti, Matteo Chiarello 

The use of the HPLC technique, coupled with high-resolution mass spectrometry technology such as an orbitrap instrument, is one of the main ways to investigate the metabolic profile and organic compound production of microorganisms. Metabolomics studies allow the discovery of new molecules of medical or industrial interest, the identification of microorganisms and the evaluation of the best environmental growth conditions to obtain better performing microbial productions. Here at UNITO, we can provide excellent support for metabolomics studies using this robust HPLC-MS based methodology.

Reference: Elena Gonella

A service of in vivo tests is offered using insect survival assays after delivery of bacterial /yeast strains or microbial products (proteins, lipids, chemical compounds, etc.). The model insect species to be used in tests will be agreed according to the requested target. Upon request, specific assays can be performed on insect cell lines. Results are usually available after 3/6 months, depending on the considered target species.

Reference: Valeria Prigione

The TUCC-UNITO Collection offers a service of isolation and identification of fungal strains from a variety of biotic and abiotic substrates. Identification is made through a polyphasic approach which combines molecular, morpho-physiological and phylogenetic analyses. Results are usually available after 2 weeks. Different culturomic techniques can be applied: dilution plate, direct isolation, enrichment, etc.

Reference: Valentina Alessandria, Davide Buzzanca

The bacterial isolates require molecular and phenotypic analyses for precise identification and description of their characteristics such as antibiotic resistance. This encompasses PCR analysis for isolate genotyping and whole genome sequencing (WGS) for taxonomy identification and detection of sequences associated with virulence, pathways, and antibiotic resistance. In the field of antibiotic resistance, our team study antibiotic resistance across various species, employing European Committee on Antimicrobial Susceptibility Testing (EUCAST) procedures. Additionally, we have experience conducting in vitro tests assessing bacterial colonization (adhesion/invasion) on human gut cell lines.

Reference: Davide Spadaro

The Laboratory of Plant Pathology, at Department of Agricultural, Forest and Food Sciences (DISAFA), University of Torino, offers a service of isolation of fungi and bacteria from plant and soil materials, and identification in pure culture with a polyphasic approach that couples molecular, morpho-physiological and metagenomic analyses. Results are usually available after 6/8 weeks. If requested, a further bioinformatic analysis of the sequenced samples can be performed. 

Reference: Alessandra Salvioli, Marco Giovannetti, Valentina Fiorilli, Andrea Genre

The team at the University of Turin – DBioS-BIO01 has a long tradition of research on the biology of symbiotic associations between plants and microorganisms, with particular attention to mycorrhizal fungi which are a crucial component of the plant microbiota in different environments, both natural and anthropogenic. The group also has profound experience in the study of both fungal and bacterial microbial populations that associate with the roots of cultivated plants. The DBioS-BIO01 can translate its scientific expertise into the following services:

• Detection of mycorrhizal fungi in formulated inocula or prototypes; assessment of the fungal viability via mycorrhization tests;
• Assessment of the mycorrhization with morphological techniques from user-provided plants/root samples via molecular and morphological approaches;
• Metabarcoding of mycorrhizal fungal communities from soil or root samples. Identification of mycorrhizal fungi on plant root samples: taxon specific metabarcoding and preliminary bioinformatic analyses (ASV table, diversity indexes);
• Consulting and access to the platform for fluorescence and confocal imaging.

Reference: Ilario Ferrocino

Based on a consolidated expertise in the field of foods, biological and environmental samples, we can offer the analytical platform to characterize the microbiome. After nucleic acid extraction we can offer: target analysis for microbial characterization (based on marker genes e.g. 16S rRNA, ITS, 26S) or untargeted (Whole genome shotgun sequencing) for functional characterization. Bioinformatic and biostatistical tools will be also available.

