The French National Institute for Agricultural Research (INRA) is a public agricultural research institute existing since 60 years, ranked one in Europe in its field of expertise. Composed of about 8000 persons, it conducts agricultural research for and with society at large, for a preserved environment, well-adapted food and nutrition and competitive and sustainable agriculture. INRA lends its expertise to public decision-making and its research results lead to innovation and know-how for society. Research on microorganisms, either food related, relevant for biotechnology uses (enzymes, biofuel…) or plant/animal pathogens are carried out to a large extent at INRA. The International Centre of Microbial Resources (CIRM) is managed by the INRA. This structure is dedicated to preservation and exploitation of microbial diversity, representing more than 15.000 strains spread over 4 dedicated sites: (i) Grignon for yeasts, (ii) Marseille for filamentous fungi, (iii) Rennes for food bacteria and (iv) Tours for pathogenic bacteria. Since 2008, all sites of the CIRM have obtained an ISO 9001:2000 certificate for the quality management systems of their collections, including accession, authentication, preservation and distribution of microorganisms.
Appropriate facilities of buildings have been developed: (i) renovation in order to respect the containment level appropriate for the risk group of the microorganisms, (ii) appropriate areas on the « no way back » principle (receipt, handling, storage, supply, delivery), (iii) environmental monitoring of laboratory air and surface and (iv) safety duplicate collection preferably in a remote building.
Different equipments are accessible in the four locations: P2 and P3 laboratories, confocal and epifluorescence microscopes, equipment dedicated to species identification and strain typing, including molecular biology, high throughput screening platform.
Tasks led by INRA are as follows: Project coordination, tasks NA3.2, JRA2.2 and JRA2.3, Transnational Access.
Institut Pasteur is a non-profit private foundation which contributes to the prevention and treatment of diseases, primarily infectious diseases, trough research, education, and public health services. Main fields of research are: microbiology, immunology, molecular biology, neuro-biology, genomics and post-genomics. Education materializes with high-level courses and welcome of trainees (over 800 a year). As to public health services, the institute houses a medical centre and 16 National Reference centres as well as 8 WHO Collaborating Centres. Valorisation of research (e.g. by improving and developing medical products, vaccines and diagnostic tests) is performed through close partnerships with industry. Institut Pasteur is operating within an independent international network of Pasteur institutes, which constitutes a unique and original autonomous body. The most important strain collections preserved in the institute gathered into a Biological Resource Centre (CRBIP) that made available for distribution more than 10000 bacterial strains, 750 cyanobacterial strains, 2700 fungal strains (filamentous fungi and yeasts) and 80 viruses (including viruses of risk group 3).
For the project, the CRBIP will benefit from all facilities offered on the Institut Pasteur campus they used to benefit from before, including technological platforms, human resources department, financial department, patent office, etc. As to informatics, the CRBIP developed specific collection management software (ARPAS). As to quality management, the CRBIP as a whole was given the ISO 9001:2000 certification as early as in 2005. Further, the bacterial collection (CIP) is operating to ISO 17025.
Tasks led by Institut Pasteur are as follows: Vice-coordination, workpackage JRA2, tasks NA1.1 and JRA2.1.2, Transnational Access.
The DSMZ houses prokaryotes, plant viruses, as well as plant, human and animal cell cultures. It is one of the few worlds’ leading centres for the systematics of prokaryotes, offering a complete spectrum of taxonomic methods and expertise for the long-term maintenance of biological material, accompanied by a research component focused on collection related fields. Molecular identification of as yet uncultured bacteria are other strong fields in the Department of Microbiology. Typical strengths are in the preservation of archaea and bacteria, storage of DNA, plasmids, and phages, in the management of databases, patent related matters and in issues relating to the acquisition, storage, handling, certification and distribution of biological material. In addition to world class expertise, the facility offers state-of-the-art equipment and support designed for phenotypic and chemotaxonomic investigations.
The DSMZ collection of microorganisms houses 13.500 strains, including archaea and bacteria, yeasts and fungi. The collection is unique in their holdings of strict anaerobes, extremophiles, actinomycetes and myxobacteria.
