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Prof. Erko Stackebrandt |
Dear all,
a labour - and (for those who were interested) a soccer-intense summer is now behind the MIRRI consortium. The MIRRI highlight of the summer 2014 clearly was the MIRRI Midterm Review, held in June. During this one-day-evaluation by representatives of the European Commission the main project outcomes of the first 18 months were presented and discussed. My thanks go to all who contributed by Work Package information, drafting, advice, as speakers in the meeting in Paris (preparatory meeting) and by contributing to the excellent atmosphere during the Evaluation meeting in Amsterdam.
The Technical Report has now been received and the expert confirms that considerable progress has been acknowledged and that the project has great potential. Members of the Steering Committee thanked the reviewer for the fair and objective assessment and for the helpful criticism mainly concerning the improvement of the MIRRI approach to the stakeholder community. Needless to say that we would have liked to have the MIRRI project be rated ‘excellent’, but we tolerate and accept the experts’ opinion on certain shortcomings. The response has been sent back to our ESFRI officer Ann Uustalu and we will now wait for the final report which will be sent to MIRRI Partners and Collaborating Parties in due time.
No time to rest! To continue in soccer jargon: ‘After the game is before the game’ meaning in MIRRI terms ‘After the EC evaluation is before the individual national stakeholder evaluation’. The evaluation momentum must be transformed into action in the following months as several issues addressed in Amsterdam were identified which need immediate attention.
Besides, work during the last months concentrated on MIRRI involvement on Horizon 2020 projects CORBEL, MBRIC and BioGHA (deadline September 2nd) which intensified the relationship of MIRRI with its members of the BMS group. Work in the next months will focus on finalisation of WP strategies, the revision of the 2nd Iteration MIRRI Business Case, and the definition of MIRRI-ERIC Statutes, the Governance Structure and of the Central Coordinating Unit (CCU) tasks and composition, as well as revision of financial plans for CCU and national nodes/networks and the ERIC legal framework. With all these elements in our hands we will encourage the Member States to sign the MIRRI Memorandum of Understanding, the first step towards the envisioned MIRRI-ERIC.
MIRRI Partner and Collaborating Parties already started to request Letters of Intent from the MIRRI stakeholder community to visualize the supported by academia as well as industry and European research projects. I would like to encourage you, the MIRRI stakeholders, to write a short Letter of Intent to emphasize the importance our envisioned infrastructure.
Keep on going - As the British say: You never walk alone.
Kind regards,
Erko Stackebrandt
MIRRI Coordinator
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Prof. Dr. Daniel Ramón |
Daniel Ramón, MIRRI stakeholder and MIRRI Advisory Board expert
Prof. Dr. Daniel Ramón is the CEO of the biotech companies Biopolis S.L. and Lifesequencing S.L. as well as member of the Advisory Board of MIRRI. He has participated in several projects that show the power of microbial Massive Genome Sequencing (MGS) in issues related to taxonomy, genotype to phenotype mapping or food safety assessment, among others. We were interested in Dr. Ramón’s opinion about the potential of this methodology and how could MIRRI add value to this field. Dr. Ramón remarked “MGS is a rapidly evolving tool with relevant applications in microbial biotechnology including biofuel production, bioremediation, soil fertilization or probiotics preparations. Furthermore, genome sequencing is becoming increasingly cheaper, faster and user-friendlier, making applied microbial genomics an affordable approach for new startups.” As Dr. Ramón says, “We are technically ready to enter a new area of massive genome sequencing of microbial culture collections. These collections hold an enormous treasure of biodiversity with social and industrial relevance that needs to be explored. MIRRI can act as a central hub for integrating resources, services and expertise, building the road from microbial raw material to biotechnological solutions.”
WP8: Data Resources Management
At present, most microbial Biological Research Centers (mBRCs) act as proprietary entities with respect to data acquisition, data quality management, data exchange and interoperability. Heterogeneous and incomplete datasets are the result. Furthermore, the lack of commonly agreed exchange formats as well as often insufficient IT-competences compromise data exchange and interoperability between mBRCs as well as public databases. As a consequence, the usage of the highly valuable knowledge stored in mBRCs is hampered for stakeholders in academia and industry. The “Data Resource Management” work package defines concepts and strategies to improve the quality, quantity, interoperability and usage of data associated with biological material. The vision is to establish the MIRRI Information System (MIRRI-IS). MIRRI-IS will manifest as an integrated, high-quality, manually annotated, non-redundant micro-biological resource database providing all relevant information and associated contextual data (metadata) about a particular biological resource stored in mBRCs. It will be designed as the central entry point for users, curators and developers that need access to the integrated knowledge of mBRCs and qualified third party databases. All mBRCs will be integrated in the MIRRI web portal “one stop shop”, while assuring that the individual strength of each mBRC stays visible. In addition an associated IT coordination and competence center will provide on-site help to balance the heterogeneity in IT capacities and offer training for curators and users. In order to achieve this goal MIRRI will collaborate with partners such as BioMedBridges and ELIXIR, as well as other infrastructure and research projects in Biological and Medical Sciences. By connecting the rich expertise of mBRCs from all over Europe, MIRRI will establish a visible trademark for high quality biological resources with associated information and expert knowledge for stakeholders in academy and industry.