Reference: Luisa Rubino

The UO03 has a long-standing expertise in plant virology, with special reference to positive strand RNA viruses and to viroids infecting grapevine and fruit trees. Specifically, CNR-IPSP_BA can provide:

• virus isolation from woody and herbaceous hosts;
• biological characterization of virus isolates: mechanical transmission, grafting, vector transmission;
• electron microscopy: observation of leaf dips and purified virus particles, cytopathology of infected tissues, immunoelectron microscopy, intracellular localization of virus replication complexes;
• extraction and molecular analysis of virus nucleic acids and proteins;
• diagnosis: serological detection, production of specific antisera, molecular hybridization, development of RNA and DNA probes and polyprobes for the detection of viruses and viroids, singly or in combination, PCR, qRT-PCR;
• “omics” technologies: high-throughput sequencing, genomics, metagenomics, transcriptomics, degradome analysis, bioinformatics;
• reverse genetics approaches for functional and structural studies of viruses and viroids: preparation of infectious clones, synthesis of biologically active transcripts from full-length cloned genome sequences of viruses and viroids, mutagenesis;
• biotechnology: functional studies of viral products through constitutive and transient expression of viral proteins in plant and yeast cells, agroinfiltration;
• fluorescence microscopy: expression and localization of viral proteins fused to the green fluorescence protein (GFP) in plant and yeast cells, immunofluorescence microscopy;
• virus taxonomy: classification of viruses and viroids;
• pest categorization of economically important viruses not present or with a restricted presence in the EU on behalf of the European Food Safety Agency.

Reference: Giancarlo Perrone, Donato Magistà

Aspergillus, Penicillium and Talaromyces are diverse, phenotypically polythetic genera encompassing species important to the environment, economy, biotechnology and medicine, causing significant social impacts. Taxonomic studies on these fungi are essential since they could provide invaluable information on their evolutionary relationships and define criteria for species recognition. These include the traditional morphological/phenotypic approach, the supplementary lipidomic, proteomic and metabolomic approaches, as well as the currently widely used phylogenetic/consolidated approach.

At ISPA-CNR we can provide valuable support for the identification and classification of these fungal genera by implementing the classical morphological (macro and micro) and ecological methods (growth on different substrate) with the phylogenetics tools using various approach like GCPSR methods by using different calculation methods for the ML and MP tree (IQ-Tree, RAxML, Bayesian).

Reference: Massimo Ferrara

High-throughput sequencing technologies coupled with Metagenomics have revolutionized the field of microbial ecology. ISPA-CNR can provide valuable support for the taxonomical and functional analysis of complex microbial community through targeted (metabarcoding) and untargeted (shotgun) approach.

Reference: Giancarlo Perrone, Massimo Ferrara 

Microbiome science represents a paradigm shift in the scientific approach from preservation of axenic samples in culture collections towards preservation of complex microbial communities. At ISPA-CNR we can provide valuable support for long term preservation of microbial consortia from fermented-food and evaluation of taxonomical and functional integrity after storing period.

Reference: Massimo Ferrara 

Microbial genomic approaches have become regular in understanding the role of functional microbial diversity. The study of the gene structure, function and their regulation in response to external stimuli and different matrices has become a fundamental aspect in microbial ecology studies. ISPA-CNR can provide valuable support for the characterization of microbial species (including bacteria, yeast and filamentous fungi) by integrating genomics, transcriptomics and bioinformatics.

Reference: Francesca Valerio, Mariaelena Di Biase

The predictive microbiology, based on mathematical approaches, studies the behavior of microorganisms in foods with the final aim of improving food quality and safety. Several microbial databases, model repositories and decision tools (as Symprevius and ComBase) have been created from microbial data sets, relevant to growth and inactivation kinetic data. Here in Bari, the growth kinetics of bacterial strains of interest, as spoilage or starter of fermentation, can be determined and used to implement microbial database of predictive tools.

Reference: Francesca Valerio, Mariaelena Di Biase 

Food matrices represent a rich source of beneficial microorganisms including the ubiquitous group of lactic acid bacteria (LAB). These microorganisms have several functions in food processing and in particular they are involved in fermentation through conversion of food components into valuable molecules with health and technological features. Here in Bari, bacterial strains can be isolated and characterized for pro-technological properties as proteolytic activity, organic acid, amino acid, protein and exopolysaccharide production, as well as other features for selecting potential candidates as starters in food fermentation.

Reference: Biancamaria Ciasca, Veronica Lattanzio 

Liquid chromatography coupled with high-resolution mass spectrometry (LC-HRMS) represents the most powerful metabolomics platform for studying biological systems. Targeted and untargeted metabolomic approaches have been applied in several research fields, including microorganism classification and identification, the study of metabolic pathways, the discovery of natural products or the investigation of host-pathogen interactions. To obtain reproducible and reliable results, the validation and harmonisation of untargeted approaches is crucial. To date, there is no standardized methods for quenching and metabolite extraction, data processing is complicated and automatic data processing platform is imperfect, in addition microorganism-specific databases are incomplete or unavailable. ISPA-CNR can provide valuable support for metabolomic studies through the development of targeted and non-targeted metabolomic approaches, the application of validation procedures and the integration of open-source tools for data processing and interpretation.

