Final Report Summary - EMBARC (European Consortium for Microbial Resource Centres)
Executive Summary:
Microbes are the primary source of genes on the planet and play a key role in addressing the big global challenges of today. Microbial domain Biological Resource Centers (mBRCs) are the professional means to preserve and deliver this crucial microbial richness as certified and traceable biological material. They also support Governments who signed the Convention on Biological Diversity (1992) and Nagoya protocol (2010) in their conservation role. Around 200 collections exist in Europe in the field of agriculture, health, biotechnology, and food, covering a large portion of biodiversity. Collections share similar challenges: how to encourage deposit of strains to protect public investment? How to cope with the breadth and depth of emerging biodiversity? How to develop quality assurance in a shared perspective as well as new technical expertise to improve services provided by microbial BRCs? How to answer all these requirements whilst funding remains at a constant level or more usually, is diminishing? How to position mBRCs as active players in a highly connected life science research community and the bioeconomy? All these questions were addressed within the EMbaRC project involving 10 partners from 7 countries.
Networking activities led to noticeable results such as the common Quality Manual and the collective evaluation of mechanisms for implementing best practices which are now on the way for ISO adoption. Guidelines for optimal formatting/annotating data were harmonized for interoperability, making about 200 000 strains accessible in existing portals. An inventory of European mBRC holdings was made to estimate the coverage rate assured by the EMbaRC partners versus the number of species described to date in the literature, leading to the identification of specific gaps to fill. A new Code of Conduct for biosecurity was provided on a European basis. In terms of research, DNA extraction and quality control were improved extending the services provided by collections and a European microbial DNA bank network was created de novo (www.microdnabank.eu). Protocols to extend the shelf life of several “delicate” species and strains were optimized as well as Identification schemes based on new molecular markers or on MALDI-TOF profiles (30 publications).
Regarding the role of mBRCs, and their connection to life sciences laboratories and the bioeconomy, several actions were made to increase interactions. An initial training offer for Europe was summarized and a new Erasmus Mundus program was created dedicated to microbial BRCs (EuroMiRC) as well as e-learning tools. A program of transnational access was delivered, 581 days of access to mBRCs to 57 European scientists or technicians coming from 10 countries. A strategy for collection expansion was defined in a collaborative way, by organizing a meeting with stakeholders including scientific editors of the main European microbial journals to stimulate and define criteria for strain deposit and long term preservation. Using a dedicated questionnaire on a two year basis, each collection was shown to have a unique funding profile, with a highly variable ratio of public support versus other sources (over the range 11% to 89 %). A long term strategy for European BRC sustainability was then established collectively. Five ETP platforms related to food, biofuels, aquaculture, animal health, and plants were in particular identified as key targets for mBRCs. To increase the visibility of mBRCs to scientists as well as to stakeholders, numerous actions of dissemination were performed, including presenting EMbaRC at 41 conferences in 10 countries and a success stories brochure. However, most importantly it is the placing of the Microbial Resources Research Infrastructure (MIRRI) on the ESFRI road map and the funding of a preparatory phase that stands out, enabling the uptake and use of the whole range of outputs from the EMbaRC project. In conclusion, this project created a strong network of professional actors sharing a vision and a common European ambition in the field of microbial collections as well as a concerted position at an international level.
Project Context and Objectives:
As microbes demonstrate all types of metabolism, the microbial world is an infinite source for innovation, able to provide solutions to some of the big global challenges of today. Microbial biodiversity thus represents a crucial richness to keep and to explore. Culture Collections have existed for over 100 years. Their aim is to secure microbial resources for research in life sciences and to support the search for interesting properties to be applied in health, agronomy, and the environment. They also offer expertise and numerous valuable services in the field of taxonomy and storage. High quality research requires access to high quality biological materials and associated data; microbial domain Biological Resource Centers (mBRCs) are the professional means to provide such certified and traceable biological materials. The use of certified materials from culture collections also reduces the costs arising from mistakes in cumulative research and, by offering immediate and easy access, it also decreases the time spent –and associated costs– in finding and isolating appropriate materials.
Governments who signed the Convention on Biological Diversity (CBD) in 1992 and the Nagoya protocol in 2010 must now meet their commitment to comply with complementing in situ conservation efforts and facilitating access by supporting bodies that are in a position to authenticate and maintain such resources. In the field of microorganisms, microbial domain Biological Resource Centers provide the professional basis to support this effort.
Around 230 collections exist in Europe in the field of agriculture, health, biotechnology, and fermented foods, covering a large portion of biodiversity. One organization, “ECCO” (European Culture Collections’ Organisation) has existed since 1981 and has been stimulating exchanges and collaboration between collections (around 60 ECCO collections); however all their resources are not yet ideally connected and structured. At the global level, the WFCC (World Federation for Culture Collections, over 600 collections from 73 countries) also stimulates culture collection development and exchange. The WFCC World Data Centre for Microorganisms provides a common access point to information on these collections and supportive data. It also encourages collaboration through its International Conference for Culture Collections held every 3 years. Additionally, to support the sustainability of culture collections, the OECD BRC task force published recommendations in 2007, stating that BRCs shall meet high standards of quality and expertise, and supporting strategies to build a Global Biological Resources Centre Network (GBRCN).
All over the world, collections share similar challenges: particularly, how to encourage deposit of strains into collections to support all published data and thus protecting the public investment made in funding the underpinning research. The literature is full of data that cannot be verified because the biological material is no longer available. An additional concern is how to cope with the breadth and depth of emerging biodiversity? Further questions arise: How to develop quality assurance in a shared perspective? How to develop new technical expertise to improve services provided by mBRCs? How to answer all these requirements whilst funding remains at a constant level or more usually, is diminishing? How to place mBRCs at the most useful position in the innovative discovery chain, i.e. as active actors highly connected to life science research and the bioeconomy?
All these questions formed the basis for the EMbaRC project work, which was initiating the European node of the GBRCN. EMbaRC “European Consortium of Microbial Resources Centres” was a three year project (2009-2012) funded by the FP7 Capacities, Research Infrastructures Action. It was composed of 10 partners from 7 countries: INRA–CIRM (France), Institut Pasteur–CRBIP (France), DSMZ (Germany), CABI (UK), the University of Valencia–CECT (Spain), the Belgian Co-ordinated Collections of Micro-organisms (BCCM/LMG and BCCM/LMBP at the University of Ghent and BCCM/MUCL at the Catholic University of Louvain), the University of Minho–MUM (Portugal) and KNAW–CBS (the Netherlands).
EMbaRC established a self-sustainable community of European Microbial Resource Centres representing a large bio-diversity and offering a wide-range of not only bio-resources but also expert services. These services enabled the development of new partnerships with public institutes in the field of biodiversity and facilitated revenue-generating partnerships with the economic sector (large food or biotech companies, research organisations, SMEs, NGO’s etc.).
Providing access to users via the project enabled EMbaRC to improve, coordinate and validate its offer to the European and International researchers from both public and private sectors and thus ensured the future sustainability of the consortium as well as the wider European BRC community at large.
Joint research to improve strain and DNA storage and to develop new microorganisms identification methods were carried out by the EMBaRC consortium. Publications disseminated the results to the broad scientific community.
At a strategic level
- EMbaRC intended to lay down the foundations for the future Global Biological Resource Centre Network (GBRCN) and the Microbial Resource Research Infrastructure (MIRRI) project, ensuring that European expertise and research are at the forefront of the International scene (via NA1, NA2 & NA3).
- EMbaRC intended to improve access to and the quality of biological resources and associated services to benefit both users past and future (all WPs)
At a coordination level
- Add-value to the current set of collections by harmonising methods for strain identification and validation of reference strains (via NA1).
- Ensure consistent quality of all European collections resources by federating current best practice, tools and operational standards and to ensure harmonisation of the quality of BRCs. EMbaRC took the current OECD best practice and emerging national standards for BRCs (e.g. French standard) to the international level (ISO) (via NA1).
- Deliver a Code of Conduct for Biosecurity for European Microbial Biological Resource Collections in order to help BRC’s avoid any direct or indirect contributions to the development, production or preservation of biological weapons (via NA1).
- Improve access to facilities by disseminating widely and managing calls for access (via NA2).
- Define the financial model of each mBRC in the project (via NA3)
At the research level EMbaRC wanted to add value to the current set of collections and related services for the benefit of all users by:
- Developing improved techniques for strain and DNA storage to enable longer shelf-life (via JRA1).
- Creating a high quality European microbial DNA bank Network : www.microdnabank.eu (JRA1)
- Creating a high quality database for eukaryotes (filamentous fungi and yeasts)
- Exploring new methods for the identification of species to ensure more accurate identification of the bioresources (via JRA2).
At the support level EMbaRC objectives was to:
- Provide the research community at large with access to high quality biological resources backed up by the joint-expertise, services and data of the project consortium to enable each individual user’s research needs to be fully addressed (via TA1-8).
- Set up a concerted outreach programme, training programme, dissemination events and project web site (via NA2) and work with users to ensure delivery of products and services to meet their current and developing needs (via TA1-8).
The EMbaRC project brought together key mBRCs in Europe to create the beginnings of a European node for a future GBRCN to support key European collections, to exploit new tools in their data and task sharing, developing common approaches to scientific endeavour, service provision and data sharing. The task of maintaining biodiversity must be shared. Importantly, EMbaRC has improved access for the researcher to high quality microbial resources to improve the quality of their research and accelerate innovation.
Governments who signed the Convention on Biological Diversity (CBD) in 1992 and the Nagoya protocol in 2010 must now meet their commitment to comply with complementing in situ conservation efforts and facilitating access by supporting bodies that are in a position to authenticate and maintain such resources. In the field of microorganisms, microbial Biological Resource Centers provide the professional basis to support this effort.
Around 200 collections exist in Europe in the field of agriculture, health, biotechnology, and fermented foods, covering a large biodiversity. One organization, “ECCO” (European Culture Collections’ Organisation) has existed since 1981 and has been stimulating exchanges and collaboration between collections; however all their resources are not yet ideally connected and structured. At international global scale, the WFCC (World Federation for Culture Collections, over 600 collections from 73 countries) also stimulates culture collection development and exchange. The WFCC World Data Centre for Microorganisms provides a common access point to information on these collections and supportive data. It also encourages collaboration through its International Conference for Culture Collections held every 3 years. Additionally, to support the sustainability of culture collections, the OECD BRC task force published recommendations in 2007, stating that BRCs shall meet high standards of quality and expertise, and supporting strategies to build a Global Biological Resources Centre Network (GBRCN).
All over the world, collections share similar challenges: particularly, how to encourage deposit of strains into collections to support all published data and thus protecting the public investment made in funding the underpinning research. The literature is full of data that cannot be verified because the biological material is no longer available. An additional concern is how to cope with the breadth and depth of emerging biodiversity? Further questions arise: How to develop quality assurance in a shared perspective? How to develop new technical expertise to improve services provided by microbial BRCs? How to answer all these requirements whilst funding remains at a constant level or more usually, is diminishing? How to place mBRCs at their most useful place in the innovative discovery chain, i.e. as active actors highly connected to life science research and the bioeconomy?
All these questions are the basis of the EMbaRC project, which is initiating the European node of the GBRCN. EMbaRC “European Consortium of Microbial Resources Centres” is a three year project (2009-2012) of the FP7 Capacities, Research Infrastructures Action. It is composed of 10 partners from 7 countries: INRA–CIRM (France), Institut Pasteur–CRBIP (France), DSMZ (Germany), CABI (UK), the University of Valencia–CECT (Spain), the Belgian Co-ordinated Collections of Micro-organisms (BCCM/LMG and BCCM/LMBP at the University of Ghent and BCCM/MUCL at the Catholic University of Louvain), the University of Minho–MUM (Portugal) and KNAW–CBS (the Netherlands).
EMbaRC comprises three kinds of activities: networking, joint research activities and transnational access.
• The main objectives of the networking activities (three work packages NA1, NA2, NA3) are to develop common standards and protocols within collections, to organize and evaluate the transnational access to users, to survey the training offered by the partners and propose a scheme to extend it, to build a strategy of dissemination and related tools, to analyse the biodiversity coverage of the consortium and to explore the different co-existing funding models
• The main objectives of the joint research activities (two work packages JRA1, JRA2) are to make collaborative progress on the state of the art in the field of microbial resources by improving the BRCs capacity to preserve microorganisms and derived products (DNA) in optimal conditions, by structuring existing DNA banks, and by improving identification schemes by varied methods, including the most innovative ones like mass spectrometry.
• Transnational Access is an opportunity for scientists to visit and use one of the 12 EMbaRC microbial BRCs (under the conditions of eligibility defined in line with the FP7 rules). By this way, scientists from another European country can benefit from expert advice and advanced equipment during a stay which includes hands-on sessions regarding collection management, identification of bacteria and fungi by state-of-the-art techniques or phenotypic screening of a collection.
Above all, the EMbaRC project aims at creating a strong network of professional actors sharing a vision and a common European ambition in the field of microbial collections and a concerted position at an international level.
Project Results:
The results achieved concern, on the one hand, mechanisms to improve the daily challenges and harmonized expertise of microbial BRCs, and on the other hand, their place and roles in the European Life Sciences and in developing the bioeconomy.
Microbial BRCs are professional entities dedicated for keeping biological resources for the long term and ensuring high quality standards. However, they need to improve their ability to keep delicate strains and to distribute them efficiently, including pathogens in a safe way. They also need to develop and provide new services adapted to the customers, and in particular to increase their expertise in taxonomy and strain identification by the most recent methods. Lastly, they need to harmonize their procedures and develop common protocols, including a code ensuring biosecurity, to be able to form a more efficient network at a European scale. Several significant results have been achieved to serve these needs:
- Standard operating procedures including protocols for culture acquisition, preservation and control were compiled, and a common Quality Manual was established (17pages, 14 sections based on ISO requirements). This generic document was made accessible on the EMbaRC website and can be provided to all collections wishing to reach high quality standards. The EMbaRC partners assessed the level to which they had implemented the OECD Best Practice Guidelines for BRCs. This served as a base line to determine their future development needs. This exercise helped provide both guidance on what the minimal requirements should be for the recognition of a culture collection becoming a BRC and the identified actions that could be coordinated and have common solutions. It facilitated the sharing of standard operation procedures where one collection had already implemented a requirement of the OECD guidelines to another which had not. The protocol for self-assessment was found useful and is now available for use by other collections wishing to set a prioritized plan of action for implementation of a quality management system.