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CABI is an inter-governmental, not-for-profit organization with 48 member countries. CABI enables national governments and organizations to tackle their agriculture and environmental problems as well as influence the global and regional development agenda. CABI’s mission is to improve people's lives worldwide by providing information and applying scientific expertise to solve problems in agriculture and the environment. CABI’s vision is to deliver high impact development projects with world class information, skills and a solid science base. This is delivered through a broad project portfolio helping to grow more and lose less with projects in managing crops, tackling pests & diseases, in soil and seed health and the Plantwise global plant health initiative. CABI empowers communities through access to knowledge, building capacity, improving communication and providing mobile advice whilst improving biodiversity and protecting livelihoods specifically by controlling invasive species and improving trade & market access. In doing this for over 100 years in 142 countries CABI has built a collection of microorganisms to share and support these actions.
The CABI culture collection is a component of the CABI Bioservices theme and is based at the CABI-UK site at Egham. The collection is a UNESCO Microbial Resource Centre (MIRCEN), and an International Depository Authority (IDA). The CABI collection holds some 28,000 living strains of more than 6,000 species, predominantly of filamentous fungi but also includes some agriculturally important bacteria. The primary focus of the collection is on strains from environmental and agricultural systems, with emphasis on species associated with agriculture, plant pathology and biotechnology. CABI supplies authenticated reference, type and test strains to businesses and research establishments, including ISO846, BS2011 Part II j and Mil Std 810G test strains from the European, the UK and US testing standards, and holds many other test and challenge strains. Fungi in the CABI collection have been isolated from a wide range of environments and sources. The CABI collection also hosts a number of internal and external culture collections including the UK National Collection of Wood Rotting Fungi and the British Antarctic Survey culture collection of environmental bacteria and fungi isolated from the Antarctic region.
CABI has been involved in European networks for over 4 decades. CABI is a member of ECCO and was a partner in the MINE and EMbaRC networks. Participation in MIRRI is of particular relevance to CABI in providing links between European skills and resources and those in CABI member countries. Examples of close links in conservation and use of microorganisms are Brunei, Chile, Ghana, Kenya, Malaysia and the United Kingdom. There are potentially major synergies and benefits that can be developed from having an integrated network of microbial resources in Europe and CABI is particularly interested in the development of specialist platforms and outreach from this. The relationship between CABI and MIRRI is a mutually beneficial one where CABI can access the vast wealth of experience, skills, technologies and resources across MIRRI and in return contribute its vast wealth of specialist skills in agriculture, particularly plant health and improving food security as well as resources and skills in knowledge and technology transfer.
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The Biological Resource Centre of the Institut Pasteur (CRBIP), created in 2001, preserves collections of biological strains and the information linked to them. The Collection of Institut Pasteur (CIP), one of the oldest collections of microorganisms in the world (some strains were isolated in 1892) and the Fungal Collection (UMIP) has been part of the CRBIP since its creation. The collection of cyanobacteria (PCC) and the group of Clinical Investigation and Access to Biological Resources (ICAReB) were included later.
At this time, more than 13,000 strains are available on stock, including type strains representative of about 4,600 different species, strains containing plasmid or genes of interest, strains having particular properties; coming either from researchers or from foreign collections.
The CIP is a member of different official organizations such as ECCO and WFCC. It develops research on identification of new species, taxonomy and preservation of bacteria, it participates in different projects such as ANVBIS (Nucleic acids, Virus and Bacteria of Interest in Standardized and Secure Storage) and it has the IBiSA label (IBiSA: Infrastructures in Health Biology and Agronomy), created in 2007.
Since 2005, the CRBIP has been certified according to the standard ISO 9001 and according to the NF 96-900 norm. It has participated in the drafting of the ISO norm in management of culture collections and Biosecurity, and it has also participated in discussions about the establishment of the Nagoya Protocol with the French parliament.
The CRBIP participates in the preparatory phase of MIRRI as a member of the steering committee, it is member of other projects such as BIOBANQUES and BIOASTER and it participated in the GBRCN project.