Reference: Vincenzo Lippolis, Salvatore Cervellieri, Annalisa De Girolamo 

High performance liquid chromatography (HPLC) alone and in combination with low- and high-resolution mass spectrometry (LC-MS) represent the most useful approaches for the identification and quantification of fungal secondary metabolites as native and/or modified forms. Moreover, headspace solid-phase microextraction and gas chromatography in combination with mass spectrometry (HS-SPME/GC-MS) has been widely used for identification and characterization of volatile organic compounds (VOCs) related to fungal contaminations. Furthermore, VOCs can be used as markers for early detection of food spoilage, fungal growth and for distinguishing between toxigenic and non-toxigenic strains. ISPA-CNR can provide valuable support for the development and validation of targeted and non-targeted methods for the determination of fungal metabolites and VOCs in both fungal culture and agro-food products.

Reference: Antonia Susca, Alessandra Villani, Antonio Moretti 

Accurate species-level identification of an etiological agent is crucial for disease diagnosis and management because knowing the agent’s identity connects it with what is known about its host range, geographic distribution, and toxin production potential.

This CNR-ISPA expertise can provide valuable support for taxonomical identification of fungi belonging to Fusarium, Alternaria, Penicillium and Aspergillus, through analyses of morphological and phenotypical characters, DNA sequencing with Sanger approach, and the analysis of whole genomes. Data generated with those approaches can be also exploited for multiple additional purposes, like: studies of population of fungi, linking genetic changes in small genomic regions to phenotype (e.g. mycotoxin production, phytopathogenicity); Genotyping of microsatellite markers; building DNA-based phylogeny to reconstruct evolution of species, especially closely related; describe new fungal species; validating results from next-generation sequencing (NGS) studies, develop DNA based assay for the detection of toxigenic fungal species in crops and food.

Reference: Alessandra Villani, Antonia Susca, Antonio Moretti

Understanding the relationships between fungal genome sequences and phenotypes and studying their evolution across species can provide valuable insights into the mechanisms driving biological diversity and diseases. CNR-ISPA expertise can provide a powerful support for addressing these questions by using phylogenetics and phylogenomics, comparative genomics tools for understanding how genomes evolve and the functional implications of genetic changes, molecular evolution tools for exploring how genes and proteins evolve at the molecular level, and genome annotation for properly identifying genes and understanding their functions.

Reference: Cristiana Sbrana 

At OU05, arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM) fungi can be isolated from soil samples or from plant roots. The obtained fungal isolates, cultured in vivo (AM) or in vitro (ECM) are identified by molecular phylogenetic analysis, after DNA extraction and sequencing of informative markers (e.g. nuclear DNA ribosomal or ITS regions) and search of sequence matching by Basic Local Alignment Search Tool (BLAST) against the available databases (NCBI, MaarjAM, SILVA). In our lab the isolates can be also characterized for their functional traits, namely host compatibility, colonization ability and efficacy in sustaining host nutrition, growth and health.

Reference: Marianna Carbone, Maria Letizia Ciavatta  

Natural products, ranging from few tens to more than 2000 Da in molecular weight, are produced by all living species including microorganisms. In microbial world, small molecules represent a niche of utmost importance with diverse functions and biological activities. Based on a consolidated expertise in the field of natural products we can offer a reproducible analytical platform to chemically characterize secondary metabolite content of microbial cultures. Extracts, prepared using different solvents, will be subjected to subsequent liquid-liquid fractionations and/or to solid phase extraction steps to get fractions that will be analyzed by hyphenated mass spectrometric (GC-MS and LC-MS) and NMR methods. Updated dereplication methods will provide fast identification of known metabolites present in the extracts and highlight the presence of new chemical entities. Pure metabolites will be obtained by using chromatographic techniques including HPLC.