DSMZ expertise in training is acknowledged by the EU (program “Improving Human Potential”).
DSMZ expertise in Access and Benefit Sharing proven within the CBD regarding microorganisms.
DSMZ bioinformation resources
DSMZ sequencing and authentification facilities, including all techniques for assessing microbial diversity at the phenetic and genomic level
DSMZs facility managed under ISO 9001-2000 quality management since 2005
Tasks led by DSMZ are as follows: task JRA1.2, sub-task JRA2.1.3, Transnational Access.
CABI is an international organisation whose mission is to improve people’s lives worldwide by providing information and applying scientific expertise to solve problems in agriculture and the environment. CABI creates and collates knowledge in agriculture and related fields and makes it widely available in usable forms. CABI has a history of supporting the establishment and enhancement of in-country microbial collections. CABI runs in excess of 140 projects in over 40 countries through it its regional centres and offices across the world. CABI is a regular partner of EU RTD projects (e.g. European Biological Resource Centre Network, MOSAICS, CONTROCAM, INCHECO, and TRICHOES in FP5, ALARM, REBECA, and DIABR-ACT). The inclusion of CABI as an International Organisation headquartered in the UK is justified by bringing its international networking experience (its 45 member country network) and the scientific networking links e.g. the World Federation for Culture Collections, to the partnership. The experience and knowledge gained through the leadership of aspects of the OECD Biological Resource Centre Initiative is unmatched. Experience in invasive species management, microbial auditing and sampling to ISO 17025, knowledge management and improving production in commodities is unique to CABI in this partnership. CABI will lead work package NA1 Develop common standard and protocols and Task NA2.3: Dissemination and outreach to users. CABI will input to all work packages in the project but primarily will provide services and products through the transnational access and service activities and will lead networking activities on implementation of common best practices. Additionally CABI will provide input to DNA banking research and out reach activities.
CABIs collection of 28,000 strains, from over 370 substrates and over 5000 hosts
CABIs links to collections world-wide via the WFCC - 524 in 67 countries - 1.3 million strains)
CABIs expertise in Access and Benefit Sharing within the CBD regarding microorganisms
CABIs information resources
CABIs sequencing and screening facilities
CABI has laboratories operating to ISO 17025 and manages its projects to PRINCE2 (internationally accepted standard for good practice in project management)
Tasks led by CABI are as follows: workpackage NA1, tasks NA1.2 and NA2.3, Transnational Access.
The Spanish Type Culture Collection (CECT), a service of the University of Valencia (UVEG) since 1991, is the only collection of microorganisms that is official and of public nature in Spain, which maintains and supplies bacteria, filamentous fungi and yeasts. Founded in 1960, is a member of the World Federation on Culture Collections (WFCC) since 1977 (wdcm.nig.ac.jp/wfcc) and has belonged to the European Culture Collection Organization (ECCO) since 1983 (www.eccosite.org). In 1992 it gained recognition as an International Depository Authority (IDA) for storing microorganisms for patent purposes in accordance with the Budapest Treaty (www.wipo.int/about-ip/en/budapest/guide/index.htm). The CECT currently maintains over 7000 microbial strains. An on-line catalogue is available on the web (www.cect.org) with relevant information about the main features of the CECT and its activities. These include the preservation of microbial resources, research conducted upon them, and several services. The main ones are the deposit of strains under three modalities (public, restricted and under the Budapest treaty), supply of strains for many different purposes (research, teaching, quality control, biotechnological applications, etc.), identification of isolates, training and counselling on conservation and taxonomy.