- Improved protocols to raise recovery rates and extend the shelf life of several “delicate” species and strains for which conventional methods give poor results were obtained collectively. Regarding prokaryotes, six delicate species were chosen as experimental models and the choice of the lyoprotectant had the biggest impact on viability. Regarding eukaryotes, 15 delicate species were studied and for ectomycorrhizal fungi, the pre-growth in cryovials, avoiding handling, gave improved results for their long term maintenance. All these results were published and made available for the scientific community; to be taken up by BRCs as new daily practice for the storage of delicate strains. Example of publications of improved preservation protocols resulting from EMbaRC collaborative work:
Lalaymia, I., Cranenbrouck, S., Draye, X., Declerck, S. (2012). Preservation at ultra-low temperature of in vitro cultured arbuscular mycorrhizal fungi via encapsulation-drying. Fungal Biology 116 (10), pp. 1032-1041
Lalaymia I., Declerck S., Naveau F., Cranenbrouck S. Cryopreservation of arbuscular mycorrhizal fungi from root organ and plant cultures. (2014). Mycorrhiza 24 (3), pp. 233-237
Matthew J. Ryan*, Daiva Kasulyte-Creasey, Anthony Kermode, Shwe Phue San and Alan G. Buddie (2014) Controlled rate cooling of fungi using a Stirling cycle freezer CryoLetters 35 (1), 63-68
J. Peiren, J. Buyse, P. De Vos, E. Lang, D. Clermont, S. Hamon, E. Bégaud, C. Bizet, J. (2014) Pascual, M. A. Ruvira, M. C. Macián, D. R. Arahal. Improving survival and storage stability of bacteria recalcitrant to freeze-drying –a coordinated study by European culture collections. Biopreservation and Biobanking (in press )
- Several mechanisms for implementing best practices were evaluated and compared. For example, Deliverable D.NA1.1.1 Standard operating procedures and methods used for culture, characterization/control, and preservation by partners provided consolidated approaches for growth, preservation and storage of biological material. Deliverable D. NA1.1.2 Guidelines for optimal formatting/annotation of data related to the biological materials addressed best practice in data management. The OECD guidance for the operation of mBRC was converted into an operational standard suitable for consideration for the adoption under the International Standards Organization (ISO) which is now underway. ISO/TC 276 Biotechnology is under development its scope includes biobanks and bioresources; analytical methods; bioprocessing; data processing including annotation, analysis, validation, comparability and integration; and metrology. ISO/TC 276 Biotechnology will work closely with related committees in order to identify standardization needs and gaps, and collaborate with other organisations to avoid duplications and overlapping standardization activities.
- Guidelines for optimal formatting/annotating data were harmonized for interoperability. In parallel, a synthesis of the different existing portals to make widely accessible these data was made; 11 out of the 12 EMbaRC BRCs, which represent together more than 200000 strains, registered to one or all of these portals (see below, further explained).
- After an overview of existing legislations, guidelines and websites regarding biosecurity, a new Code of Conduct for biosecurity was provided and approved by all members of EMbaRC consortium. This document (18 pages) is accessible on the website of EMbaRC. It was finalized and approved during a biosecurity workshop organized by the partners in September 2011 in Utrecht and is now published (Christine Rohde, David Smith, Dunja Martin, Dagmar Fritze, and Joost Stalpers (2013). Code of Conduct on Biosecurity for Biological Resource Centres: procedural implementation. International Journal of Systematic and Evolutionary Microbiology 63, 2374-2382. http://ijs.sgmjournals.org/content/63/Pt_7/2374.long
- A shared approach to improve DNA extraction, storage and quality control, was achieved, extending the services provided by mBRCs and allowing taxonomic and genomic studies directly based on DNA samples (which distribution is much simpler in particular in case of pathogenic strains).
Clermont, D. et al. Assessment of DNA Encapsulation, a New Room-Temperature DNA Storage Method. Biopreservation and Biobanking 12, 176–183 (2014).
- Improved identification schemes based on new molecular markers, and an implemented high quality data base of gene sequences was collectively created for fungi, which will be a precious tool for research projects in the field of biodiversity., in silico approaches for identification candidate marker gene targets for the fungal kingdom have been tested and reported in scientific papers. New set of primers for the ITS, D1/D2 sequences and the actin gene have been tested for two genera : Coniothyrium-like anamorphs and Candida. Moreover a A well-resolved phylogeny of the complex white-rot Trametes group, relevant for its high lignolytic potential, was constructed based on concatenate sequences of ITS region and RBP2 gene from a wide sampling of temperate and tropical strains. In addition, a reference phylogenetic tree was constructed with traditionally used molecular loci (ITS region and b-tubulin gene) for the well-known Aspergilli section Nigri group in order to authenticate the selected strains including a large range of type strains and species.
- Improved identification schemes based on MALDI-TOF was provided for several species and valorized through publications. Comparative experimental work showed that MALDI-TOF profiles were machine dependent and hence not portable unless standardized conditions were linked to the use of the same type of apparatuses. Specific databases were created for MALDI-TOF spectra. MALDI MS/MS experiments were also developed on five bacteria genera: Lactobacillus, Streptococcus, Lactococcus, Enterococcus and Propionibacterium. A total of 26 species of food interest, represented by type strains where then studied with promising results that should be confirmed before publication. After clearance of the ExCom to provide access to the database for all interested users in June 2012, UVEG-CECT offered to host the ftp server for download, cared for the curation of the database and uploaded it to the server. The database can now be accessed after requesting username and password by email to the address maldi_embarc@cect.org. Users of the database are requested to acknowledge the EMbaRC project that enabled the built of the public database. The pending Deliverable D15.33 “Release of an accessible database of MALDI-TOF spectra of strains investigated” was drafted by DSMZ and UVEG-CECT and submitted for agreement by ExCom on September 12, 2012.The public release of the database of MALDI-TOF mass spectra of bacterial strains will be announced at the EMbaRC homepage.
Regarding the role of mBRCs, and their connection with life sciences laboratories and the bioeconomy, several actions were made to increase interactions.
- The access to a larger set of microorganisms and their associated data was facilitated via joining different existing portals : CABRI, StrainInfo.net or WDCM (World Data Center of Microorganisms). Specifically a link to EMbaRC mBRC data has been made via the WDCM Global Microorganism Catalogue (http://gcm.wfcc.info/embarc). This collaboration with the WDCM provides “A one-stop access” to the collections of EMbaRC strain catalogue data providing better access to authentic microorganisms and validated associated data from this consortium of European collections.
- A European microbial DNA bank network was created de novo, and made accessible via a Central web portal (www.microdnabank.eu). A complementary DNA bank with shared roles and common practices will develop the principle of shared activities to benefit the user. Enabling a joint accession policy and development of a unique and validated sequence databank linked to state-of-the-art preserved biological materials.
- Initial training offer in Europe was summarized and a new Erasmus Mundus program was created dedicated to microbial BRCs (EuroMiRC) as well as e-learning tools concerning basic technics used in a collection.
- A program of transnational access was built and 581 days of access in mBRCs were delivered to 57 European scientists or technicians coming from 20 countries, after a selection of their project on scientific basis. 90% were academic users. Each site proposed services corresponding to its particular field of expertise and research excellence. These services represent the state-of-art in a given domain and therefore users had access to this ‘collective’ state-of-the-art via EMbaRC. They could achieve different kind of expertise and ressources for their projects, as indicated below :
- High Throughput Screening of food bacteria and filamentous fungi
- Strain identification on pathogenic bacteria
- Handling risk group 3 microorganisms
- Taxonomy of pathogenic bacteria -food safety
- Management of microbial strains in ex situ collections
- State of the art techniques in bacteriology
- Identification - Authentication, characterisation, preservation, databasing storage of micro-organisms
- Analytical and microbiological services
- Theoretical, practical and regulatory aspects of a plasmid collection management
- In vitro Culture of Arbuscular Mycorrhizal Fungi
- An inventory of European mBRC holdings was made to estimate the coverage rate assured by the BRC partners of EMbaRC versus the number of species described up to date in the literature as well as to identify specific gaps to fill.
- A strategy of collection expansion was defined in a collaborative way and by organizing a meeting with stakeholders including scientific editors of the 8 main European microbial journals (Braunschweig, 02-2012) in order to stimulate and define criteria of strain deposit and long term preservation.
- Using a dedicated questionnaire on a two year basis, each collection was shown to have a unique funding profile, with a highly variable ratio of public support versus other sources (11%/89 % to the contrary). A long term strategy for European BRC sustainability was established collectively. Five ETP platforms related to food, biofuels, aquaculture, animal health, and plants were in particular identified as key targets for microbial BRCs. They will serve now within the MIRRI demonstration project.
- In order to increase the visibility of mBRC for scientists as well as for stakeholders numerous actions of dissemination were performed, including 49 conferences in 15 countries, as well as the edition of a success stories brochure. However, most importantly it is the recognition of the Microbial Resources Research Infrastructure (MIRRI) as part of the ESFRI road map and the funding of a preparatory phase that stands out, enabling the uptake and use of the whole range of outputs from the EMbaRC project.
List of publications done within the EMbaRC project
Casaregola, S., Weiss, S. & Morel, G. New perspectives in hemiascomycetous yeast taxonomy. Comptes Rendus Biologies 334, 590–598 (2011).
Clermont, D. et al. Assessment of DNA Encapsulation, a New Room-Temperature DNA Storage Method. Biopreservation and Biobanking 12, 176–183 (2014).
Cousin S, Clermont D, Creno S, Ma L, Loux V, Bizet C, Bouchier C. Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76T. Genome Announc. 2013 Aug 22;1(4). pii: e00660-13. doi: 10.1128/genomeA.00660-13.
Cousin S, Creno S, Ma L, Clermont D, Loux V, Bizet C, Bouchier C. Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T Isolated from Human Intestine. Genome Announc. 2013 Aug 22;1(4). pii: e00662-13. doi: 10.1128/genomeA.00662-13.
Cousin S, Loux V, Ma L, Creno S, Clermont D, Bizet C, Bouchier C. Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137 Isolated from Thoroughbred Racehorse Feces and Human Urine, Respectively. Genome Announc. 2013 Aug 22;1(4). pii: e00663-13. doi: 10.1128/genomeA.00663-13.
Cousin, S. et al. Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T Isolated from a Chicken Crop. Journal of Bacteriology 194, 5973–5973 (2012).
Cousin, S. et al. Lactobacillus gigeriorum sp. nov., isolated from chicken crop. International Journal of Systematic and Evolutionary Microbiology 62, 330–334 (2012).
Cousin, S. et al. Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. International Journal of Systematic and Evolutionary Microbiology 63, 53–59 (2013).
Crahay, C. Wevers, J., Munaut F., Colpaert, J.V. & Declerck, S. Cryopreservation of ectomycorrhizal fungi has minor effects on rootcolonization of Pinus sylvestris plantlets and their subsequent nutrientuptake capacity Mycorrhiza 23 (6), 463-471 (2013).
Crahay, C., Declerck, S., Colpaert, J.V. Pigeon, M. & Munaut F. Viability of ectomycorrhizal
David Smith, Kevin McCluskey and Erko Stackebrandt. Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres. SpringerPlus 2014, 3:81 doi:10.1186/2193-1801-3-81
Dequin, S. & Casaregola, S. The genomes of fermentative Saccharomyces. Comptes Rendus Biologies 334, 687–693 (2011).
Falentin H, Cousin S, Clermont D, Creno S, Ma L, Chuat V, Loux V, Rüdiger P, Bizet C, Bouchier C. Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13T Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin. Genome Announc. 2013 Aug 22;1(4). pii: e00658-13. doi: 10.1128/genomeA.00658-13
fungi following cryopreservation. Fungal Biology117(2),103-111 (2013).
J. Peiren, J. Buyse, P. De Vos, E. Lang, D. Clermont, S. Hamon, E. Bégaud, C. Bizet, J. Pascual, M. A. Ruvira, M. C. Macián, D. R. Arahal. Improving survival and storage stability of bacteria recalcitrant to freeze-drying –a coordinated study by European culture collections. Biopreservation and Biobanking (in the process of resubmission after reviewers comments)
Janssens, D., Arahal, D. R., Bizet, C. & Garay, E. The role of public biological resource centers in providing a basic infrastructure for microbial research. Research in Microbiology 161, 422–429 (2010).
Mallet, S. et al. Insights into the Life Cycle of Yeasts from the CTG Clade Revealed by the Analysis of the Millerozyma (Pichia) farinosa Species Complex. PLoS ONE 7, e35842 (2012).
Pereira, L., Dias, N., Santos, C. & Lima, N. The use of MALDI-TOF ICMS as an alternative tool for Trichophyton rubrum identification and typing. Enfermedades Infecciosas y Microbiología Clínica 32, 11–17 (2014).
Robert, V. The Quest for a General and Reliable Fungal DNA Barcode. The Open Applied Informatics Journal 5, 45–61 (2011).
Rodrigues, P., Santos, C., Venâncio, A. & Lima, N. Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches: Aspergillus section Flavi polyphasic identification. Journal of Applied Microbiology 111, 877–892 (2011).
Rohde, C., Smith, D., Martin, D., Fritze, D., Stalpers J. Code of Conduct on Biosecurity for BiologicalResource Centres: procedural implementation. International Journal of Systematics and Evolutionary Microbiology 63, 2374–2382 (2013).
Santos, C., Fraga, M. E., Kozakiewicz, Z. & Lima, N. Fourier transform infrared as a powerful technique for the identification and characterization of filamentous fungi and yeasts. Research in Microbiology 161, 168–175 (2010).