Reference: Giuliana d’Ippolito

Lipids (e.g glycerolipids, fatty acids) mediate many biological processes, playing key roles in the survival of the producing organisms and determinant interactions within their environment. Their regulation can explain variations in cell structure, energy storage mechanisms and photosynthetic efficiency. Here at CNR-ICB, analysis, isolation and structural elucidation of lipids is performed by NMR, LCMS and GCMS, obtaining detailed information of cell lipid coverage.

Reference: Annarita Poli, Ida Romano, Ilaria Finore, Luigi Leone 

Extremophiles cultivation implies the capability to grow the microorganisms in extreme condition in terms of temperatures, pH values, high salt concentration, absence of oxygen, etc. We are specialized in fermentation of Extremophilic microorganisms including psychrophiles, thermophiles, halophiles, alkalophiles and anaerobic bacteria, with the possibility to scale up the processes starting from 0.5 up to 50 liters in controlled fermenters system by batch, fed batch or continuous models, in order to obtain microbial cells.

Reference: Giuseppina Tommonaro, Gennaro Roberto Abbamondi

Unlock the hidden language of bacteria. We specialize in screening and chemically characterizing signal molecules involved in Quorum Sensing mechanisms, with a particular focus on N-Acyl homoserine lactones (AHLs). Our state-of-the-art approach involves preliminary screenings using specific assays based on bacterial bioreporters (including TLC overlay, T-Streak, and Lux screen), to detect AHLs and other signal molecules. Subsequently, we utilize spectroscopic methods such as NMR and LC-MS to chemically identify these molecules. This service empowers researchers and organizations to gain a deeper understanding of microbial communication and regulation, contributing to the ultimate metabolic mapping of the microorganisms under study.

Reference: Laura Miozzi, Marco Forgia 

The detection of viral pathogens infecting a given plant sample, obtained through high-throughput sequencing (HTS) followed by appropriate bioinformatics analyses, allows to verify the phytosanitary status of plants and is particularly useful for the identification of viruses involved in diseases with unknown etiology or for the certification of seed and planting material. The UO07 has expertise to perform the analysis of plant samples by HTS and the downstream bioinformatic analysis, up to the identification of sequences of viral origin.

Reference: Marina Ciuffo

Diagnosis of plant viruses is achieved using several different techniques, that have rapidly evolved in the recent years. The results of a diagnostic assay has to be rapid and inexpensive. Above that, the quality (specificity and sensitivity) of the result and the possibility to be quantitative are desirable features. The UO07 has long-term expertise in plant virus diagnostics, and nowadays utilizes routinely a number of techniques such as ELISA, tissue-printing hybridization, dot-blot hybridization, preparation of non-radioactive probes, PCR, RT-PCR. UO07 can provide the diagnostic service per se, or a residential hands-on training course to learn the techniques.

Reference: Laura Garzoli 

The UO08 has expertise in identification of marine and freshwater Ascomycetes, cave microfungi including pathogenic microrganisms as Pseudogymnoasus destructans, and the plant pathogen Pyricularia oryzae. Taxonomic and phylogenetic assignment based on morphological features and analyses of barcode marker and genes specific to each fungal class.

Reference: Ester M. Eckert

Expertise in identification of prokaryotes with genetic markers. Taxonomic and phylogenic placement of prokaryotes based on single marker genes of whole genome analysis. Optimization of DNA extraction for specific strains. Analysis of prokaryotic genomes with focus on antibiotic and other resistance genes.

Reference: Diego Fontaneto

In the last two decades, the use of DNA sequence data for the identification and delimitation of taxa, namely DNA taxonomy, has found consensus and applications in various fields. After the advent of DNA barcoding, which showed the potential of using short DNA sequences for species identification across multiple groups of organisms, different methods and approaches made DNA taxonomy flourishing as a mature discipline. The UO08 can provide expertise in DNA-based delimitation of independent evolutionary units, akin to species. Such approach on DNA taxonomy can be used for performing taxonomic revisions and combined with morphology and ecology in the description of new species covering all groups of organisms, including prokaryotes and microscopic eukaryotes.

Reference: Emanuele Ferrari

In the last years, proteomics become increasingly important in different topics: drug discovery, biomarker discovery, analysis of microbial community (e.g. metaproteomics on human microbiome or environmental samples). Proteomics relies on data obtained from high resolution Mass Spectrometer coupled with Liquid Chromatography (LC-MS). To obtain reliable and reproducible results, an effective preparation of the samples is crucial. The OU08 can provide support in set up the experimental design for proteomics experiments and the protocol for the preparation of samples. In particular, our expertise could be useful in protein isolation from different matrixes and their digestion and purification.