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The Mycotheca Universitatis Taurinensis (MUT) is a filamentous fungi culture collection established in 1999 and is hosted by the Department of Life Science and Systems Biology of the University of Turin. The collection hosts about 5,300 strains belonging to almost all classes of filamentous fungi and representing over 1,100 species.
MUT is a historical collection affiliated for several years with the ECCO and WFCC. It is one of the largest biological resource centres in Italy and complies with the internationally recognized quality norm ISO 9001:2008.
Our Fungal strains have been isolated from very different habitats and substrates in arctic, temperate, tropical and subtropical zones and about a quarter of the collection is represented by fungi isolated from marine environments. Many of the strains have been screened for specific secondary metabolites production, i.e. plant growth promoting molecules, siderophores, redox enzymes (laccase, ene-reductase, etc.) important for both bioremediation and biocatalysts purposes. Moreover, fungi are investigated for the presence of different genes whose presence is considered predictive of the capability to produce useful pharmaceutical metabolites, e. g. polyketide synthases genes (PKS), non-ribosomial peptide synthases gene (NRPS) and terpene synthase genes (TP).
MUT performs three basic functions: acquisition, conservation (in conditions that guarantee survival and preservation of genetic integrity) and distribution of cultures and related information. In addition, MUT explores and exploits the great genetic plasticity and physiological versatility of fungi to support the new bio-based economy providing scientific services, teaching and training, consultancy services to support research and technology transfer for both Academia and Industrial stakeholders.
Currently, MUT is a partner of MIRRI, and is involved in several national/international projects, e.g. BRIO - Banking rhizosphere micro-organisms, a European-Russian initiative to set up a network of rhizosphere microbiological resources centres; FIRB 2013 - In situ bio-augmentation to exploit the combination of fungi and bacteria for recalcitrant compounds removal; Galileo Italy/France 2014 – Discovering marine mycobiota: identification, characterization, and preservation of fungi associated to algae for future biotechnological exploitation.
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Beyond the microbe's world |
The European Marine Biological Resource Centre (EMBRC) is a sister Research Infrastructure of MIRRI, placed on the ESFRI roadmap in 2008. Currently establishing the legal framework (ERIC) for the operation of the infrastructure, EMBRC will provide a strategic delivery mechanism for the provision of excellent, large-scale marine science in Europe.
It is known that marine organisms are the source for novel compounds of importance for a range of biological, medical and industrial applications, but a better coordination and long-term, strategic planning and common development of marine research stations and laboratories are urgently needed to exploit the existing resources in an optimal way. Combining the strengths of all participating European partners, EMBRC aims to provide not only access to European coastal marine biota and their ecosystems, marine model species and state-of-the-art research services, the infrastructure also focuses on knowledge and technology transfer to the user community.
From the very beginning there has been a strong dialogue between EMBRC and MIRRI in order to identify synergies and shared strategies. Up to date, several options for collaboration have been identified including coordination of marine microbial resource holdings to avoid unnecessary duplication, development of new marine microbial model organisms, sharing best practices as well as expertise, interoperability of databases. Currently both infrastructures (together with other ESFRI projects) have teamed up to apply for H2020 funding to develop projects that aim at increasing the interoperability of research infrastructure clusters and at improving access to harmonized, high-level services for a large community of users from academia, industry, policy and the wider society.
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During the Preparatory Phase of MIRRI (2012-2015) work is allocated to specific workpackages (WP), each of them aiming to develop strategies for implementation of a mature and sustainable infrastructure. This section provides the MIRRI stakeholders with important achievements and results in a concise form.
Within the first 21 months of the project the basics for the development of strategies have been defined:
- WP2 revised the definition of membership criteria and the future operational structure
- WP3 finalised the Memorandum of Understanding and starts preparation of the MIRRI-ERIC Statues, the MIRRI Partner Charter and other relevant documents
- WP4 revised the Second Iteration Business Case of MIRRI and MIRRI participants provided it to relevant stakeholders; if you are interested in this document, please contact us
- WP5 held the first expert group meeting back-to-back with the General Meeting
- WP6 started to compile a list of experts in the different fields of microbiology
- WP7 finalised the deliverable “Report on available and potential new electronic tools for training”
- WP8 discussed strategies for data evaluation and validation as well as potential mechanisms and improvements of ICT
- WP9 determined gaps in biosecurity issues
Further information about the WPs can be obtained by the WP leaders
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In this issue, the series continues with highlights from MIRRI partners CBS, INRA-CIRM and IAFB:
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Penicillium vanoranjei (CBS 134406) makes Top 10 list of new species described in 2013
In 2013, scientists at the CBS-KNAW Fungal Biodiversity Centre, the Netherlands, published their research in a paper named “Five new Penicillium species in section Sclerotiora: a tribute to the Dutch Royal family” (Visagie et al. 2013; Persoonia 31: 42–62). As the title hinted, they named five species after the Dutch royal family. One of them produced bright orange (Dutch = oranje) sclerotia and was thus named Penicillium vanoranjei (photo credit C. Visagie) to coincide with the inauguration of King Willem Alexander of The Netherlands, Prins van Oranje. This event was big news in the Netherlands and the story was covered in newspapers, online media and social sites, as well as receiving television and radio coverage. In these, the positive impact that Penicillium has on everyday life was emphasised, above the negatives of some species. Positive impacts include the production of antibiotics, other various important extrolites, and the production of speciality cheeses and fermented sausages. On a whole, the “event” was unexpectedly worthwhile for creating public awareness about fungi.