Santos, C., Lima, N., Sampaio, P. & Pais, C. Matrix-assisted laser desorption/ionization time-of-flight intact cell mass spectrometry to detect emerging pathogenic Candida species. Diagnostic Microbiology and Infectious Disease 71, 304–308 (2011).
Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences 109, 6241–6246 (2012).
Smith, D. & Day, P. (2012). European Consortium of Microbial Resource Centres: Microbial Resources Success Stories. EMbaRC, CABI, UK, http://www.embarc.eu/embarc-update-16.pdf.
Smith, D. & Fritze, D. European Culture Collections – The Future is MIRRI. Microbiology Today 37, 256–258 (2010).
Smith, D. & Ryan, M. Implementing Best Practices and Validation of Cryopreservation Techniques for Microorganisms. The Scientific World Journal 2012, 1–9 (2012).
Smith, D. (2012) A new look at Microorganisms. Insight Publications, Projects 20, 18-19. http://viewer.zmags.com/publication/4c7a6b67#/4c7a6b67/19; SEED Research Library: http://www.seedresearchlibrary.com/biology-medicine-research-projects/174/embarc-improves-microbial-resource-delivery
Smith, D. in Advances in Applied Microbiology 79, 73–118 (Elsevier, 2012).
Smith, D., Fritze, D. & Stackebrandt, E. in the Prokaryotes 267–304 (Springer, 2013).
Smith, David. Research Resources Help To Drive Innovation in Microbiology. Microbe Magazine 6, 486–490 (2011).
Stackebrandt E, Smith D, Casaregola S, Varese GC, Verkleij G, Lima N, Bridge P. (2014). Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science. SpringerPlus 2014, 3:208 doi:10.1186/2193-1801-3-208
Stackebrandt, E. Diversification and focusing: strategies of microbial culture collections. Trends in Microbiology 18, 283–287 (2010).
Stackebrandt, E. Editorial. Archives of Microbiology 193, 155–156 (2011).
Stackebrandt, E. Hinterlegung von Mikroorganismen – ein Dienst an der Wissenschaft. Biospektrum 363 (2011).
Stackebrandt, E. Responsibilities of Culture Collections. Microbiology Today 37, 259 (2010).
Stackebrandt, E. Towards a strategy to enhance access to microbial diversity. International Journal of Systematic and Evolutionary Microbiology 61, 479–481 (2011).
Verkley G.J.M. Dukik K., Renfurm R., Göker M., Stielow J.B. Novel genera and species of Coniothyrium-like fungi in the Montagnulaceae (Ascomycota). Persoonia 32, 25–51 (2014).
Welti, S. et al. Molecular phylogeny of Trametes and related genera, and description of a new genus Leiotrametes. Fungal Diversity 55, 47–64 (2012).
Potential Impact:
Potential impact, main dissemination activities and exploitation results
EMbaRC has delivered tools to improve the management and operation of mBRCs, improve access to the microbial resources and expertise within them and by working with the scientific community has demonstrated how mBRCs can help accelerate discovery of active compounds and microbial solutions to societal challenges.
A key outcome is the recognition of the responsibilities of scientists, editors and the European mBRCs themselves to continuously improve the coverage and preservation of biodiversity. Through the coordinated efforts within EMbaRC, mBRCs already provide better access through virtual catalogues to high quality resources and their associated data to the world’s scientific community. Involved in initial or vocational training, they also better contribute to the maintenance of skills in taxonomy and long term strain preservation. More than before, mBRCs are drivers in the challenge of promoting “reference collections”, in particular by helping collections willing to develop their Quality Management System.
Biological resources are no longer just associated with scientific and medical purposes, providing reference strains. They are open spaces offering multiple uses and are mobilized in a variety of application contexts carrying other issues and unpublished values. The OECD Guidance designs the BRCs as a place where new interactions between academic research, industry and market are experienced. Since the 1970s, scientific activity has changed dramatically, and so exacerbated the life sciences. Socio-political and economic changes have led to the expansion of market transactions through the patentability of biological materials, renewing logical appropriation of knowledge. The biological resources are gradually moved from simply being a tool for scientific and medical research, a holder of legal issues requiring legal regulations, to become a political instrument promoting economic growth. Primarily subject to local business regulations, collections of biological resources have gradually fallen between several forms of regulation (professional, state, market) at national and international levels. These arrangements have fundamentally changed the status and market potential of biological resources, but also the way to collect living resources. The networking of BRCs during EMbaRC reinforced the emergence of this new system of knowledge production. However, coordinating the collection of living resources does not happen by itself. First of all, the era of large-scale biology, the development of "reference collections" is a practical necessity. Without them, no common benchmarks to evaluate multiple samples now available exists, nor the potential to develop batteries of performance tests. Different concepts of value co-exist: a mBRC may be of interest to researchers for the advancement of knowledge, to physicians for diagnoses and therapy provision, to pharmaceutical firms exploring opportunities in drug discovery, or to governments that focus on synergies between science, medicine and industry. Finally, legal standards, best practice guides, quality procedures, certification schemes, access policies are ways to regulate the production and distribution of biological resources.
BRCs have also the opportunity to conduct themselves or in collaboration R & D on biological resources they hold. This can directly contribute to progress in life sciences or lead to useful products generating revenue to support the functions of the broader BRC. However, as we have seen within the project the balance between internal R & D and service activities is delicate to reach as regular public funding is not sufficient to support BRC activities. One of the BRC mission is thus to involve industry in a "long term vision" to harmonize their royalty regimes, and develop marketable products and services, in various domains like health, food, biotechnology and environment. Taking this crucial point into consideration, MIRRI was built on the foundations set by EMbaRC’s achievements.
Concrete impacts
The EMbaRC partnership as key BRCs in Europe harmonised structure and activities on several levels: harmonisation of characterisation and preservation techniques, harmonisation of quality processes and procedures via best practice implementation guidelines and standards, creation of a common web portal and one-stop-shop to the collections resources, expertise and service, and development of a common approach and plan to self-sustainability further to a mapping of current governance, and costing policies of the BRCs.
This can now be useful to:
- the end users (researchers, SMEs and large industrials) providing them with a coherent and consistent service no matter which BRC they approach in terms of the quality of the resources provided, the procedures for strain deposit and preservation and IPR policies.
- the other EU collections, particularly the small collections which do not have the means to invest in new techniques and cumbersome quality processes can benefit from EMbaRC know–how and results. This is delivered on several fronts from sharing sustainable business models to best practices and standard operating procedures; providing short cuts and reducing the investment needed will help to ensure their continued existence.
- The EU research community, as they can access high quality resources and associated services more easily via the web portal, allowing them to find a particular resource with the reassurance that the quality and procedures will be the same from one collection to another. Via the dissemination, training and outreach activities EMbaRC partners tried that the wider research community and SMEs see strains as an asset and worth maintaining and depositing to which the BRC can ‘add value’. This should encourage a more systematic depositing of strains from the wider community reassured with a common and fair IPR policy to enable the BRCs to propose larger strain sets and access to several collection services therefore ensuring a greater biodiversity.
- The EU biological research area through a coordinated infrastructure and complementarity of mBRCs. There are vast numbers of microbes still to be discovered, the majority of which are not yet culturable. However, it is clear that we need a better understanding of biological diversity in particular to enable us to harness their properties to the benefit of humankind at a time when other natural resources are depleted. EMbaRC proposed a strategy to fill the gap and increase the coverage by sharing in a complementary way the task of maintaining biodiversity. Improved data and greater access to a wider range and better maintained resources as proposed by EMbaRC results will provide European industry with a huge advantage over the rest of the world and a road to delivering the bioeconomy.
- The protection of the citizen against biological weapons. Indeed biological weapons are devices which disseminate disease-causing organisms or poisons to kill or harm humans, animals or plants. Almost any disease-causing (such as bacteria, viruses, fungi, prions or rickettsiae) or toxin-producing micro-organism (poisons derived from organisms, or produced in response to micro-organisms) can be used in biological weapons. There are many different disease-causing organisms that are potential candidates for biological weapons. On the other hand, many of these organisms are extremely important for research and development in the domains of medicine, biology and agriculture. These organisms can therefore be used for two purposes. The term used by the international community for these types of organism is `dual use'. OECD has seen the necessity that especially BRC’s as guardians of many potentially dual use strains should have at least common minimum guidelines. National and international bodies (e.g. the States Parties to the BTWC) have formulated the necessity to come to a code of conduct on biosecurity. Before EMbaRC, only three of those countries (Albania, France, and the Netherlands), have started drafting a national code of conduct on biosecurity. EMbaRC worked with the collection community, particularly the GBRCN consortium and ECCO to publish a code of conduct for biosecurity to raise awareness and to put in place manageable and appropriate best practices. These were discussed in various fora and have been accepted at the European level. In December 2011, the code was introduced at the 7th Review Conference to BTWC, United Nations, Geneva, together with an NGO (non-governmental organization) statement (available in IJSEM Online) and was well received by the review conference. The universal uptake of this code by mBRCs will prevent them from directly or indirectly contributing to the development, production or preservation of biological weapons, as described in the Biological and Toxin Weapons Convention (BTWC), or to any other misuse of biological material or derivatives.
- There are several other societal and economic benefits that will arise from the EMbaRC project in the future. The Microbial Resource Research Infrastructure is now in its preparatory phase. This infrastructure has several goals and builds on the outputs of EMbaRC and its collaborations with GBRCN and ECCO. Microbiological diversity and well described microbial resources will play a key role in underpinning the bioeconomy and driving economic growth through successful biotechnological innovation. Harvesting the full value in such organisms is fundamental to agribusiness, industrial biotechnology health technology, biofuel production and, more fundamentally to new industrial policy and green growth. These are in turn fundamental to the delivery of continuing European success in a world that is globalising at a startlingly unprecedented pace. Realizing sustained growth and harnessing a successful bioeconomy will not, however, happen spontaneously and will require private and public sectors to work together to develop specific initiatives plus a supportive environment for the bioeconomy to emerge. A well-integrated research infrastructure that underpins such efforts will be essential. Improved understanding, use and uptake of microbial resources will accelerate innovation and discovery and thus lead to a more successful biotechnology in Europe. The European Commission Directorate General for Research and Innovation Research Infrastructures estimates that there are around 500 000 life scientists in the research landscape. Many of whom are microbiologists reliant on high quality microbial resources. The “bioeconomy” as a whole is worth nearly €2 trillion and provides approximately 22million jobs in Europe alone across sectors as diverse as agriculture, forestry, fisheries, food, chemicals and biofuels (EuropaBio (2012) The tax, finance and regulatory framework and global policy comparison. European Commission. http://www.europabio.org/biotechnology-europe-tax-finance-and-regulatory-framework-and-global-policy-comparison). The provision of well characterised strains in a targeted and coordinated fashion can only accelerate the growth in this area.
- Answering the global challenges; effort is often fragmented and thus inefficient and costly, therefore the coordinated effort through MIRRI can focus the discovery of solutions to the challenges. The idea of releasing the “full value” in microbial resources is pivotal to delivery of the bioeconomy. Simply put, such value is the potential for use of microbial resources, as well as the biological systems and components therein, in basic and applied science as well as in innovation (for example, the potential that may be inherent in some fungal metabolites to act as new generation antimicrobials). There is a need to be able to focus the expertise and capacity of mBRCs to provide the specific resources to facilitate discovery of solutions to some of our grand challenges such as antimicrobials for control of resistant diseases and accelerate discovery in healthcare. Greater rigour and greater cooperation is required to ensure that research matches industry and societal demand. The broader user community need to be brought into a strategic discussion with MIRRI on addressing such gaps in the short, medium and longer terms. The G8 Science Ministers’ Statement (https://www.gov.uk/government/news/g8-science-ministers-Statement) made 12 June 2013, highlighted the need to improve transparency, coherence and coordination of the global scientific research enterprise to address global challenges. They focused on antimicrobial drug resistance as a major health-security challenge, and the need to work together to reduce antimicrobial resistance. They stressed that Research Infrastructures are key elements in research and innovation policies. Iniitiated by EMbaRC, MIRRI will also assist in turning new data into new knowledge and making that knowledge available through integrated and open knowledge networks. Knowledge presents the hidden value in recognisable terms for investment. It envisages the creation of a knowledge collaboration based on data networking. It is the gold standard of a publicly-funded shared knowledge in a way that casts light on G8 aspirations for new antimicrobials.
Dissemination of results
EMbaRC key outputs
Implementing best practice
Standard operating procedures and methods used for culture, characterization/control, and preservation by the partners
A BRC operational standard based on the OECD best practice guidelines for Biological Resource Centres as a working draft for an ISO Standard
Code of conduct for Biosecurity
Improving methods
Recommendation of best protocols for preservation
Report on the dissemination of information and common access to current DNA banks
Common optimised methodology for the storage of DNA
Method validation exercise via inter-laboratory tests
Report on strain authentication by MALDI-TOF and identification of accurate and misclassified/mislabelled strains in consortium holdings
Guidelines for optimal formatting/annotation of data related to biological materials
Supporting users
Transnational access: study visits to utilise partner expertise and technologies
Report on the survey of training courses and a proposal to implement a common training programme
EMbaRC Web site
EMbaRC workshop for emerging collections in Romania
Report on the learning materials to support the teaching/training activities
Supporting science
A strategy for increasing collection holdings with scientifically relevant resources
Publication on comparative genomic analysis of prokaryote targeted species
Report on phylogenetic approach using enzymes of industrial interest
Supporting culture collections/BRCs
A model strategy for sustainability of BRC services
Overview of existing legislation, guidelines, best practices etc. connected with biosecurity
Dissemination tools
EMbaRC utilised many tools to disseminate its outputs to the various stakeholders:
End-User level stakeholder
The research community including SMEs and research labs of large corporates who are current and or potential users (and clients) of the EMbaRC infrastructure and services were a key target group. Partners attended partnering events, conferences and trade shows to interact with representatives from academia and bioindustry (see below). Additionally, work with scientific journal editors has helped promote the deposit of strains cited in publications to ensure their continued availability for confirmation of results and further studies. The main dissemination tools used for this target group were the EMbaRC Web portal and Newsletter, presentations at key bio- industry events and targeted email shots.