Reference: Emanuele Ferrari

The increasing amount of LC-MS-based proteomics experiments poses the issue of how to handle the great amount of data that is being generated. A careful and precise analysis workflow has to be set up in order to have consistent and reliable data. In this context, OU08 can support and perform the identification of proteins from raw data coming from LC-MS-based proteomics experiments. Furthermore, we can assist and perform statistics and bioinformatic analysis of proteomics and metaproteomics data, in order to evaluate the biological significance of these data.

Reference: Tomasa Sbaffi

The increasing quality and amount of data produced by Illumina and other sequencing platforms has set in past decade the need of a range of bioinformatic tools and pipelines to treat such data and obtain the required information out of it which can vary dependently on the research topic. We can assist in developing and curate a pipeline that accommodates the researcher needs, we are specialized in the topic of antimicrobial resistance and functional annotation. We also work with WGS (Whole Genome Sequencing) data deriving from microbial isolates. We can further assist with the data analysis of the bioinformatic outcome.

Reference: Daniela Cuna

The Laboratory for AgriFood Sustainability, Quality and Safety at ENEA Brindisi offers a service for phenotypical identification and characterization of microorganisms isolated from diverse environments (compost, soil and sea water) by using The MicroStation™ Identification System BIOLOG. Results are usually available after 3-4 days. 

Reference: Andrea Visca

The Laboratory for AgriFood Sustainability, Quality and Safety at ENEA Casaccia offers a service of targeted DNA sequencing (16S rRNA and ITS regions) with Oxford Nanopore technology (third generation sequencing – long reads). Results are usually available after 2/3 weeks. If requested, a further bioinformatic analysis of the sequenced samples can be performed. The same Laboratory also offers support in case of optimizing scripts to be run in R, as well as the bioinformatic support in terms of analysis of microbial community structure. 

Reference: Luciana Di Gregorio

The Laboratory for AgriFood Sustainability, Quality and Safety at ENEA Casaccia offers a service for identifying the culture-uninvestigable microbial physiological state by using Flow Cytometry (FCM). By means of selected probes, FCM allows to monitor several cellular parameters (i.e. membrane permeability, metabolic activity, DNA/RNA content, etc.), getting a deeper knowledge of the microbial physiological state and related subpopulation viability state on both planktonic and sessile cells.  

Reference: Giulia Massini

The Biotechnological Processes for Energy and Industry laboratory at ENEA Casaccia offers a service for analyzing microbial communities using direct methods, i.e. epifluorescence microscopy, for the determination of the total microbial abundance, the abundance of the fungal and bacterial component, the determination of the viable fraction of the community and the enumeration of specific metabolically active microbial components (respectively after DAPI, Calcofluor, Live/Dead staining and applying FISH technique). If requested, results will be accompanied by micrographs obtained using the Axiovision image processing system. 

Reference: Patrizia Casella

The Laboratory Bio-products and Bio-processes at ENEA Portici offers a service of cultivation of microalgae in indoor photobioreactors (bubble column) (1.2 L and 28 L), on the main cultivation parameters, the treatment and the storage as lyophilized strains. The ENEA Portici offers a service on microalgae characterization and extraction of bioactive compounds as carotenoids and fatty acids and analytical methodologies for the measurements of total protein content, carbohydrates, fatty acids, total dietary fibers, carotenoids. 

Reference: Mario Trupo

The Laboratory Bio-products and Bio-processes at ENEA Trisaia offers a service for the preparation of bacterial starters in bioreactors (biomass and freeze-drying) for agricultural or novel food at the Technological Hall hosting several operating pilot units working as stand-alone plants or as integrated process units: bioreactors and fermentation systems, from lab-scale (2 – 5 L) to pilot-scale (50 and 500 L); freeze-drying systems (lab-scale lyophilizer: about 5 L bulk capacity; pilot-scale freeze dryer: about 60 L bulk capacity). 

Reference: Federica Cerino, Elena Di Poi 

The CoSMi collection makes available numerous species of unicellular marine microalgae with a special focus on potentially toxic dinoflagellates and diatoms responsible for blooms.

