MIRRI - Microbial Resource Research Infrastructure


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MIRRI NEWS | Issue 5

Editorial | MIRRI Insights | Hunters & Gatherers | Beyond the microbe's world | Work Package Update | Microbe Highlights | News & Events | Meet MIRRI | Publications | Reports


Prof. Erko Stackebrandt

Dear all,

following the summer vacation and facing the last two months of the MIRRI Preparatory Phase the entire consortium needs to combine its energy to enable a smooth transition to the upcoming Interim Phase. MIRRI’s latest progress was acknowledged by the ESFRI Working Group on Implementation, which stated that MIRRI ‘has the enormous potential to support a broad range of biology related research activities across all of Europe. If successfully implemented, it will add significantly to building a real and effective European Research Area. (…) MIRRI also has the potential to dramatically expand innovation activities in numerous strategical industrial sectors, while at the same time advancing state-of-the-art knowledge in microbial research. (…) We strongly recommend the involved countries to formally express their commitment and to initiate selection for the host with pre-defined evaluation criteria and to decide on the host country before the end of the preparatory phase by October 2015.’ We are using this momentum to continue the dialogue with the national stakeholders (e.g. during the upcoming Annual Meeting in October) to listen to their expectations of the envisaged MIRRI-ERIC. Some stakeholders may follow specific national strategies, others may have financial constraints, yet others may want to see MIRRI develop towards financial sustainability. All these thoughts will be dealt with by national representatives in the Governing Board who need to find a compromise on administrative and financial matters. However, before this Board is established MIRRI must now finalize the text of governing documents and combine individual strategies into the holistic offer that will make MIRRI irresistible to users: the next months will be exciting.

In the meantime, MIRRI partners will start their work in the H2020 projects CORBEL, EMBRIC and RItrain, thereby assuring MIRRI’s position within the European research infrastructure landscape.

The MIRRI story will turn over a new leaf – stay tuned to receive the latest updates!


Kind regards,

Erko Stackebrandt
MIRRI Coordinator


MIRRI Insights

Work package 3: Define governance structure, legal status and operational practice

The definition of the legal status of a research infrastructure and its underlying governance structure and operational practices are an essential premise for entering the Implementation Phase. The MIRRI consortium decided to establish an European Research Infrastructure Consortium (ERIC) as its legal status and WP3 contributed elaborating the statutes. The Rules of Operation, another important document complementary to the statutes, is also being elaborated by this WP. This was done in close collaboration with the other Preparatory Phase work packages to ensure the consideration of their developed strategies for a future operational MIRRI. The way towards setting up the ERIC is well set by the European Commission; therefore it is now up to the participating Member States to start discussing necessary details, e.g. on financial issues. The current model foresees that the number of participants who will succeed in convincing their government to join actively the consortium will determine in how many parts the MIRRI-ERIC budget will be divided. The more participants you get, the lower the contribution of each country will be, knowing that the contribution of a country to the budget of the Central Coordinating Unit (CCU) is made of a fixed part and a part calculated on the basis of the GDP. At the same time, countries need to invest in their own facilities.
The envisaged governance structure elaborated together with work packages 2 and 4 foresees a CCU at which the ERIC is located. The CCU, consisting of the Executive Director and other personnel, will coordinate the work of MIRRI-ERIC. On the national level, National Nodes will be established and the relevant National Coordinators will monitor that participating partners are compliant with the MIRRI Partner Charter. The Governing Board as well as several Advisory Bodies will provide advice to the MIRRI General Assembly in order to support the success of MIRRI-ERIC.
Another key factor for a service provider is the envisaged MIRRI-ERIC has a high level of quality. In collaboration with other work packages a harmonised quality management system (QMS) concept for CCs and mBRCs is under development.