Network level stakeholder
The outreach activities extended to the global, regional and national federations of culture collections. A presence at their conferences and business meetings ensured a two-way dialogue on the network activities of EMbaRC and the transfer of project results. The key dissemination tools used were presentations at ECCO meetings, the EMbaRC Workshop in Romania and publications.
Political level stakeholder
National Authorities were a key collaborator in the design of the code of conduct on biosecurity and issues on the impending implementation of the Nagoya Protocol and Access and Benefit Sharing. Research programme funders were consulted regarding the protection of their investments made in research and collection of biological materials. Relevant international organisations were consulted directly for example the BTWC and WHO (on the biosecurity code) and others through News/articles, lobbying by EMbaRC partners at national level, web site and presentations at key events (see the table below).
Main Dissemination tools:
EMbaRC Newsletter: 4 issues were distributed to the full EMbaRC distribution list
EMbaRC Web portal: www.embarc.eu: Visitors to the web site can access electronic catalogues of the partner mBRCs, an information resource, news and relevant events. The key resources presented are technical training videos are available on gram staining, fungi observation under the optical microscope and preservation techniques; Access to the European microbial DNA Bank Network at
www.microdnabank.eu; The Code of Conduct on Biosecurity for BRCs; The Database for Molecular Taxonomy and Phylogeny of Yeasts (YeastIP) and the EMbaRC Brochure Microbial Resources Success stories
EMbaRC presentations at key conferences
EMbaRC was present at 41 conferences in more than 10 countries presenting over 40 papers or posters. Key events are listed below and some of them were then detailed for their special importance :
• Colóquio do Instituto Nacional dos Recursos Biológicos I.P. (INRB)
• The GBRCN Regional Seminar
• Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)
• Simpósio de Coleções Culturas at the 25th Congresso Brasileiro de Microbiologie (Brazilian Microbiology Congress) held in Porto de Galinhas, Brazil, 3-11 November 2009
• EUPHRESCO – Europe Wide Workshop on Building and Influencing Transnational Phytosanitary Research Strategies
• 3rd FEMS Congress for European Microbiologists Microbes and Man: Interdependence and Future Challenges
• Science Collections International, Brussels, Belgium
• 8th Meeting of the French Society for Microbiology (SFM)
• ECCO XXVIII, Göteborg, Sweden,July 2nd - 3rd ; ECCO XXIX Annual Meeting of the European Culture Collection’s Organisation
• BTWC 7th Review Conference
• International Society for Microbial Ecology (ISME) Annual conference
EMbaRC Workshop: Institut Cantacuzén, Romania (for East EU collections) in 2009 and a Workshop associated with ICCC12, the WFCC international Culture Collection Conference in Brazil in 2010
The GBRCN Annual Meeting, Braunschweig, Germany, 22-26 February 2010
The meeting brought together the Global Biological Resource Centre Network (GBRCN) Demonstration Project partners with related projects and initiatives across Europe, in Australia, Asia, the USA and Eastern Europe. There were 46 participants from 16 countries on 5 continents. Representatives from the GBRCN Demonstration Project, the European Consortium of Microbial Resources Centres (EMbaRC, EU Seventh Framework Programme Research Infrastructures (INFRA-2008-1.1.2.9: Biological Resources Centres (BRCs) for microorganisms), and the CABRI (Common Access to Biological Resources and Information) network discussed together with the ESFRI (http://cordis.europa.eu/esfri/) initiatives BBMRI (http://www.bbmri.eu/) and ERINHA http://asso.orpha.net/HBSL/) and with representatives from the EU, the OECD and the EUPHRESCO ERA Network. Parties interested in the networking initiative came from Russia, Taiwan, Australia and the USA. Topics revolved around issues on biosecurity, information systems, and governance structures and implementation of best practice and other potential areas of collaboration. Several actions arose to help define the work of the GBRCN Demonstration Project and outline areas of collaboration with other initiatives.
EMbaRC progress was discussed and the opportunity for Transnational access reported to participants..
Science Collections International Brussels
SciColl is an international initiative devoted to increasing the benefits that object-based scientific collections and their associated information produce for science and society. It brings together major museums and proposes an international co-ordination mechanism that will enable the uptake of best practices, stimulate collaborations and identify and open new areas of research that rely on scientific collections. SciColl is an OECD Global Science Forum initiative and has formulated a strategy, drafted infrastructure, budget and outreach documents. It presents itself as a Research Infrastructure for collections and thus has similar goals to GBRCN and the Microbial Resources Research Infrastructure (MIRRI)
i. Steering Group meeting, Berlin, 02-05 September 2009
ii. GBRCN mechanisms for improving quality in BRCs at the Scientific Collections International Organisation (SciColl) Outreach Conference in Brussels, 07-09 February 2010
Talks presented at both on the GBRCN but emphasising the role of EMbaRC to develop the European platform
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)
Stakeholders Meeting, Brussels, 16 September 2009
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) is addressing the networking and best practice issues. BBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources (http://bbmri.eu/bbmri/index.php). Its mission is:
• To benefit European health-care, medical research, and, ultimately, the health of the citizens of the European Union.
• To have a sustainable legal and financial conceptual framework for a pan-European Biobank infrastructure.
• To increase scientific excellence and efficacy of European research in the life sciences, especially in biomedical research.
• To expand and secure competitiveness of European research and industry in a global context, especially in the field of medicine and biology.
EMbaRC and the GBRCN demonstration project are exploring with BBMRI how the initiatives can best work together.
Simpósio de Coleções Culturas at the 25th Congresso Brasileiro de Microbiologie (Brazilian Microbiology Congress) held in Porto de Galinhas, Brazil, 3-11 November 2009
A special session on culture collections included presentations on the Brazilian BRC network development project and further opportunities for funding. The latter was covered by Luiz Antonio Rodrigues Elias representing the Executive Secretary of the Ministry of Science and Technology. The discussion session generated lively and enthusiastic debate (all in Portuguese) but and executive summary provided by Vanderlei Canhos said everything had gone extremely well and that all were pleased with the Brazilian projects and participation in the GBRCN demonstration project. Fritze and Smith’s presentations covered EMbaRC’s contribution to establishment of the global network (GBRCN). The report on the special session and the participants list will appear on the CRIA web site.
EUPHRESCO - Europe Wide Workshop on ‘Building and Influencing Transnational Phytosanitary Research Strategies, 26 – 27 May 2009, Braunschweig, Germany
This is a Coordination Action funded by the European Union's ERA-NET Scheme under the 6th Framework Programme (FP6). It presently involves a partnership of 24 organisations involved with funding or managing phytosanitary (quarantine/regulated plant health) research programmes in 17 European countries. It is policy-led and involves the European Commission's Directorate General for Health and Consumer Protection (DG SANCO), the European and Mediterranean Plant Protections Organisation (EPPO) and the European Food Safety Authority (EFSA) through an Expert Advisory Group. EUPHRESCO aims to coordinate its trans-national activities with EU-funded programmes to ensure overlaps are avoided and optimal research is commissioned. EMbaRC, ECCO and the GBRCN can provide the microbial resources to underpin activities and EUPHRESCO can be approached to contribute to support MIRRI if it succeeds on getting on the Pan-European road map as a global research infrastructure.
3rd FEMS Congress for European Microbiologists: Microbes and Man: Interdependence and Future Challenges 2009 June 28 – July 2 Göteborg Convention Centre, Göteborg, Sweden
Smith and Fritze (GBRCN Secretariat) participated in the FEMS and ECCO meetings held in Göteborg, Sweden to present oral presentations and posters on the GBRCN and, EMbaRC projects
To present:
Posters:
Managing Microbes an E-Learning Experience
The Global Biological Resource Centre Network Demonstration Project
Biorisk: how Culture Collections deal with Biosafety & Biosecurity
Correct packaging for microorganisms
Would your collection join the Global Biological Resource Centre Network?
European Consortium of Microbial Resources Centres – EMbaRC (
European Culture Collection’s Organisation – ECCO
European Culture Collection’s compliance with the CBD and Access and Benefit Sharing
Oral presentations:
The background of the OECD GBRCN demonstration project
The Vision and Current activities of the GBRCN demonstration project
Access and Benefit Sharing, a micoorganism perspective
ECCO XXVIII, Göteborg, Sweden,July 2nd - 3rd
CABI, DSMZ, MUM, LMG and other partners attended the European Culture Collections’ Organisation (ECCO) meeting held back to back with FEMS to present some of the posters and presentations to a new and more focussed group of participants at the ECCO annual meeting. The poster: The European Consortium of Microbial Resources Centres – EMbaRC was presented (Annexe 1 Abstract text 2) and presentations highlighted the role of EMbaRC in delivering a microbial resource to underpin European research.
The GBRCN Regional Seminar, Guimarães, Portugal, 12-16 May 2009
The programme of the meeting was designed to address a few key issues to get the partner work in the GBRCN fully underway. The meeting was the first of the GBRCN outreach seminars and was arranged by Esperanza Garay, Spain and Nelson Lima, Portugal, the latter making all the local arrangements for the meeting at Ave Park which is located in Taipas, Guimarães. The Ave Park is a new Science Park where the University of Minho has its biotechnology spin off and shares conference facilities. The GBRCN seminar was held back to back with a MALDI-TOF workshop, the second day of the latter being open to participants; the GBRCN Secretariat were allowed to make two presentations on the GBRCN project. The GBRCN seminar was split into a day of informative presentations on the background and progress, including country reports. The second day included a working meeting with certification/accreditation bodies to define the work programme in this area and presentations on Biosecurity and options for a GBRCN information system. The presentations addressed the input of EMbaRC to the development and establishment of the GBRCN.
The MicroBiotec 11 meeting in Braha (Portugal) 2011 (http://microbiotec11.files.wordpress.com/2011/12/e-microbiotec11.pdf). In this meeting of the Portuguese society for Microbiology and the Portuguese Society for Biotechnology, the EMbaRC project was presented in a Keynote lecture.
Exploitation of the EMbaRC results
Exploitation results:
- A one-stop access to the collections of EMbaRC and the wider European BRC community via a searchable web portal (Deliverable NA2.3.2)
- Access and high-quality support and training to research teams via an open call for access delivering 57 access opportunities to research teams from 20 countries (Via TA1 – 8 and the support of NA2)
- Improved methods for strain and DNA preservation (Deliverable JRA.1.2.2/3)
- Novel approaches for identifying species methods such as mass spectrometry, screening and high throughput sequencing). (Deliverable JRA.2.1.1)
- A complementary DNA bank with shared roles and common practices developed the principle of shared activities to benefit the user.
- A creation of a high quality database for eukaryotes (filamentous fungi and yeasts) which is a precious tool for research projects in the field of biodiversity.
- A working draft ISO standard for microbial resource centres and accompanying implementation guidelines and training material (Deliverable NA.1.2.2)
- A code of conduct for biosecurity for European BRCs (Deliverable NA.1.3.3)
- A strategic plan for the role of EMbaRC and the wider EU BRC community in the GBRCN (Deliverable NA.3.2.4)
- A set of financial models for the self-sustainability of BRC (Deliverable NA.3.2.4)
The above outputs have been made available for further exploitation. Several tools have already been adopted by the MIRRI consortium in the preparation phase prior to the implementation of this ESFRI infrastructure. Particularly taken up are the Code of conduct for biosecurity, the further development of quality management standards and the financial models. Other elements have been incorporated in MIRRI strategies for future implementation. All the outputs will constitute the first steps to forming the Global Biological Resource Centre Network; MIRRI is the European regional node for the GBRCN and is closely linked with initiatives in South and North America, Asia and Africa. The EMbaRC outputs have been promulgated globally through these linkages. The research results (JRA1 and 2) have added value to the partners' current collections and related services enabling them to attract a wider customer base. The scientific results have been published in key journals
The most significant development instigated by EMbaRC, GBRCN demonstration project consortium and ECCO has been Microbial Resources Research Infrastructure (MIRRI). A joint proposal was tabled by the French European Strategy Forum on Research Infrastructures (ESFRI) delegate and MIRRI is now on the Biological and Medical Sciences Road Map. A workshop at the Leibnitz Association Brussels with EU officers on the 14-16 December 2009 was organised by the GBRCN to discuss funding. Discussions focussed on the ESFRI route for development funding for MRRI. Other opportunities were the EU Capacities Programme, a proposal to the DG Justice and Home Affairs, Counter Terrorism II for a Biosecurity database and a proposal on an information system for the GBRCN to the e Infrastructures programme. Presentations included EMbaRC’s contribution to global networking. The European Commission´s representatives were Jean-Emmanuelle Faure, Research Directorate General Research Infrastructures (Unit B3), Annika Thies, DG Research, Research Infrastructure, Garbine Guiu, DG Research, Biotechnologies, Patrick Dietz, Directorate-General Justice and Home Affairs Directorate F: Security Unit F1, Susanna Kantas, DG Internal Market and Services Industrial, Property Unit and Carlos Morais, DG Infso, Geant and e-Infrastructures.
List of Websites:
http://www.embarc.eu
Sylvie.lortal@rennes.inra.fr (coordinator) / Chantal.bizet@pasteur.fr / d.smith@cabi.org
Microbes are the primary source of genes on the planet and play a key role in addressing the big global challenges of today. Microbial domain Biological Resource Centers (mBRCs) are the professional means to preserve and deliver this crucial microbial richness as certified and traceable biological material. They also support Governments who signed the Convention on Biological Diversity (1992) and Nagoya protocol (2010) in their conservation role. Around 200 collections exist in Europe in the field of agriculture, health, biotechnology, and food, covering a large portion of biodiversity. Collections share similar challenges: how to encourage deposit of strains to protect public investment? How to cope with the breadth and depth of emerging biodiversity? How to develop quality assurance in a shared perspective as well as new technical expertise to improve services provided by microbial BRCs? How to answer all these requirements whilst funding remains at a constant level or more usually, is diminishing? How to position mBRCs as active players in a highly connected life science research community and the bioeconomy? All these questions were addressed within the EMbaRC project involving 10 partners from 7 countries.