Reference: Eugenio Parente  

Amplicon targeted high-throughput sequencing is one of the main set of techniques used for the analysis of the structure and dynamics of microbial communities. Beyond processing of raw sequences and taxonomic assignment using reference databases it requires bioinformatic and statistical skills for the representation and interpretation of results. Prof. Parente at UO14 has developed significant expertise in creating automated pipelines for sequence processing and descriptive and inferential statistical analysis of metataxonomic data, including inference of microbial association networks and can provide support in this area in the framework of scientific collaborations.

Reference: Rocchina Pietrafesa 

UO14 offers the service of yeast characterization for parameters of technological interest, such as the resistance level to antimicrobial compounds, the qualitative and quantitative determination of enzymatic activities (such as glucosidase, protease, lipase, amylase, …). Furthermore, a procedure for the characterization of metabolic profile of yeast strains is available. At this aim, gas chromatographic techniques are used for determination of secondary compounds produced by yeast starter during fermentation and affecting aromatic profile of fermented beverages. The contents of secondary compounds present at high level are quantified by direct injection gas chromatography, whereas other compounds present in low amounts are determined by SPME–GC technique. The results are available in few weeks, depending on the number of samples.

Reference: Teresa Zotta

UO14 offers support for the study and exploitation of metabolic features of lactic acid bacteria (LAB), to be used as starter and/or adjunct cultures for the production of fermented and functional foods, and/or as biofactories for the production of different high-value compounds. Optimization and boost of biomass yield, cell robustness and metabolite production may include cultivation and growth trials in controlled conditions (by using laboratory-scale bioreactor systems). Strain performances may be also improved (whenever possible) by using methodologies based on adaptive evolution assays and/or metabolic shifts.  The type of support/service and timing will differ depending on the strain, metabolic properties and number of samples/analyses.

Reference: Maria Barbara Pisano

The OU15 has gained considerable expertise in the study of health promoting properties of microbial strains, in particular lactic acid bacteria and yeasts, to be used in the production of functional foods. The following tests can be performed: bile salt hydrolase activity, simulated stomach duodenum passage, autoaggregation capacity and cell-surface hydrophobicity, adhesion to Caco-2 cells, antimicrobial activity, assimilation of cholesterol, antioxidant activity.

Reference: Maria Barbara Pisano

The OU15 has gained considerable expertise in the application of PCR-DGGE for identification and analysis of microbial community composition and dynamics in food samples.

Reference: Simone Di Piazza, Mirca Zotti

The COLD Collection offers a mycological sampling service aimed at the isolation, preservation, and characterization of the functional traits of strains from different environments:

• to obtain fungal strains able to biodegrade different pollutants and potentially exploitable in mycoremediation protocols;
• to characterize the cultivable mycobiota in indoor environment (such as workplaces and domestic environments) in order isolate biodeteriogenic fungi potentially dangerous for people and for things (such as museums artifacts or libraries).

Sampling is carried out with both active (Surface Air System biocollector, direct isolation, etc.) and passive methods, depending on the specific conditions of the sampling location. Taxonomic characterization is carried out by molecular barcoding using the ITS region as the primary barcode; to obtain precise species identifications and deepen the identification of critical species, additional gene sequences (such as beta-tubulin, calmodulin, elongation factor 1-alpha, LSU, etc.) can be generated.

Reference: Maria Gullo 

UNIMORE Microbial Culture Collection (UMCC) offers a service of identification and characterization of acetic acid bacteria strains through a polyphasic approach, both phenotypic [using conventional microbiology techniques] and genotypic [16S rRNA gene sequencing]. Moreover, the capability to synthetize biopolymers and to metabolize specific requested substrate can be also investigated. Results are usually available in 3 weeks, although the delivery times may change depending on specific cases. For more details, please see the UMCC website  https://www.umcc.unimore.it/servizi/  

Reference: Antonino Pollio, Antonino De Natale, Donato Giovannelli 

The ACUF collection offers a service of identification of strains of bacteria, cyanobacteria and microalgae using molecular taxonomy techniques (sequencing of 26S rRNA gene and of the ITS 1&2 region, including the 5.8S rRNA gene). Results are usually available after 4 weeks. Upon request, a conventional characterization procedure can be performed (cell morphology by LM and SEM microscopy, coupled with physiological tests, etc.). In this case, the results are usually available in 1 month. For more details, please see the ACUF website  www.acuf.net.