UVEG-CECT will lead work package JRA1 Improving strain and DNA storage methods and will contribute in NA1.1, NA1.2, NA2.2 NA2.3 NA3.1, NA3.2 JRA1.1, and JRA2.1 & JRA2.2
The UVEG-CECT is located on the ground floor of the Research Building on the Burjassot Campus of the University of Valencia, in Burjassot (Valencia). It covers a surface area of around 300 m2, with an office and two laboratories (one for Microbiology and the other for Molecular Biology). Adjoining the Microbiology Lab there is a kitchen where cleaning and sterilizing are carried out and an area for freeze-drying. There are also two cold chambers where the culture media and fungi are preserved, respectively, a climatic chamber for long-term preservation, and a separate space to store material and packaging. The equipment is typical of a Microbiology laboratory of these characteristics, i.e., one housing a collection of microbial cultures. To this we add, in the Molecular Biology laboratory, PCR apparatus, equipment for electrophoresis, image analysers with their corresponding analysis programs, etc. With respect to the computer equipment, the UVEG-CECT uses two servers to house the web and associated data bases, which also hold the electronic mail and the shared files. Moreover, UVEG-CECT has a molecular biology server from which one can access different programs to manipulate and align sequences. Likewise, we have a server with back-up copies which are received daily from the data-bases of the other servers.
Tasks led by UVEG-CECT are as follows: workpackage JRA1, task JRA1.1, Transnational Access.
The “Service Public Fédéral de Programmation Politique Scientifique (SPP-PS)” or Belgian Science Policy funds and coordinates the BCCM (Belgian Coordinated Collections of Micro-organisms) since 1983. BCCM is a consortium of four major collections:
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the collection of biomedical fungi and yeasts , BCCM/IHEM, established in 1980 at the Mycology Laboratory of the Institut Scientifique de Santé Publique, Brussels (Partner 11);
- the collection of agro-industrial fungi and yeasts , BCCM/MUCL, developed since 1894 at the ‘Université Catholique de Louvain’, Louvain-La-Neuve (Partner 9) ;
- the bacteria collection, BCCM/LMG, developed since the early fifties at the Laboratory for Microbiology of the Faculty of Sciences of the Universiteit Gent, Ghent (Partner 8);
- in 1990, the plasmid collection BCCM/LMBP, hosted since 1977 in the Laboratory of Molecular Biology of the Universiteit Gent (Partner 9), joined the BCCM consortium.
The SPP-PS, more precisely the BCCM coordination cell of the SPP-PS, will perform management tasks, contribute to organise the training framework and work on a sustainable funding scheme for BRCs.
The individual BCCM collections will effectively contribute to the EMbaRC research and development tasks, but since they have no direct legal existence, they will be represented by their respective host institutions: UGent and UCL.
The BCCM collections maintain over 60.000 strains of bacteria, fungi, and yeasts, including most of the routine test- and reference strains. Moreover, 3.100 recombinant plasmids useful for applied and fundamental molecular biological, immunological and biomedical research and a selection of their recommended or required host strains, as well as 20 DNA libraries from fungal to human origin are present. Most of these biological resources are offered online at http://bccm.belspo.be/.
The collections are similarly organised according to their 3 main activities: preservation & supply of microbiological material, providing scientific services, and performing research. A BCCM Direction Committee is in charge of the consortium’s strategy and operation. The BCCM collections are multisite ISO 9001:2000 certified for accessioning, quality control, preservation and supply of their biological materials.
Since 1992, BCCM has the International Depositary Authority (IDA) status from the World Intellectual Property Organisation, in the framework of international patent legislation (Budapest Treaty). The BCCM consortium is a member of the European Culture Collections' Organisation (ECCO) and the World Federation for Culture Collections (WFCC) and have staff members in the boards. BCCM participates in the UNESCO Microbial Resources Centres Network (MIRCEN), and contributed to several international BRC-related projects e.g. Common Access to Biological Resources and Information (CABRI), the European Biological Resource Centres Network (EBRCN), the MOSAICC Code of Conduct and the MOSAICS project, and the OECD Best Practice Guidelines for Biological Resource Centres.
For material resources see partners 9 UGent and 10.
Tasks led by SPP-PS are as follows: workpackage NA3 and task NA2.2.