Networking activities led to noticeable results such as the common Quality Manual and the collective evaluation of mechanisms for implementing best practices which are now on the way for ISO adoption. Guidelines for optimal formatting/annotating data were harmonized for interoperability, making about 200 000 strains accessible in existing portals. An inventory of European mBRC holdings was made to estimate the coverage rate assured by the EMbaRC partners versus the number of species described to date in the literature, leading to the identification of specific gaps to fill. A new Code of Conduct for biosecurity was provided on a European basis. In terms of research, DNA extraction and quality control were improved extending the services provided by collections and a European microbial DNA bank network was created de novo (www.microdnabank.eu). Protocols to extend the shelf life of several “delicate” species and strains were optimized as well as Identification schemes based on new molecular markers or on MALDI-TOF profiles (30 publications).
Regarding the role of mBRCs, and their connection to life sciences laboratories and the bioeconomy, several actions were made to increase interactions. An initial training offer for Europe was summarized and a new Erasmus Mundus program was created dedicated to microbial BRCs (EuroMiRC) as well as e-learning tools. A program of transnational access was delivered, 581 days of access to mBRCs to 57 European scientists or technicians coming from 10 countries. A strategy for collection expansion was defined in a collaborative way, by organizing a meeting with stakeholders including scientific editors of the main European microbial journals to stimulate and define criteria for strain deposit and long term preservation. Using a dedicated questionnaire on a two year basis, each collection was shown to have a unique funding profile, with a highly variable ratio of public support versus other sources (over the range 11% to 89 %). A long term strategy for European BRC sustainability was then established collectively. Five ETP platforms related to food, biofuels, aquaculture, animal health, and plants were in particular identified as key targets for mBRCs. To increase the visibility of mBRCs to scientists as well as to stakeholders, numerous actions of dissemination were performed, including presenting EMbaRC at 41 conferences in 10 countries and a success stories brochure. However, most importantly it is the placing of the Microbial Resources Research Infrastructure (MIRRI) on the ESFRI road map and the funding of a preparatory phase that stands out, enabling the uptake and use of the whole range of outputs from the EMbaRC project. In conclusion, this project created a strong network of professional actors sharing a vision and a common European ambition in the field of microbial collections as well as a concerted position at an international level.
Project Context and Objectives:
As microbes demonstrate all types of metabolism, the microbial world is an infinite source for innovation, able to provide solutions to some of the big global challenges of today. Microbial biodiversity thus represents a crucial richness to keep and to explore. Culture Collections have existed for over 100 years. Their aim is to secure microbial resources for research in life sciences and to support the search for interesting properties to be applied in health, agronomy, and the environment. They also offer expertise and numerous valuable services in the field of taxonomy and storage. High quality research requires access to high quality biological materials and associated data; microbial domain Biological Resource Centers (mBRCs) are the professional means to provide such certified and traceable biological materials. The use of certified materials from culture collections also reduces the costs arising from mistakes in cumulative research and, by offering immediate and easy access, it also decreases the time spent –and associated costs– in finding and isolating appropriate materials.
Governments who signed the Convention on Biological Diversity (CBD) in 1992 and the Nagoya protocol in 2010 must now meet their commitment to comply with complementing in situ conservation efforts and facilitating access by supporting bodies that are in a position to authenticate and maintain such resources. In the field of microorganisms, microbial domain Biological Resource Centers provide the professional basis to support this effort.
Around 230 collections exist in Europe in the field of agriculture, health, biotechnology, and fermented foods, covering a large portion of biodiversity. One organization, “ECCO” (European Culture Collections’ Organisation) has existed since 1981 and has been stimulating exchanges and collaboration between collections (around 60 ECCO collections); however all their resources are not yet ideally connected and structured. At the global level, the WFCC (World Federation for Culture Collections, over 600 collections from 73 countries) also stimulates culture collection development and exchange. The WFCC World Data Centre for Microorganisms provides a common access point to information on these collections and supportive data. It also encourages collaboration through its International Conference for Culture Collections held every 3 years. Additionally, to support the sustainability of culture collections, the OECD BRC task force published recommendations in 2007, stating that BRCs shall meet high standards of quality and expertise, and supporting strategies to build a Global Biological Resources Centre Network (GBRCN).
All over the world, collections share similar challenges: particularly, how to encourage deposit of strains into collections to support all published data and thus protecting the public investment made in funding the underpinning research. The literature is full of data that cannot be verified because the biological material is no longer available. An additional concern is how to cope with the breadth and depth of emerging biodiversity? Further questions arise: How to develop quality assurance in a shared perspective? How to develop new technical expertise to improve services provided by mBRCs? How to answer all these requirements whilst funding remains at a constant level or more usually, is diminishing? How to place mBRCs at the most useful position in the innovative discovery chain, i.e. as active actors highly connected to life science research and the bioeconomy?
All these questions formed the basis for the EMbaRC project work, which was initiating the European node of the GBRCN. EMbaRC “European Consortium of Microbial Resources Centres” was a three year project (2009-2012) funded by the FP7 Capacities, Research Infrastructures Action. It was composed of 10 partners from 7 countries: INRA–CIRM (France), Institut Pasteur–CRBIP (France), DSMZ (Germany), CABI (UK), the University of Valencia–CECT (Spain), the Belgian Co-ordinated Collections of Micro-organisms (BCCM/LMG and BCCM/LMBP at the University of Ghent and BCCM/MUCL at the Catholic University of Louvain), the University of Minho–MUM (Portugal) and KNAW–CBS (the Netherlands).
EMbaRC established a self-sustainable community of European Microbial Resource Centres representing a large bio-diversity and offering a wide-range of not only bio-resources but also expert services. These services enabled the development of new partnerships with public institutes in the field of biodiversity and facilitated revenue-generating partnerships with the economic sector (large food or biotech companies, research organisations, SMEs, NGO’s etc.).
Providing access to users via the project enabled EMbaRC to improve, coordinate and validate its offer to the European and International researchers from both public and private sectors and thus ensured the future sustainability of the consortium as well as the wider European BRC community at large.
Joint research to improve strain and DNA storage and to develop new microorganisms identification methods were carried out by the EMBaRC consortium. Publications disseminated the results to the broad scientific community.
At a strategic level
- EMbaRC intended to lay down the foundations for the future Global Biological Resource Centre Network (GBRCN) and the Microbial Resource Research Infrastructure (MIRRI) project, ensuring that European expertise and research are at the forefront of the International scene (via NA1, NA2 & NA3).
- EMbaRC intended to improve access to and the quality of biological resources and associated services to benefit both users past and future (all WPs)
At a coordination level
- Add-value to the current set of collections by harmonising methods for strain identification and validation of reference strains (via NA1).
- Ensure consistent quality of all European collections resources by federating current best practice, tools and operational standards and to ensure harmonisation of the quality of BRCs. EMbaRC took the current OECD best practice and emerging national standards for BRCs (e.g. French standard) to the international level (ISO) (via NA1).
- Deliver a Code of Conduct for Biosecurity for European Microbial Biological Resource Collections in order to help BRC’s avoid any direct or indirect contributions to the development, production or preservation of biological weapons (via NA1).
- Improve access to facilities by disseminating widely and managing calls for access (via NA2).
- Define the financial model of each mBRC in the project (via NA3)
At the research level EMbaRC wanted to add value to the current set of collections and related services for the benefit of all users by:
- Developing improved techniques for strain and DNA storage to enable longer shelf-life (via JRA1).
- Creating a high quality European microbial DNA bank Network : www.microdnabank.eu (JRA1)
- Creating a high quality database for eukaryotes (filamentous fungi and yeasts)
- Exploring new methods for the identification of species to ensure more accurate identification of the bioresources (via JRA2).
At the support level EMbaRC objectives was to:
- Provide the research community at large with access to high quality biological resources backed up by the joint-expertise, services and data of the project consortium to enable each individual user’s research needs to be fully addressed (via TA1-8).
- Set up a concerted outreach programme, training programme, dissemination events and project web site (via NA2) and work with users to ensure delivery of products and services to meet their current and developing needs (via TA1-8).
The EMbaRC project brought together key mBRCs in Europe to create the beginnings of a European node for a future GBRCN to support key European collections, to exploit new tools in their data and task sharing, developing common approaches to scientific endeavour, service provision and data sharing. The task of maintaining biodiversity must be shared. Importantly, EMbaRC has improved access for the researcher to high quality microbial resources to improve the quality of their research and accelerate innovation.
Governments who signed the Convention on Biological Diversity (CBD) in 1992 and the Nagoya protocol in 2010 must now meet their commitment to comply with complementing in situ conservation efforts and facilitating access by supporting bodies that are in a position to authenticate and maintain such resources. In the field of microorganisms, microbial Biological Resource Centers provide the professional basis to support this effort.
Around 200 collections exist in Europe in the field of agriculture, health, biotechnology, and fermented foods, covering a large biodiversity. One organization, “ECCO” (European Culture Collections’ Organisation) has existed since 1981 and has been stimulating exchanges and collaboration between collections; however all their resources are not yet ideally connected and structured. At international global scale, the WFCC (World Federation for Culture Collections, over 600 collections from 73 countries) also stimulates culture collection development and exchange. The WFCC World Data Centre for Microorganisms provides a common access point to information on these collections and supportive data. It also encourages collaboration through its International Conference for Culture Collections held every 3 years. Additionally, to support the sustainability of culture collections, the OECD BRC task force published recommendations in 2007, stating that BRCs shall meet high standards of quality and expertise, and supporting strategies to build a Global Biological Resources Centre Network (GBRCN).
All over the world, collections share similar challenges: particularly, how to encourage deposit of strains into collections to support all published data and thus protecting the public investment made in funding the underpinning research. The literature is full of data that cannot be verified because the biological material is no longer available. An additional concern is how to cope with the breadth and depth of emerging biodiversity? Further questions arise: How to develop quality assurance in a shared perspective? How to develop new technical expertise to improve services provided by microbial BRCs? How to answer all these requirements whilst funding remains at a constant level or more usually, is diminishing? How to place mBRCs at their most useful place in the innovative discovery chain, i.e. as active actors highly connected to life science research and the bioeconomy?
All these questions are the basis of the EMbaRC project, which is initiating the European node of the GBRCN. EMbaRC “European Consortium of Microbial Resources Centres” is a three year project (2009-2012) of the FP7 Capacities, Research Infrastructures Action. It is composed of 10 partners from 7 countries: INRA–CIRM (France), Institut Pasteur–CRBIP (France), DSMZ (Germany), CABI (UK), the University of Valencia–CECT (Spain), the Belgian Co-ordinated Collections of Micro-organisms (BCCM/LMG and BCCM/LMBP at the University of Ghent and BCCM/MUCL at the Catholic University of Louvain), the University of Minho–MUM (Portugal) and KNAW–CBS (the Netherlands).
EMbaRC comprises three kinds of activities: networking, joint research activities and transnational access.
• The main objectives of the networking activities (three work packages NA1, NA2, NA3) are to develop common standards and protocols within collections, to organize and evaluate the transnational access to users, to survey the training offered by the partners and propose a scheme to extend it, to build a strategy of dissemination and related tools, to analyse the biodiversity coverage of the consortium and to explore the different co-existing funding models
• The main objectives of the joint research activities (two work packages JRA1, JRA2) are to make collaborative progress on the state of the art in the field of microbial resources by improving the BRCs capacity to preserve microorganisms and derived products (DNA) in optimal conditions, by structuring existing DNA banks, and by improving identification schemes by varied methods, including the most innovative ones like mass spectrometry.
• Transnational Access is an opportunity for scientists to visit and use one of the 12 EMbaRC microbial BRCs (under the conditions of eligibility defined in line with the FP7 rules). By this way, scientists from another European country can benefit from expert advice and advanced equipment during a stay which includes hands-on sessions regarding collection management, identification of bacteria and fungi by state-of-the-art techniques or phenotypic screening of a collection.
Above all, the EMbaRC project aims at creating a strong network of professional actors sharing a vision and a common European ambition in the field of microbial collections and a concerted position at an international level.
Project Results:
The results achieved concern, on the one hand, mechanisms to improve the daily challenges and harmonized expertise of microbial BRCs, and on the other hand, their place and roles in the European Life Sciences and in developing the bioeconomy.
Microbial BRCs are professional entities dedicated for keeping biological resources for the long term and ensuring high quality standards. However, they need to improve their ability to keep delicate strains and to distribute them efficiently, including pathogens in a safe way. They also need to develop and provide new services adapted to the customers, and in particular to increase their expertise in taxonomy and strain identification by the most recent methods. Lastly, they need to harmonize their procedures and develop common protocols, including a code ensuring biosecurity, to be able to form a more efficient network at a European scale. Several significant results have been achieved to serve these needs:
- Standard operating procedures including protocols for culture acquisition, preservation and control were compiled, and a common Quality Manual was established (17pages, 14 sections based on ISO requirements). This generic document was made accessible on the EMbaRC website and can be provided to all collections wishing to reach high quality standards. The EMbaRC partners assessed the level to which they had implemented the OECD Best Practice Guidelines for BRCs. This served as a base line to determine their future development needs. This exercise helped provide both guidance on what the minimal requirements should be for the recognition of a culture collection becoming a BRC and the identified actions that could be coordinated and have common solutions. It facilitated the sharing of standard operation procedures where one collection had already implemented a requirement of the OECD guidelines to another which had not. The protocol for self-assessment was found useful and is now available for use by other collections wishing to set a prioritized plan of action for implementation of a quality management system.