Reference: Antonino Pollio, Antonino De Natale

Bioprospecting of ACUF cyanobacteria and microalgae strains for properties of biotechnological interest may be performed upon request. The screening can be carried out also on other strains provided by people or organizations requesting this service. For more details, please see the ACUF website  www.acuf.net

Reference: Giovanni Giammanco

Public deposit: this service is offered to scientists wishing to deposit a strain at UNIPA – PROMISE collection. If the strain fits the criteria for deposit, the strain may be included. The collection itself may ask a potential depositor for a strain of educational, industrial, or scientific interest. Please contact us at  microbiologia@policlinico.pa.it, prior to sending strains to determine if they can be accepted. Strains will not be accepted without prior approval. In case PROMISE is interested in accepting a strain, an accession form is sent to the potential depositor inviting inclusion of the strain into the Collection. The potential depositor is requested to return the completed accession form to the collection at the time the strain is dispatched. Upon receiving it UNIPA-PROMISE acknowledges the receipt of the strain.

Safe deposit: this service is offered for long-term preservation of microorganisms where the distribution of the strains is restricted at the discretion of the depositor. Microorganisms for Safe Deposit remain the property of the depositor. All information concerning the deposit and the nature of the organism are treated in strict confidence. Microorganisms for Safe Deposit will not be included in the public collection and in the UNIPA-PROMISE catalogue. Access to Safe Deposits must be requested from the depositor. It is at the discretion of the depositor to terminate the deposit at any time and ask the UNIPA-PROMISE Collection to destroy the stored cultures. The fee of the Safe Deposit will be calculated according to the length of the deposit and the number and risk group of strains. No refund will be provided for early termination of the deposit.

This kind of deposit does not comply with the requirements of a patent deposit.

Reference: Giovanni Giammanco

Evaluation will provide the measurement of the performance capabilities of a system/test method, comparing different systems/test methods designed to perform the same marker/target, different culture media to isolate the same organism, or different equipment with the same function. Evaluation findings will be fed back to interested parties via written reports and/or publication of results. Comparison of performance characteristics could include the following: easier to use, cheaper, faster or requires a more easily obtainable sample. Access to the Evaluation service must be requested at  microbiologia@policlinico.pa.it. Upon acceptance of the Evaluation service request, a formal agreement will be signed and a Project Manager will be assigned. The Project Manager will have overall responsibility for the evaluation work including production of the protocol, data collection and analysis, writing the report and ensuring that there is peer group assessment of the protocol and report. The Project Manager will document any conclusions made based on the results analysis. The report could have the support of stakeholders identified in the protocol design. The fee of the Evaluation service will be calculated based on the performance requested and will be included in the formal agreement.

Reference: Paola Quatrini

This service is offered by the Laboratory of Environmental Microbiology and Microbial Ecology to scientists, public and private entities that need to implement a bioremediation strategy for hydrocarbons at laboratory or pilot scale using bacterial bioaugmentation. The contaminated matrices include soil, water and sediment that are already chemically characterized: the contaminants have to be identified and quantified before the service is started. The service will consist in a preliminary verification of the biodegradation potential intrinsic to the matrix in order to start enrichment cultures aiming to isolate the best performing biodegraders already present in the matrix. The HC biodegrading consortia will be tested and produced as liquid inocula for laboratory and pilot scale bioaugmentation trials. Alternatively biodegrading bacterial strains/consortia will be made up starting from the UNIPA-EMMELAB culture collection and produced as liquid inocula for laboratory and pilot scale bioaugmentation trials. Costs and times of production will be calculated for each specific project.

Reference: Benedetta Turchetti, Pietro Buzzini 

The DBVPG collection offers a service of identification of yeast strains using molecular taxonomy techniques (sequencing of the D1/D2 domain of the 26S rRNA gene and of the ITS 1&2 region, including the 5.8S rRNA gene). Results are usually available after 2/3 weeks. Upon request, a conventional characterization procedure can be performed (i.e. cell morphology by photomicrographs, determination of the mating type and physiological tests, etc.). In this case, the results are usually available in a few weeks, also depending on the considered species. For more details, please see the DBVPG website  www.dbvpg.unipg.it  