Then, the SUNY-ESF International Institute for Species Exploration (IISE) released their top 10 species described in 2013 to coincide with Carolus Linnaeus’ birthday on 23 May. This list is prepared by an international committee of taxonomists and from the 18,000 species described in 2013, Penicillium vanoranjei was chosen as one of the top 10. This news created worldwide awareness on the wonderful world of microfungi. Who knows what species await to be described in 2014?
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Genome sequencing of four strains of Escherichia coli: in search of the specificities of bovine mastitis strains
Abundant literature is dedicated to the intraspecific diversity within E. coli. In particular, pathogenic strains can be classified into several pathotypes causing distinct diseases. For example, entero-hemorrhagic E. coli (‘EHEC’ pathotype) are frequently associated to foodborne outbreaks causing severe human cases. Each of those pathotypes is expected to carry specific virulence factors. Beside these numerous pathologies, E. coli is also known as one of the main pathogenic agents involved in bovine mastitis, along with Staphylococcus aureus and Streptococcus uberis. This inflammation of the cow's mammary gland is causing important economic losses with estimates ranging from €61 to €97 per cow/year across the world. By contrast to other pathotypes' strains, mastitis strains apparently do not share specific virulence factors. This leads to the common acceptation that every E. coli strain can be virtually involved in mastitis, depending on the host immune system. Nevertheless, a renewed interest is arising from comparative genomic approaches investigating specific phenotypes associated with some strains isolated from mastitis cases.
The model mastitis strain (E. coli P4) has been recently sequenced. In the frame of a project funded by INRA grant three strains (E. coli D6-113.11, D6-117.07, D6-117.29) isolated from acute clinical bovine mastitis cases were sequenced (Kempf et al., submitted). The inference of genetic relations showed that these three strains could be clustered with different unrelated strains whatever the method considered (e.g. MLST, core genes absence or presence). Besides, the comparison of our data to other E. coli published genomes did not reveal any obvious differences at functional or gene family level. These preliminary results thus did not argue for the pathotype hypothesis. Further analyses will now target particular genes and mechanisms potentially involved in the mastitis strains specific phenotypes.
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Adoption to sulphur dioxide-induced stress as selection criteria for Saccharomyces cerevisiae used in wine production
The Culture Collection of Industrial Microorganisms of the Institute of Agricultural and Food Biotechnology (Warsaw, Poland) keeps strains which are used in wine, bakery, brewery and distilling industry, with a major focus on yeast.
A significant part of our Saccharomyces cerevisiae strains are used in the wine industry. One of the essential steps in industrial scale wine production is the addition of sulphur dioxide (SO2) to the freshly pressed grape juice. SO2 acts as a growth inhibitor of bacteria and wild spoilage yeasts, antioxidant, and it also inactivates certain enzymes during the wine making process. Furthermore, during storage, it inhibits haze formation, re-fermentation of sweet wines as well as unintentional malo-lactic fermentation. The use of SO2 in wine production resulted in the adaptation of several S. cerevisiae strains to high amounts of this compound, and they are associated with wines with higher production of alcohol. Sulphur resistance is thus a desired feature in the metabolic pathways of wince yeast strains and one of the selective features.
SO2-resistant strains have developed mechanisms (i.e. certain gene expression regulations) to reduce the stress conditions induced by high contents of this compound. It is well known that the gene SSU1 mediates efflux of sulphur in S. cerevisiae and therefore assures resistance against sulphur compounds. It is also proven that in the reference strain S. cerevisiae S288c the SSU1 gene shows lower expression levels than in preferred wine yeast strains. We have performed detailed investigations on 12 S. cerevisiae strains (photo credit: left A. Misiewicz, right: A. Terebieniec) and detected the presence of SSU1 gene (or its allele – SSU1-R) in three of them. We observed that the expression level of the SSU1 gene was correlated with increasing sulfite resistance and followed with studies on the promotor sequences of the SSU1 gene.