- Improved protocols to raise recovery rates and extend the shelf life of several “delicate” species and strains for which conventional methods give poor results were obtained collectively. Regarding prokaryotes, six delicate species were chosen as experimental models and the choice of the lyoprotectant had the biggest impact on viability. Regarding eukaryotes, 15 delicate species were studied and for ectomycorrhizal fungi, the pre-growth in cryovials, avoiding handling, gave improved results for their long term maintenance. All these results were published and made available for the scientific community; to be taken up by BRCs as new daily practice for the storage of delicate strains. Example of publications of improved preservation protocols resulting from EMbaRC collaborative work:
Lalaymia, I., Cranenbrouck, S., Draye, X., Declerck, S. (2012). Preservation at ultra-low temperature of in vitro cultured arbuscular mycorrhizal fungi via encapsulation-drying. Fungal Biology 116 (10), pp. 1032-1041
Lalaymia I., Declerck S., Naveau F., Cranenbrouck S. Cryopreservation of arbuscular mycorrhizal fungi from root organ and plant cultures. (2014). Mycorrhiza 24 (3), pp. 233-237
Matthew J. Ryan*, Daiva Kasulyte-Creasey, Anthony Kermode, Shwe Phue San and Alan G. Buddie (2014) Controlled rate cooling of fungi using a Stirling cycle freezer CryoLetters 35 (1), 63-68
J. Peiren, J. Buyse, P. De Vos, E. Lang, D. Clermont, S. Hamon, E. Bégaud, C. Bizet, J. (2014) Pascual, M. A. Ruvira, M. C. Macián, D. R. Arahal. Improving survival and storage stability of bacteria recalcitrant to freeze-drying –a coordinated study by European culture collections. Biopreservation and Biobanking (in press )
- Several mechanisms for implementing best practices were evaluated and compared. For example, Deliverable D.NA1.1.1 Standard operating procedures and methods used for culture, characterization/control, and preservation by partners provided consolidated approaches for growth, preservation and storage of biological material. Deliverable D. NA1.1.2 Guidelines for optimal formatting/annotation of data related to the biological materials addressed best practice in data management. The OECD guidance for the operation of mBRC was converted into an operational standard suitable for consideration for the adoption under the International Standards Organization (ISO) which is now underway. ISO/TC 276 Biotechnology is under development its scope includes biobanks and bioresources; analytical methods; bioprocessing; data processing including annotation, analysis, validation, comparability and integration; and metrology. ISO/TC 276 Biotechnology will work closely with related committees in order to identify standardization needs and gaps, and collaborate with other organisations to avoid duplications and overlapping standardization activities.
- Guidelines for optimal formatting/annotating data were harmonized for interoperability. In parallel, a synthesis of the different existing portals to make widely accessible these data was made; 11 out of the 12 EMbaRC BRCs, which represent together more than 200000 strains, registered to one or all of these portals (see below, further explained).
- After an overview of existing legislations, guidelines and websites regarding biosecurity, a new Code of Conduct for biosecurity was provided and approved by all members of EMbaRC consortium. This document (18 pages) is accessible on the website of EMbaRC. It was finalized and approved during a biosecurity workshop organized by the partners in September 2011 in Utrecht and is now published (Christine Rohde, David Smith, Dunja Martin, Dagmar Fritze, and Joost Stalpers (2013). Code of Conduct on Biosecurity for Biological Resource Centres: procedural implementation. International Journal of Systematic and Evolutionary Microbiology 63, 2374-2382. http://ijs.sgmjournals.org/content/63/Pt_7/2374.long
- A shared approach to improve DNA extraction, storage and quality control, was achieved, extending the services provided by mBRCs and allowing taxonomic and genomic studies directly based on DNA samples (which distribution is much simpler in particular in case of pathogenic strains).
Clermont, D. et al. Assessment of DNA Encapsulation, a New Room-Temperature DNA Storage Method. Biopreservation and Biobanking 12, 176–183 (2014).
- Improved identification schemes based on new molecular markers, and an implemented high quality data base of gene sequences was collectively created for fungi, which will be a precious tool for research projects in the field of biodiversity., in silico approaches for identification candidate marker gene targets for the fungal kingdom have been tested and reported in scientific papers. New set of primers for the ITS, D1/D2 sequences and the actin gene have been tested for two genera : Coniothyrium-like anamorphs and Candida. Moreover a A well-resolved phylogeny of the complex white-rot Trametes group, relevant for its high lignolytic potential, was constructed based on concatenate sequences of ITS region and RBP2 gene from a wide sampling of temperate and tropical strains. In addition, a reference phylogenetic tree was constructed with traditionally used molecular loci (ITS region and b-tubulin gene) for the well-known Aspergilli section Nigri group in order to authenticate the selected strains including a large range of type strains and species.
- Improved identification schemes based on MALDI-TOF was provided for several species and valorized through publications. Comparative experimental work showed that MALDI-TOF profiles were machine dependent and hence not portable unless standardized conditions were linked to the use of the same type of apparatuses. Specific databases were created for MALDI-TOF spectra. MALDI MS/MS experiments were also developed on five bacteria genera: Lactobacillus, Streptococcus, Lactococcus, Enterococcus and Propionibacterium. A total of 26 species of food interest, represented by type strains where then studied with promising results that should be confirmed before publication. After clearance of the ExCom to provide access to the database for all interested users in June 2012, UVEG-CECT offered to host the ftp server for download, cared for the curation of the database and uploaded it to the server. The database can now be accessed after requesting username and password by email to the address maldi_embarc@cect.org. Users of the database are requested to acknowledge the EMbaRC project that enabled the built of the public database. The pending Deliverable D15.33 “Release of an accessible database of MALDI-TOF spectra of strains investigated” was drafted by DSMZ and UVEG-CECT and submitted for agreement by ExCom on September 12, 2012.The public release of the database of MALDI-TOF mass spectra of bacterial strains will be announced at the EMbaRC homepage.
Regarding the role of mBRCs, and their connection with life sciences laboratories and the bioeconomy, several actions were made to increase interactions.
- The access to a larger set of microorganisms and their associated data was facilitated via joining different existing portals : CABRI, StrainInfo.net or WDCM (World Data Center of Microorganisms). Specifically a link to EMbaRC mBRC data has been made via the WDCM Global Microorganism Catalogue (http://gcm.wfcc.info/embarc). This collaboration with the WDCM provides “A one-stop access” to the collections of EMbaRC strain catalogue data providing better access to authentic microorganisms and validated associated data from this consortium of European collections.
- A European microbial DNA bank network was created de novo, and made accessible via a Central web portal (www.microdnabank.eu). A complementary DNA bank with shared roles and common practices will develop the principle of shared activities to benefit the user. Enabling a joint accession policy and development of a unique and validated sequence databank linked to state-of-the-art preserved biological materials.
- Initial training offer in Europe was summarized and a new Erasmus Mundus program was created dedicated to microbial BRCs (EuroMiRC) as well as e-learning tools concerning basic technics used in a collection.
- A program of transnational access was built and 581 days of access in mBRCs were delivered to 57 European scientists or technicians coming from 20 countries, after a selection of their project on scientific basis. 90% were academic users. Each site proposed services corresponding to its particular field of expertise and research excellence. These services represent the state-of-art in a given domain and therefore users had access to this ‘collective’ state-of-the-art via EMbaRC. They could achieve different kind of expertise and ressources for their projects, as indicated below :
- High Throughput Screening of food bacteria and filamentous fungi
- Strain identification on pathogenic bacteria
- Handling risk group 3 microorganisms
- Taxonomy of pathogenic bacteria -food safety
- Management of microbial strains in ex situ collections
- State of the art techniques in bacteriology
- Identification - Authentication, characterisation, preservation, databasing storage of micro-organisms
- Analytical and microbiological services
- Theoretical, practical and regulatory aspects of a plasmid collection management
- In vitro Culture of Arbuscular Mycorrhizal Fungi
- An inventory of European mBRC holdings was made to estimate the coverage rate assured by the BRC partners of EMbaRC versus the number of species described up to date in the literature as well as to identify specific gaps to fill.
- A strategy of collection expansion was defined in a collaborative way and by organizing a meeting with stakeholders including scientific editors of the 8 main European microbial journals (Braunschweig, 02-2012) in order to stimulate and define criteria of strain deposit and long term preservation.
- Using a dedicated questionnaire on a two year basis, each collection was shown to have a unique funding profile, with a highly variable ratio of public support versus other sources (11%/89 % to the contrary). A long term strategy for European BRC sustainability was established collectively. Five ETP platforms related to food, biofuels, aquaculture, animal health, and plants were in particular identified as key targets for microbial BRCs. They will serve now within the MIRRI demonstration project.
- In order to increase the visibility of mBRC for scientists as well as for stakeholders numerous actions of dissemination were performed, including 49 conferences in 15 countries, as well as the edition of a success stories brochure. However, most importantly it is the recognition of the Microbial Resources Research Infrastructure (MIRRI) as part of the ESFRI road map and the funding of a preparatory phase that stands out, enabling the uptake and use of the whole range of outputs from the EMbaRC project.
List of publications done within the EMbaRC project
Casaregola, S., Weiss, S. & Morel, G. New perspectives in hemiascomycetous yeast taxonomy. Comptes Rendus Biologies 334, 590–598 (2011).
Clermont, D. et al. Assessment of DNA Encapsulation, a New Room-Temperature DNA Storage Method. Biopreservation and Biobanking 12, 176–183 (2014).
Cousin S, Clermont D, Creno S, Ma L, Loux V, Bizet C, Bouchier C. Draft Genome Sequence of Lactobacillus pasteurii CRBIP 24.76T. Genome Announc. 2013 Aug 22;1(4). pii: e00660-13. doi: 10.1128/genomeA.00660-13.
Cousin S, Creno S, Ma L, Clermont D, Loux V, Bizet C, Bouchier C. Draft Genome Sequence of Lactobacillus hominis Strain CRBIP 24.179T Isolated from Human Intestine. Genome Announc. 2013 Aug 22;1(4). pii: e00662-13. doi: 10.1128/genomeA.00662-13.
Cousin S, Loux V, Ma L, Creno S, Clermont D, Bizet C, Bouchier C. Draft Genome Sequences of Lactobacillus equicursoris CIP 110162T and Lactobacillus sp. Strain CRBIP 24.137 Isolated from Thoroughbred Racehorse Feces and Human Urine, Respectively. Genome Announc. 2013 Aug 22;1(4). pii: e00663-13. doi: 10.1128/genomeA.00663-13.
Cousin, S. et al. Draft Genome Sequence of Lactobacillus gigeriorum CRBIP 24.85T Isolated from a Chicken Crop. Journal of Bacteriology 194, 5973–5973 (2012).
Cousin, S. et al. Lactobacillus gigeriorum sp. nov., isolated from chicken crop. International Journal of Systematic and Evolutionary Microbiology 62, 330–334 (2012).
Cousin, S. et al. Lactobacillus pasteurii sp. nov. and Lactobacillus hominis sp. nov. International Journal of Systematic and Evolutionary Microbiology 63, 53–59 (2013).
Crahay, C. Wevers, J., Munaut F., Colpaert, J.V. & Declerck, S. Cryopreservation of ectomycorrhizal fungi has minor effects on rootcolonization of Pinus sylvestris plantlets and their subsequent nutrientuptake capacity Mycorrhiza 23 (6), 463-471 (2013).
Crahay, C., Declerck, S., Colpaert, J.V. Pigeon, M. & Munaut F. Viability of ectomycorrhizal
David Smith, Kevin McCluskey and Erko Stackebrandt. Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres. SpringerPlus 2014, 3:81 doi:10.1186/2193-1801-3-81
Dequin, S. & Casaregola, S. The genomes of fermentative Saccharomyces. Comptes Rendus Biologies 334, 687–693 (2011).
Falentin H, Cousin S, Clermont D, Creno S, Ma L, Chuat V, Loux V, Rüdiger P, Bizet C, Bouchier C. Draft Genome Sequences of Five Strains of Lactobacillus acidophilus, Strain CIP 76.13T Isolated from Humans, Strains CIRM-BIA 442 and CIRM-BIA 445, Isolated from Dairy Products, and Strains DSM 20242 and DSM 9126 of Unknown Origin. Genome Announc. 2013 Aug 22;1(4). pii: e00658-13. doi: 10.1128/genomeA.00658-13
fungi following cryopreservation. Fungal Biology117(2),103-111 (2013).
J. Peiren, J. Buyse, P. De Vos, E. Lang, D. Clermont, S. Hamon, E. Bégaud, C. Bizet, J. Pascual, M. A. Ruvira, M. C. Macián, D. R. Arahal. Improving survival and storage stability of bacteria recalcitrant to freeze-drying –a coordinated study by European culture collections. Biopreservation and Biobanking (in the process of resubmission after reviewers comments)
Janssens, D., Arahal, D. R., Bizet, C. & Garay, E. The role of public biological resource centers in providing a basic infrastructure for microbial research. Research in Microbiology 161, 422–429 (2010).
Mallet, S. et al. Insights into the Life Cycle of Yeasts from the CTG Clade Revealed by the Analysis of the Millerozyma (Pichia) farinosa Species Complex. PLoS ONE 7, e35842 (2012).
Pereira, L., Dias, N., Santos, C. & Lima, N. The use of MALDI-TOF ICMS as an alternative tool for Trichophyton rubrum identification and typing. Enfermedades Infecciosas y Microbiología Clínica 32, 11–17 (2014).
Robert, V. The Quest for a General and Reliable Fungal DNA Barcode. The Open Applied Informatics Journal 5, 45–61 (2011).
Rodrigues, P., Santos, C., Venâncio, A. & Lima, N. Species identification of Aspergillus section Flavi isolates from Portuguese almonds using phenotypic, including MALDI-TOF ICMS, and molecular approaches: Aspergillus section Flavi polyphasic identification. Journal of Applied Microbiology 111, 877–892 (2011).
Rohde, C., Smith, D., Martin, D., Fritze, D., Stalpers J. Code of Conduct on Biosecurity for BiologicalResource Centres: procedural implementation. International Journal of Systematics and Evolutionary Microbiology 63, 2374–2382 (2013).