The Universidade do Minho (UM - www.uminho.pt) is a public, state-funded, academic institution in the Northwest of Portugal, 70 km from the northern border with Spain. It is the fifth largest university in Portugal, with about 17000 students, and courses in almost all disciplines. MUM was established in 1996 and is hosted by the Biological Engineering Research Centre (www.deb.uminho.pt) which is a centre of excellence (top classification) integrated in the Institute for Biotechnology and Bioengineering (IBB - www.ibb.pt/). This centre has 58 of 146 researchers having a Ph.D. degree. The Mycology and Molecular Biology Laboratory is one of the working groups of this centre. This laboratory has a long experience in applied mycology studies, namely in food and drink mycology and, in recent years efforts have also focused on mycotoxins and others secondary metabolites as well as in molecular mycology. Furthermore, in this laboratory is located the Micoteca da Universidade do Minho. The main mission is maintain and provide fungal strains for research and teaching and wish act as a centre of expertise, information and training (MSc and PhD) in mycology. Nowadays in the Universidade do Minho the training atmosphere is related with lifelong education, e-learning, long-distance training which using new educational technologies and platforms. MUM is also involved in these new educational programmes and teaching approaches.
Mycology laboratory and other related laboratories of Biological Engineering Research Centre of the University of Minho (www.deb.uminho.pt).
Tasks led by UMinho-MUM are as follows: workpackage NA2, task NA2.1, Transnational access.
The Centraalbureau voor Schimmelcultures (KNAW-CBS) is an institute of the Royal Netherlands Academy of Arts and Sciences (RNAAS), studying biosystematics, with research focused on its unique living collection of fungi. Currently it maintains 60.000 fungal strains, 10.000 bacterial strains, and also smaller collections of plasmids and phages, The collection is an IDA for patented strains and ISO 9001:2000 certified. Research projects should add new material to the collection, be it strains or valuable information, including genetic and other datasets.
KNAW-CBS is an active partner in numerous national and international collaborative projects, and aims to use these projects to broaden its scope to include functional fungal biodiversity. Related projects are on a wide range of topics: evolutionary and developmental biology of fungi; the elucidation of structure, function and morphogenesis in phylogenetically relevant cellular components; and the exploration of developments in the “-omics” sciences.
As a partner of the Consortium for European Taxonomic Facilities (CETAF), KNAW-CBS participated in the SYNTHESYS project aimed at facilitating scientific exchange.
KNAW-CBS has in the past participated in many collection-oriented EU (CABRI, EBRCN) and other (OECD) projects, all aimed at improving the quality of both materials and management.
Software package Biolomics
Laboratory equipment for testing
Tasks led by KNAW-CBS are as follows: tasks NA1.3 and JRA2.1, Transnational access.
Universiteit Gent hosts two of the BCCM collections:
The BCCM (Belgian Coordinated Collections of Micro-organisms) is a consortium of four major collections funded and coordinated since 1983 by the Service Public Fédéral de Programmation Politique scientifique (Partner 6 SPP-PS).
BCCM/LMBP holds
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over 3.100 publicly available, recombinant plasmids that can be used as valuable tools for applied and fundamental molecular biological, immunological and biomedical research. These plasmids represent two groups: the vector and the cloned genes groups.
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a selection of recommended or required host strains.
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20 unique DNA libraries, from fungal to human origin.
BCCM/LMG
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Holds and offers over 23.000 bacterial strains, representing some 380 genera and 2.700 species, subspecies or pathovars, encompassing plant associated and phytopathogenic bacteria (pseudomonads, xanthomonads, erwiniae, agrobacteria, coryneforms, etc.), bacteria of medical or veterinary importance (Arcobacter, Campylobacter, Helicobacter, aeromonads, flavobacteria, bordetellae, enterococci, streptococci), marine bacteria (Vibrionaceae) and various groups of biotechnological interest (such as lactic acid bacteria and acetic acid bacteria, N2 fixers, clostridia, bacilli, streptomycetes, agrobacteria, etc.). Most of the commonly used control, test and bioassay strains are available. BCCM/LMG also distributes the complete experimental strain panel of the Burkholderia cepacia complex.
The majority of these biological resources is offered online at http://bccm.belspo.be/.
The collections are similarly organised according to their 3 main activities: preservation and supply of microbiological material, providing scientific services and performing research. A BCCM Direction Committee is in charge of the consortium’s strategy and operation. The BCCM are multisite ISO 9001:2000 certified for accessioning, quality control, preservation and supply of their biological materials.