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- After the successful first meeting of European mBRC Heads, organised by MIRRI in February 2014, a follow-up meeting in envisaged for the end of 2014. The directors of participating mBRCs will continue discussion on the impact of MIRRI on the future landscape of microbial holdings and how it will affect their daily business.
- In September there has been a closed meeting of the MIRRI Steering Committee and WP leaders to discuss the developed strategies of each WP and their implications on the MIRRI Business Plan. The constructive discussions resulted in advanced drafts of the MIRRI-ERIC Statutes, the MIRRI Partner Charter and the MIRRI Rules of Operations. MIRRI Partners will now start negotiations with Member States to ensure a smooth transfer into the Implementation Phase.
- Call for Letter of Intent: MIRRI participants started a call to receive Letters of Intent from its various kinds of stakeholders. If you want to support MIRRI and its vision, please send us your Letter of Intent!
- MIRRI is preparing the incorporation of a new collaborating party: HAMBI, Finland.
- As a SERVICE FOR USERS of microbial resources, the MIRRI website was amended with two preliminary databases: provision of links to the online catalogues of MIRRI participants as well as a list of services currently offered by MIRRI participants. Please feel free to forward this information to your colleagues.
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7th Global Microbial Identifier Meeting, September 11-12, 2014 in York (UK); MIRRI will be represented by the Russian Partner VKM
4th Joint Conference of the Association for General and Applied Microbiology (VAAM) and the society of Hygiene and Microbiology (DGHM), October 5-8, 2014 in Dresden (Germany); representation at the exhibition of the German Partner Leibniz Institute DSMZ
Carnot Meetings 2014, October 08-09, 2014 in Lyon (France); MIRRI will be represented by the French Partner Institut Pasteur
ESBB Annual Meeting, October 21-24, 2014 in Leipzig (Germany); poster presentation will be given by the French Partner Institut Pasteur
Enzymes Innovations Industries, October 27-28, 2014 in Romainville (France); exhibition by the French Partner Institut Pasteur
XXII Latin American Congress of Microbiology and 4th Colombian Congress of Microbiology, November 5-8, 2014 in Cartagena (Colombia); poster presentation by the Spanish Partner CECT
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Participants of the CTLS 2014 meeting |
The Core Technology for Life Science (CTLS) 2014 meeting was the first Pan-European Core Facility Congress dedicated to core facility staff as well as other life science research staff. This year’s program focused on Research and Development with and within Core Technology Facilities, Core Technology Facility management for long-term sustainability and National and Trans-national Core Facility Networking. MIRRI was represented by exhibition, poster (R. Hurtado; IP) as well as by a lecture (E. Stackebrandt; DSMZ).
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Participants of the ECCO XXXIII meeting |
ECCO XXXIII - This year’s ECCO (European Culture Collection Organization) annual meeting was held in Valencia (Spain) with the motto ‘Molecular Taxonomy: from biodiversity to biotechnology’. During the meeting, presentations about MIRRI overall progress, policy about Access and Benefit Sharing, membership criteria, data management and training offer were exposed. The lecture “The MIRRI project and its status halftime” by Erko Stackebrandt (DSMZ) is accessible here. The next ECCO annual meeting will probably take place in Paris (France).
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Participants of the 3rd MIRRI General Meeting |
Intermediate Review/3rd General Meeting – After the first half of the project’s Preparatory Phase the Intermediate Review took place on June 18th in Amsterdam. The ESFRI project officer as well as a scientific expert evaluated the current status of MIRRI. Subsequent to the Intermediate Review the 3rd MIRRI General Meeting took place on 19th/20 June in Amsterdam. All Work Packages provided a preview of work load in the second half of the Preparatory Phase and welcomed the constructive discussions. Invited lectures were given by Juncai Ma (WFCC), Wiebe Koistra (EMBRC) and Barend Mons (ELIXIR).
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Discussion @ the MIRRI stand |
In July, MIRRI participated in the 16th European Congress on Biotechnology. During this four-day conference the project was presented to the attending delegates by an exhibition stand as well as by a poster. Researchers from academia and industry were interested in MIRRI and M. Schüngel (DSMZ) and A. Antunes (UMinho-MUM) were successful in establishing new contacts to our stakeholders.
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This publication reflects the view only of the author(s), and the European Union cannot be held responsible for any use which may be made of the information contained therein.
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European Strategy Forum on Research Infrastructures |
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This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 312251. |
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