Santos, C., Fraga, M. E., Kozakiewicz, Z. & Lima, N. Fourier transform infrared as a powerful technique for the identification and characterization of filamentous fungi and yeasts. Research in Microbiology 161, 168–175 (2010).
Santos, C., Lima, N., Sampaio, P. & Pais, C. Matrix-assisted laser desorption/ionization time-of-flight intact cell mass spectrometry to detect emerging pathogenic Candida species. Diagnostic Microbiology and Infectious Disease 71, 304–308 (2011).
Schoch, C. L. et al. Nuclear ribosomal internal transcribed spacer (ITS) region as a universal DNA barcode marker for Fungi. Proceedings of the National Academy of Sciences 109, 6241–6246 (2012).
Smith, D. & Day, P. (2012). European Consortium of Microbial Resource Centres: Microbial Resources Success Stories. EMbaRC, CABI, UK, http://www.embarc.eu/embarc-update-16.pdf.
Smith, D. & Fritze, D. European Culture Collections – The Future is MIRRI. Microbiology Today 37, 256–258 (2010).
Smith, D. & Ryan, M. Implementing Best Practices and Validation of Cryopreservation Techniques for Microorganisms. The Scientific World Journal 2012, 1–9 (2012).
Smith, D. (2012) A new look at Microorganisms. Insight Publications, Projects 20, 18-19. http://viewer.zmags.com/publication/4c7a6b67#/4c7a6b67/19; SEED Research Library: http://www.seedresearchlibrary.com/biology-medicine-research-projects/174/embarc-improves-microbial-resource-delivery
Smith, D. in Advances in Applied Microbiology 79, 73–118 (Elsevier, 2012).
Smith, D., Fritze, D. & Stackebrandt, E. in the Prokaryotes 267–304 (Springer, 2013).
Smith, David. Research Resources Help To Drive Innovation in Microbiology. Microbe Magazine 6, 486–490 (2011).
Stackebrandt E, Smith D, Casaregola S, Varese GC, Verkleij G, Lima N, Bridge P. (2014). Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science. SpringerPlus 2014, 3:208 doi:10.1186/2193-1801-3-208
Stackebrandt, E. Diversification and focusing: strategies of microbial culture collections. Trends in Microbiology 18, 283–287 (2010).
Stackebrandt, E. Editorial. Archives of Microbiology 193, 155–156 (2011).
Stackebrandt, E. Hinterlegung von Mikroorganismen – ein Dienst an der Wissenschaft. Biospektrum 363 (2011).
Stackebrandt, E. Responsibilities of Culture Collections. Microbiology Today 37, 259 (2010).
Stackebrandt, E. Towards a strategy to enhance access to microbial diversity. International Journal of Systematic and Evolutionary Microbiology 61, 479–481 (2011).
Verkley G.J.M. Dukik K., Renfurm R., Göker M., Stielow J.B. Novel genera and species of Coniothyrium-like fungi in the Montagnulaceae (Ascomycota). Persoonia 32, 25–51 (2014).
Welti, S. et al. Molecular phylogeny of Trametes and related genera, and description of a new genus Leiotrametes. Fungal Diversity 55, 47–64 (2012).
Potential Impact:
Potential impact, main dissemination activities and exploitation results
EMbaRC has delivered tools to improve the management and operation of mBRCs, improve access to the microbial resources and expertise within them and by working with the scientific community has demonstrated how mBRCs can help accelerate discovery of active compounds and microbial solutions to societal challenges.
A key outcome is the recognition of the responsibilities of scientists, editors and the European mBRCs themselves to continuously improve the coverage and preservation of biodiversity. Through the coordinated efforts within EMbaRC, mBRCs already provide better access through virtual catalogues to high quality resources and their associated data to the world’s scientific community. Involved in initial or vocational training, they also better contribute to the maintenance of skills in taxonomy and long term strain preservation. More than before, mBRCs are drivers in the challenge of promoting “reference collections”, in particular by helping collections willing to develop their Quality Management System.
Biological resources are no longer just associated with scientific and medical purposes, providing reference strains. They are open spaces offering multiple uses and are mobilized in a variety of application contexts carrying other issues and unpublished values. The OECD Guidance designs the BRCs as a place where new interactions between academic research, industry and market are experienced. Since the 1970s, scientific activity has changed dramatically, and so exacerbated the life sciences. Socio-political and economic changes have led to the expansion of market transactions through the patentability of biological materials, renewing logical appropriation of knowledge. The biological resources are gradually moved from simply being a tool for scientific and medical research, a holder of legal issues requiring legal regulations, to become a political instrument promoting economic growth. Primarily subject to local business regulations, collections of biological resources have gradually fallen between several forms of regulation (professional, state, market) at national and international levels. These arrangements have fundamentally changed the status and market potential of biological resources, but also the way to collect living resources. The networking of BRCs during EMbaRC reinforced the emergence of this new system of knowledge production. However, coordinating the collection of living resources does not happen by itself. First of all, the era of large-scale biology, the development of "reference collections" is a practical necessity. Without them, no common benchmarks to evaluate multiple samples now available exists, nor the potential to develop batteries of performance tests. Different concepts of value co-exist: a mBRC may be of interest to researchers for the advancement of knowledge, to physicians for diagnoses and therapy provision, to pharmaceutical firms exploring opportunities in drug discovery, or to governments that focus on synergies between science, medicine and industry. Finally, legal standards, best practice guides, quality procedures, certification schemes, access policies are ways to regulate the production and distribution of biological resources.
BRCs have also the opportunity to conduct themselves or in collaboration R & D on biological resources they hold. This can directly contribute to progress in life sciences or lead to useful products generating revenue to support the functions of the broader BRC. However, as we have seen within the project the balance between internal R & D and service activities is delicate to reach as regular public funding is not sufficient to support BRC activities. One of the BRC mission is thus to involve industry in a "long term vision" to harmonize their royalty regimes, and develop marketable products and services, in various domains like health, food, biotechnology and environment. Taking this crucial point into consideration, MIRRI was built on the foundations set by EMbaRC’s achievements.
Concrete impacts
The EMbaRC partnership as key BRCs in Europe harmonised structure and activities on several levels: harmonisation of characterisation and preservation techniques, harmonisation of quality processes and procedures via best practice implementation guidelines and standards, creation of a common web portal and one-stop-shop to the collections resources, expertise and service, and development of a common approach and plan to self-sustainability further to a mapping of current governance, and costing policies of the BRCs.
This can now be useful to:
- the end users (researchers, SMEs and large industrials) providing them with a coherent and consistent service no matter which BRC they approach in terms of the quality of the resources provided, the procedures for strain deposit and preservation and IPR policies.
- the other EU collections, particularly the small collections which do not have the means to invest in new techniques and cumbersome quality processes can benefit from EMbaRC know–how and results. This is delivered on several fronts from sharing sustainable business models to best practices and standard operating procedures; providing short cuts and reducing the investment needed will help to ensure their continued existence.
- The EU research community, as they can access high quality resources and associated services more easily via the web portal, allowing them to find a particular resource with the reassurance that the quality and procedures will be the same from one collection to another. Via the dissemination, training and outreach activities EMbaRC partners tried that the wider research community and SMEs see strains as an asset and worth maintaining and depositing to which the BRC can ‘add value’. This should encourage a more systematic depositing of strains from the wider community reassured with a common and fair IPR policy to enable the BRCs to propose larger strain sets and access to several collection services therefore ensuring a greater biodiversity.
- The EU biological research area through a coordinated infrastructure and complementarity of mBRCs. There are vast numbers of microbes still to be discovered, the majority of which are not yet culturable. However, it is clear that we need a better understanding of biological diversity in particular to enable us to harness their properties to the benefit of humankind at a time when other natural resources are depleted. EMbaRC proposed a strategy to fill the gap and increase the coverage by sharing in a complementary way the task of maintaining biodiversity. Improved data and greater access to a wider range and better maintained resources as proposed by EMbaRC results will provide European industry with a huge advantage over the rest of the world and a road to delivering the bioeconomy.
- The protection of the citizen against biological weapons. Indeed biological weapons are devices which disseminate disease-causing organisms or poisons to kill or harm humans, animals or plants. Almost any disease-causing (such as bacteria, viruses, fungi, prions or rickettsiae) or toxin-producing micro-organism (poisons derived from organisms, or produced in response to micro-organisms) can be used in biological weapons. There are many different disease-causing organisms that are potential candidates for biological weapons. On the other hand, many of these organisms are extremely important for research and development in the domains of medicine, biology and agriculture. These organisms can therefore be used for two purposes. The term used by the international community for these types of organism is `dual use'. OECD has seen the necessity that especially BRC’s as guardians of many potentially dual use strains should have at least common minimum guidelines. National and international bodies (e.g. the States Parties to the BTWC) have formulated the necessity to come to a code of conduct on biosecurity. Before EMbaRC, only three of those countries (Albania, France, and the Netherlands), have started drafting a national code of conduct on biosecurity. EMbaRC worked with the collection community, particularly the GBRCN consortium and ECCO to publish a code of conduct for biosecurity to raise awareness and to put in place manageable and appropriate best practices. These were discussed in various fora and have been accepted at the European level. In December 2011, the code was introduced at the 7th Review Conference to BTWC, United Nations, Geneva, together with an NGO (non-governmental organization) statement (available in IJSEM Online) and was well received by the review conference. The universal uptake of this code by mBRCs will prevent them from directly or indirectly contributing to the development, production or preservation of biological weapons, as described in the Biological and Toxin Weapons Convention (BTWC), or to any other misuse of biological material or derivatives.
- There are several other societal and economic benefits that will arise from the EMbaRC project in the future. The Microbial Resource Research Infrastructure is now in its preparatory phase. This infrastructure has several goals and builds on the outputs of EMbaRC and its collaborations with GBRCN and ECCO. Microbiological diversity and well described microbial resources will play a key role in underpinning the bioeconomy and driving economic growth through successful biotechnological innovation. Harvesting the full value in such organisms is fundamental to agribusiness, industrial biotechnology health technology, biofuel production and, more fundamentally to new industrial policy and green growth. These are in turn fundamental to the delivery of continuing European success in a world that is globalising at a startlingly unprecedented pace. Realizing sustained growth and harnessing a successful bioeconomy will not, however, happen spontaneously and will require private and public sectors to work together to develop specific initiatives plus a supportive environment for the bioeconomy to emerge. A well-integrated research infrastructure that underpins such efforts will be essential. Improved understanding, use and uptake of microbial resources will accelerate innovation and discovery and thus lead to a more successful biotechnology in Europe. The European Commission Directorate General for Research and Innovation Research Infrastructures estimates that there are around 500 000 life scientists in the research landscape. Many of whom are microbiologists reliant on high quality microbial resources. The “bioeconomy” as a whole is worth nearly €2 trillion and provides approximately 22million jobs in Europe alone across sectors as diverse as agriculture, forestry, fisheries, food, chemicals and biofuels (EuropaBio (2012) The tax, finance and regulatory framework and global policy comparison. European Commission. http://www.europabio.org/biotechnology-europe-tax-finance-and-regulatory-framework-and-global-policy-comparison). The provision of well characterised strains in a targeted and coordinated fashion can only accelerate the growth in this area.
- Answering the global challenges; effort is often fragmented and thus inefficient and costly, therefore the coordinated effort through MIRRI can focus the discovery of solutions to the challenges. The idea of releasing the “full value” in microbial resources is pivotal to delivery of the bioeconomy. Simply put, such value is the potential for use of microbial resources, as well as the biological systems and components therein, in basic and applied science as well as in innovation (for example, the potential that may be inherent in some fungal metabolites to act as new generation antimicrobials). There is a need to be able to focus the expertise and capacity of mBRCs to provide the specific resources to facilitate discovery of solutions to some of our grand challenges such as antimicrobials for control of resistant diseases and accelerate discovery in healthcare. Greater rigour and greater cooperation is required to ensure that research matches industry and societal demand. The broader user community need to be brought into a strategic discussion with MIRRI on addressing such gaps in the short, medium and longer terms. The G8 Science Ministers’ Statement (https://www.gov.uk/government/news/g8-science-ministers-Statement) made 12 June 2013, highlighted the need to improve transparency, coherence and coordination of the global scientific research enterprise to address global challenges. They focused on antimicrobial drug resistance as a major health-security challenge, and the need to work together to reduce antimicrobial resistance. They stressed that Research Infrastructures are key elements in research and innovation policies. Iniitiated by EMbaRC, MIRRI will also assist in turning new data into new knowledge and making that knowledge available through integrated and open knowledge networks. Knowledge presents the hidden value in recognisable terms for investment. It envisages the creation of a knowledge collaboration based on data networking. It is the gold standard of a publicly-funded shared knowledge in a way that casts light on G8 aspirations for new antimicrobials.
Dissemination of results
EMbaRC key outputs
Implementing best practice
Standard operating procedures and methods used for culture, characterization/control, and preservation by the partners
A BRC operational standard based on the OECD best practice guidelines for Biological Resource Centres as a working draft for an ISO Standard
Code of conduct for Biosecurity
Improving methods
Recommendation of best protocols for preservation
Report on the dissemination of information and common access to current DNA banks
Common optimised methodology for the storage of DNA
Method validation exercise via inter-laboratory tests
Report on strain authentication by MALDI-TOF and identification of accurate and misclassified/mislabelled strains in consortium holdings
Guidelines for optimal formatting/annotation of data related to biological materials
Supporting users
Transnational access: study visits to utilise partner expertise and technologies
Report on the survey of training courses and a proposal to implement a common training programme
EMbaRC Web site
EMbaRC workshop for emerging collections in Romania
Report on the learning materials to support the teaching/training activities
Supporting science
A strategy for increasing collection holdings with scientifically relevant resources
Publication on comparative genomic analysis of prokaryote targeted species
Report on phylogenetic approach using enzymes of industrial interest
Supporting culture collections/BRCs
A model strategy for sustainability of BRC services
Overview of existing legislation, guidelines, best practices etc. connected with biosecurity
Dissemination tools
EMbaRC utilised many tools to disseminate its outputs to the various stakeholders:
End-User level stakeholder
The research community including SMEs and research labs of large corporates who are current and or potential users (and clients) of the EMbaRC infrastructure and services were a key target group. Partners attended partnering events, conferences and trade shows to interact with representatives from academia and bioindustry (see below). Additionally, work with scientific journal editors has helped promote the deposit of strains cited in publications to ensure their continued availability for confirmation of results and further studies. The main dissemination tools used for this target group were the EMbaRC Web portal and Newsletter, presentations at key bio- industry events and targeted email shots.