BCCM/LMBP and BCM/LMG will contribute in work packages
Besides the microbiological material, the BCCM platform operates a large range of research equipment. (see more detailed description at TA9 Transnational Access form).
The BCCM platform disposes of facilities equipped with a broad range of techniques - from conventional to advanced biomolecular – allowing extensive characterization and analysis of biorisk 1, 2 and 3 organisms, including quarantine and other pest organisms (see TA 9)
BCCM has central and local server facilities, develops tailored software for data management, and is the nursery of the innovating StrainInfo.net web-tool. BCCM can rely on the informatics team of the Belgian EMBL node (BEN).
Tasks led by UGent are as follows: Transnational access to BCCM/LMBP and BCCM/LMG installations.
Université Catholique de Louvain hosts the collection of agro-industrial fungi and yeasts , BCCM/MUCL, developed since 1894 at the ‘Université catholique de Louvain’, Louvain-La-Neuve.
BCCM /MUCL holds over 26,000 strains of filamentous and yeast-like fungi, representing over 3 300 species of Ascomycetes, Basidiomycetes, Hyphomycetes and Zygomycetes, numerous type strains and isolates of ecological and/or biotechnological importance. The collection's agro-industrial focus is reflected by its extensive holding of starter cultures for e.g. the manufacture of fermented foods, animal feed, biopesticides and biofertilisers (i.e. mycorrhizae), as well as by the availability of cultures for the cultivation of edible mushrooms or the production of important primary and secondary metabolites (i.e. antibiotics, enzymes and polysaccharides). Test and control strains used in bioassays, biodeterioration and biodegradation tests are also available.
GINCO (Glomales in vitro collection) is the first international collection of arbuscular mycorrhizal fungi (AMF) based exclusively on in vitro produced species. This unique collection is aimed at providing the scientific community and industrial sectors with high-quality contaminant-free in vitro-produced AMF".
The majority of these biological resources is offered online at http://bccm.belspo.be/.
BCCM collections are similarly organised according to their 3 main activities: preservation and supply of microbiological material, providing scientific services and performing research. A BCCM Direction Committee is in charge of the consortium’s strategy and operation. The BCCM are multisite ISO 9001:2000 certified for accessioning, quality control, preservation and supply of their biological materials. Thanks to the BCCM multisite organization, the BCCM collections benefit from the additional expertise of their host institutes.
Since 1992, BCCM has the International Depositary Authority (IDA) status from the World Intellectual Property Organisation, in the framework of international patent legislation (Budapest Treaty). The BCCM consortium is a member of the European Culture Collections' Organisation (ECCO) and the World Federation for Culture Collections (WFCC) and have staff members in the boards. BCCM participates in the UNESCO Microbial Resources Centres Network (MIRCEN), and contributed to several international BRC-related projects e.g. Common Access to Biological Resources and Information (CABRI), the European Biological Resource Centres Network (EBRCN), the Micro-Organisms Sustainable use and Access regulation International Code of Conduct (MOSAICC), and the OECD Best Practice Guidelines for Biological Resource Centres.
BCCM/MUCL will contribute in work packages
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NA.1.1: Harmonization of data associated to the biological material. Design and implementation of standardized information exchange format to facilitate automated processing of data.
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NA1.2: Implementation of network best practice and customer delivery
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JRA1. Improving strain and DNA storage methods
Besides the microbiological material, the BCCM platform operates a large range of research equipment. (see more detailed description at TA10 Transnational Access form).
The BCCM platform disposes of facilities equipped with a broad range of techniques - from conventional to advanced biomolecular – allowing extensive characterization and analysis of biorisk 1, 2 and 3 organisms, including quarantine and other pest organisms (see TA 10)
BCCM has central and local server facilities, develops tailored software for data management, and is the nursery of the innovating StrainInfo.net web-tool. BCCM can rely on the informatics team of the Belgian EMBL node (BEN).
Task led by UCL is as follows: Transnational access to BCCM/MUCL installation.
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