Reference: Benedetta Turchetti, Pietro Buzzini

The exploration for specific useful properties of biotechnological interest may be performed upon request using the strains conserved in the DBVPG collection or other strains provided by people or organizations requesting this service. DBVPG is willing to develop joint research projects in collaboration with other parties on topics involved in DBVPG research activities. For more details, please see the DBVPG website  www.dbvpg.unipg.it  

Reference: Camilla Lazzi 

The laboratory of Food Microbiology at University of Parma offers a service for phenotypical characterization of microorganism isolated from  various origins, particularly lactic acid bacteria of food origin, useful to describe the growth phenotype in response to various environmental conditions (temperature, pH, salt concentration) as well as the capability to metabolize different substrates using commercial high throughput biochemical tests (Biolog GenIII test panel, Biolog Phenotype Microarrays). 

Reference: Valentina Bernini

The laboratory of Food Microbiology at University of Parma can perform challenge test analysis on different microorganisms and food substrates. The Unit has expertise in planning and execution on different type of matrices, with quantitative assessment of microbial growth in conditions that simulate the shelf life of products. 

Reference: Annalisa Ricci

The laboratory of Food Microbiology at University of Parma can perform assessment of bacterial susceptibility to antimicrobials following the guidelines provided by EFSA guidance document. Microplates assays are performed to evaluate minimum inhibitory concentrations (MIC) and minimum bactericidal concentration (MBC). The same type of assessment can be performed to evaluate the effect of similar treatments on bacteria, such as new antimicrobial compounds, detergents, etc. 

Reference: Alessia Levante

The laboratory of Food Microbiology at University of Parma can perform identification and genotypic characterization of bacteria by using a combination of techniques including 16S identification of strains, fingerprinting (REP-PCR, AFLP) and whole-genome sequencing and comparative analysis by using bioinformatics tools. 

Reference: Marilena Budroni, Giacomo Zara

Among the various microbial species present in the MBDS-UNISSCC collection, of particular interest are the flor yeasts ascribed to the Saccharomyces cerevisiae species, isolated in over 50 years of study from wines aged under biofilm. Flor yeasts constitute a unique asset of microbial diversity. Biofilm is interesting to study and preserve both in unicellular form and as a multicellular community and for this reason specific study and conservation protocols are needed. This research group has contributed to the optimization of these specific protocols. The OU23 can provide excellent support for or perform microbial identification of flor yeast and others yeast able to produce biofilm, by using this methodology.

Reference: Elisa Salvetti 

The antimicrobial overuse in the food chain has been associated with the emergence of resistance mechanisms, not only in several pathogens, but also in other microorganisms, including food bacteria. As reported by the EFSA (European Food Safety Authority), whole genome sequencing is a valid technique to assess the safety of bacteria used in the food chain. Here Verona, UO24, we can provide a thorough safety assessment following EFSA guidance, combining both genomic as well as phenotypic data, thanks also to the availability of antibiotic resistant strains in VUCC-DBT that can be used as references.

Reference: Giovanna Felis 

Lactic acid bacteria (LAB) are a functional group of fermentative prokaryotic microorganisms, which are differently related from a phylogenetic point of view. They are normal constituent of food microbiota and could be a reservoir of strains with an applied relevance. Indeed, several LAB are of utmost importance for food/feed and supplement (probiotics) industry. For those reasons, species-level identification is pivotal not only for the discovery of biodiversity but also with respect to the deliberate use in food and feed; in fact, only strains belonging to species in EFSA QPS list can be used (EFSA – European Food Safety Authority; QPS – Qualified Presumption of Safety). Gene sequencing and/or whole genome sequencing and analysis in comparison with a reliable set of controls is the most valid approach to identify LAB strains. Here in Verona, UO24, we can provide reliable identification of LAB strains, supported by an internationally recognized expertise.

Reference: Silvia Lampis, Marco Andreolli 

In the last years the evaluation of the antibiofilm efficiency of new compounds gained an important scientific and industrial interest. Biofilm formation by means of contaminant or even pathogenic strains can be of great impact for food and industrial production. Determination of the ability to inhibit biofilm formation as well as to eradicate an already formed biofilm can be assessed through the measurement of the MBIC (Minimum Biofilm Inhibitory concentration) and MBEC (Minimum Biofilm Eradication concentration) by means of appropriate devices. UO24 can provide support for or perform studies regarding analysis on potential antibiofilm compounds.