Network level stakeholder
The outreach activities extended to the global, regional and national federations of culture collections. A presence at their conferences and business meetings ensured a two-way dialogue on the network activities of EMbaRC and the transfer of project results. The key dissemination tools used were presentations at ECCO meetings, the EMbaRC Workshop in Romania and publications.
Political level stakeholder
National Authorities were a key collaborator in the design of the code of conduct on biosecurity and issues on the impending implementation of the Nagoya Protocol and Access and Benefit Sharing. Research programme funders were consulted regarding the protection of their investments made in research and collection of biological materials. Relevant international organisations were consulted directly for example the BTWC and WHO (on the biosecurity code) and others through News/articles, lobbying by EMbaRC partners at national level, web site and presentations at key events (see the table below).
Main Dissemination tools:
EMbaRC Newsletter: 4 issues were distributed to the full EMbaRC distribution list
EMbaRC Web portal: www.embarc.eu: Visitors to the web site can access electronic catalogues of the partner mBRCs, an information resource, news and relevant events. The key resources presented are technical training videos are available on gram staining, fungi observation under the optical microscope and preservation techniques; Access to the European microbial DNA Bank Network at
www.microdnabank.eu; The Code of Conduct on Biosecurity for BRCs; The Database for Molecular Taxonomy and Phylogeny of Yeasts (YeastIP) and the EMbaRC Brochure Microbial Resources Success stories
EMbaRC presentations at key conferences
EMbaRC was present at 41 conferences in more than 10 countries presenting over 40 papers or posters. Key events are listed below and some of them were then detailed for their special importance :
• Colóquio do Instituto Nacional dos Recursos Biológicos I.P. (INRB)
• The GBRCN Regional Seminar
• Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)
• Simpósio de Coleções Culturas at the 25th Congresso Brasileiro de Microbiologie (Brazilian Microbiology Congress) held in Porto de Galinhas, Brazil, 3-11 November 2009
• EUPHRESCO – Europe Wide Workshop on Building and Influencing Transnational Phytosanitary Research Strategies
• 3rd FEMS Congress for European Microbiologists Microbes and Man: Interdependence and Future Challenges
• Science Collections International, Brussels, Belgium
• 8th Meeting of the French Society for Microbiology (SFM)
• ECCO XXVIII, Göteborg, Sweden,July 2nd - 3rd ; ECCO XXIX Annual Meeting of the European Culture Collection’s Organisation
• BTWC 7th Review Conference
• International Society for Microbial Ecology (ISME) Annual conference
EMbaRC Workshop: Institut Cantacuzén, Romania (for East EU collections) in 2009 and a Workshop associated with ICCC12, the WFCC international Culture Collection Conference in Brazil in 2010
The GBRCN Annual Meeting, Braunschweig, Germany, 22-26 February 2010
The meeting brought together the Global Biological Resource Centre Network (GBRCN) Demonstration Project partners with related projects and initiatives across Europe, in Australia, Asia, the USA and Eastern Europe. There were 46 participants from 16 countries on 5 continents. Representatives from the GBRCN Demonstration Project, the European Consortium of Microbial Resources Centres (EMbaRC, EU Seventh Framework Programme Research Infrastructures (INFRA-2008-1.1.2.9: Biological Resources Centres (BRCs) for microorganisms), and the CABRI (Common Access to Biological Resources and Information) network discussed together with the ESFRI (http://cordis.europa.eu/esfri/) initiatives BBMRI (http://www.bbmri.eu/) and ERINHA http://asso.orpha.net/HBSL/) and with representatives from the EU, the OECD and the EUPHRESCO ERA Network. Parties interested in the networking initiative came from Russia, Taiwan, Australia and the USA. Topics revolved around issues on biosecurity, information systems, and governance structures and implementation of best practice and other potential areas of collaboration. Several actions arose to help define the work of the GBRCN Demonstration Project and outline areas of collaboration with other initiatives.
EMbaRC progress was discussed and the opportunity for Transnational access reported to participants..
Science Collections International Brussels
SciColl is an international initiative devoted to increasing the benefits that object-based scientific collections and their associated information produce for science and society. It brings together major museums and proposes an international co-ordination mechanism that will enable the uptake of best practices, stimulate collaborations and identify and open new areas of research that rely on scientific collections. SciColl is an OECD Global Science Forum initiative and has formulated a strategy, drafted infrastructure, budget and outreach documents. It presents itself as a Research Infrastructure for collections and thus has similar goals to GBRCN and the Microbial Resources Research Infrastructure (MIRRI)
i. Steering Group meeting, Berlin, 02-05 September 2009
ii. GBRCN mechanisms for improving quality in BRCs at the Scientific Collections International Organisation (SciColl) Outreach Conference in Brussels, 07-09 February 2010
Talks presented at both on the GBRCN but emphasising the role of EMbaRC to develop the European platform
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI)
Stakeholders Meeting, Brussels, 16 September 2009
Biobanking and Biomolecular Resources Research Infrastructure (BBMRI) is addressing the networking and best practice issues. BBMRI is a pan-European and internationally broadly accessible research infrastructure and a network of existing and de novo biobanks and biomolecular resources (http://bbmri.eu/bbmri/index.php). Its mission is:
• To benefit European health-care, medical research, and, ultimately, the health of the citizens of the European Union.
• To have a sustainable legal and financial conceptual framework for a pan-European Biobank infrastructure.
• To increase scientific excellence and efficacy of European research in the life sciences, especially in biomedical research.
• To expand and secure competitiveness of European research and industry in a global context, especially in the field of medicine and biology.
EMbaRC and the GBRCN demonstration project are exploring with BBMRI how the initiatives can best work together.
Simpósio de Coleções Culturas at the 25th Congresso Brasileiro de Microbiologie (Brazilian Microbiology Congress) held in Porto de Galinhas, Brazil, 3-11 November 2009
A special session on culture collections included presentations on the Brazilian BRC network development project and further opportunities for funding. The latter was covered by Luiz Antonio Rodrigues Elias representing the Executive Secretary of the Ministry of Science and Technology. The discussion session generated lively and enthusiastic debate (all in Portuguese) but and executive summary provided by Vanderlei Canhos said everything had gone extremely well and that all were pleased with the Brazilian projects and participation in the GBRCN demonstration project. Fritze and Smith’s presentations covered EMbaRC’s contribution to establishment of the global network (GBRCN). The report on the special session and the participants list will appear on the CRIA web site.
EUPHRESCO - Europe Wide Workshop on ‘Building and Influencing Transnational Phytosanitary Research Strategies, 26 – 27 May 2009, Braunschweig, Germany
This is a Coordination Action funded by the European Union's ERA-NET Scheme under the 6th Framework Programme (FP6). It presently involves a partnership of 24 organisations involved with funding or managing phytosanitary (quarantine/regulated plant health) research programmes in 17 European countries. It is policy-led and involves the European Commission's Directorate General for Health and Consumer Protection (DG SANCO), the European and Mediterranean Plant Protections Organisation (EPPO) and the European Food Safety Authority (EFSA) through an Expert Advisory Group. EUPHRESCO aims to coordinate its trans-national activities with EU-funded programmes to ensure overlaps are avoided and optimal research is commissioned. EMbaRC, ECCO and the GBRCN can provide the microbial resources to underpin activities and EUPHRESCO can be approached to contribute to support MIRRI if it succeeds on getting on the Pan-European road map as a global research infrastructure.
3rd FEMS Congress for European Microbiologists: Microbes and Man: Interdependence and Future Challenges 2009 June 28 – July 2 Göteborg Convention Centre, Göteborg, Sweden
Smith and Fritze (GBRCN Secretariat) participated in the FEMS and ECCO meetings held in Göteborg, Sweden to present oral presentations and posters on the GBRCN and, EMbaRC projects
To present:
Posters:
Managing Microbes an E-Learning Experience
The Global Biological Resource Centre Network Demonstration Project
Biorisk: how Culture Collections deal with Biosafety & Biosecurity
Correct packaging for microorganisms
Would your collection join the Global Biological Resource Centre Network?
European Consortium of Microbial Resources Centres – EMbaRC (
European Culture Collection’s Organisation – ECCO
European Culture Collection’s compliance with the CBD and Access and Benefit Sharing
Oral presentations:
The background of the OECD GBRCN demonstration project
The Vision and Current activities of the GBRCN demonstration project
Access and Benefit Sharing, a micoorganism perspective
ECCO XXVIII, Göteborg, Sweden,July 2nd - 3rd
CABI, DSMZ, MUM, LMG and other partners attended the European Culture Collections’ Organisation (ECCO) meeting held back to back with FEMS to present some of the posters and presentations to a new and more focussed group of participants at the ECCO annual meeting. The poster: The European Consortium of Microbial Resources Centres – EMbaRC was presented (Annexe 1 Abstract text 2) and presentations highlighted the role of EMbaRC in delivering a microbial resource to underpin European research.
The GBRCN Regional Seminar, Guimarães, Portugal, 12-16 May 2009
The programme of the meeting was designed to address a few key issues to get the partner work in the GBRCN fully underway. The meeting was the first of the GBRCN outreach seminars and was arranged by Esperanza Garay, Spain and Nelson Lima, Portugal, the latter making all the local arrangements for the meeting at Ave Park which is located in Taipas, Guimarães. The Ave Park is a new Science Park where the University of Minho has its biotechnology spin off and shares conference facilities. The GBRCN seminar was held back to back with a MALDI-TOF workshop, the second day of the latter being open to participants; the GBRCN Secretariat were allowed to make two presentations on the GBRCN project. The GBRCN seminar was split into a day of informative presentations on the background and progress, including country reports. The second day included a working meeting with certification/accreditation bodies to define the work programme in this area and presentations on Biosecurity and options for a GBRCN information system. The presentations addressed the input of EMbaRC to the development and establishment of the GBRCN.
The MicroBiotec 11 meeting in Braha (Portugal) 2011 (http://microbiotec11.files.wordpress.com/2011/12/e-microbiotec11.pdf). In this meeting of the Portuguese society for Microbiology and the Portuguese Society for Biotechnology, the EMbaRC project was presented in a Keynote lecture.
Exploitation of the EMbaRC results
Exploitation results:
- A one-stop access to the collections of EMbaRC and the wider European BRC community via a searchable web portal (Deliverable NA2.3.2)
- Access and high-quality support and training to research teams via an open call for access delivering 57 access opportunities to research teams from 20 countries (Via TA1 – 8 and the support of NA2)
- Improved methods for strain and DNA preservation (Deliverable JRA.1.2.2/3)
- Novel approaches for identifying species methods such as mass spectrometry, screening and high throughput sequencing). (Deliverable JRA.2.1.1)
- A complementary DNA bank with shared roles and common practices developed the principle of shared activities to benefit the user.
- A creation of a high quality database for eukaryotes (filamentous fungi and yeasts) which is a precious tool for research projects in the field of biodiversity.
- A working draft ISO standard for microbial resource centres and accompanying implementation guidelines and training material (Deliverable NA.1.2.2)
- A code of conduct for biosecurity for European BRCs (Deliverable NA.1.3.3)
- A strategic plan for the role of EMbaRC and the wider EU BRC community in the GBRCN (Deliverable NA.3.2.4)
- A set of financial models for the self-sustainability of BRC (Deliverable NA.3.2.4)
The above outputs have been made available for further exploitation. Several tools have already been adopted by the MIRRI consortium in the preparation phase prior to the implementation of this ESFRI infrastructure. Particularly taken up are the Code of conduct for biosecurity, the further development of quality management standards and the financial models. Other elements have been incorporated in MIRRI strategies for future implementation. All the outputs will constitute the first steps to forming the Global Biological Resource Centre Network; MIRRI is the European regional node for the GBRCN and is closely linked with initiatives in South and North America, Asia and Africa. The EMbaRC outputs have been promulgated globally through these linkages. The research results (JRA1 and 2) have added value to the partners' current collections and related services enabling them to attract a wider customer base. The scientific results have been published in key journals
The most significant development instigated by EMbaRC, GBRCN demonstration project consortium and ECCO has been Microbial Resources Research Infrastructure (MIRRI). A joint proposal was tabled by the French European Strategy Forum on Research Infrastructures (ESFRI) delegate and MIRRI is now on the Biological and Medical Sciences Road Map. A workshop at the Leibnitz Association Brussels with EU officers on the 14-16 December 2009 was organised by the GBRCN to discuss funding. Discussions focussed on the ESFRI route for development funding for MRRI. Other opportunities were the EU Capacities Programme, a proposal to the DG Justice and Home Affairs, Counter Terrorism II for a Biosecurity database and a proposal on an information system for the GBRCN to the e Infrastructures programme. Presentations included EMbaRC’s contribution to global networking. The European Commission´s representatives were Jean-Emmanuelle Faure, Research Directorate General Research Infrastructures (Unit B3), Annika Thies, DG Research, Research Infrastructure, Garbine Guiu, DG Research, Biotechnologies, Patrick Dietz, Directorate-General Justice and Home Affairs Directorate F: Security Unit F1, Susanna Kantas, DG Internal Market and Services Industrial, Property Unit and Carlos Morais, DG Infso, Geant and e-Infrastructures.
List of Websites:
http://www.embarc.eu
Sylvie.lortal@rennes.inra.fr (coordinator) / Chantal.bizet@pasteur.fr / d.smith@cabi.org