Work package 9: Legal operational framework for access to microbial resources

Countdown to the EU Implementing Act on Access and Benefit Sharing
The Nagoya Protocol entered into effect for all member states of the EU on 12 October 2014. On that day, the "Regulation No 511/2014 on compliance measures for users from the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization in the Union" entered into effect according to a Council Decision adopting the Protocol. Thus since this day all users and collections are expected to implement the EU regulation. Still in development and expected to enter into force in the second half of October 2015 is the EU Implementing Regulation which will contain measures on some specific aspects, concerning registered collections, best practices as well as monitoring of user compliance. Guidance documents will be developed by the EU involving a Consultation Forum, which will be convened in the third quarter of 2015, once the Implementing Regulation is adopted.
Although the legislative process in the EU Council and in the European countries is not finished yet, the EU Regulation No. 511/2014 is compulsory for all users in the European Union and appropriate measurements must be considered by the users and the collections as well. Waiting for the Implementing Act would only postpone the problem and responsibility and disposes precious time to think about the most adequate implementation in your own institution. Many parameters are set, especially for those sourcing, collecting and using genetic resources, thus databases can be expanded to incorporate required information and document and/or information management systems can be elaborated to handle the required legal documents and information accompanying genetic resources in the future. WP 9.1 thus started to draft an ABS manual on handling Genetic Resources in a legally compliant way. On September 15 and 16, 2015 the “International Workshop on Access and Benefit Sharing in the microbial domain” was held to finalize the MIRRI Policy and Best Practice on ABS. On the eve of the final EU legislative, MIRRI is facing the challenge especially for the European collections and their users, which is emerging with the act of law.
Stakeholders consider the EU Regulation 511/2014 much too bureaucratic, extending beyond the principles set out in the Nagoya Protocol. They fear huge restrictions on access to genetic resources for European users and collections, and that international scientific exchange of biological resources is at stake. On the positive side, the EU Regulation can make the exchange of genetic material more transparent and lead to measures to secure this transparency in a sustainable and trackable way. Of course, this means it could be considerably more difficult for science and industry to work with genetic resources. However, by starting early to set out organizational rules and appropriate processes and to interchange with colleagues on the most appropriate measures will reduce the burden for individual organizations. MIRRI is taking its responsibility for the European collections and users to set an important impact for the research community in the academic and commercial fields and to support the research infrastructure on genetic resources in the European Union. The MIRRI Policy on ABS and the ABS Manual will be brought into public circulation in the following weeks – we will keep everyone updated with this development.

Developing a biosecurity risk assessment and compliance policy
MIRRI seeks to engender trust from the user community by being transparent in how it answers to all relevant laws and regulatory requirements, including those on biosecurity. Building on existing tools such as the Code of Conduct for Biosecurity for BRCs, it will work in collaboration with experts in the MIRRI-expert cluster and external partners towards developing and implementing protocols for adequate biosecurity risk assessment of holdings and normative compliance in MIRRI-mBRCs. Also, MIRRI will work to strengthen the ethical basis for biosecurity in the scientific community, and adopt existing or develop new educational tools to raise awareness among mBRC staff. An expert cluster workshop on “Biosecurity implementation strategies and Compliance Management in microbial Biological Resource Centres” (mBRCs) held in December 2014, organized by Workpackages 3 and 9 brought together experts and representatives from government, science, industry, public health, standardization and ethics, with a focus on Biosecurity and Legal Compliance to discuss some of the key-issues for biosecurity, such as education and awareness-raising, problems and approaches in laboratory biorisk assessment, and to take steps forward in designing a MIRRI policy on risk assessment and an overall compliance strategy.


Hunters & Gatherers

Who are the people, “hunting” microorganisms and collating them in public culture collections? Where are they located? And why do they participate in MIRRI?

In today’s issue these questions will be answered by the G.K. Skryabin Institute of Biochemistry and Physiology of Microorganisms (IBPM-VKM), the Institut Mediterrani d’Estudis Avançats (CSIC-IMEDEA) and the Koninklijke Nederlandse Akademie van Wetenschappen – Centraalbureau voor Schimmelcultures (KNAW-CBS).

The All-Russian Collection of Microoganisms (VKM) operates (since 1980) as a Department of the G. K. Skryabin Institute of Biochemistry and Physiology of Microorganisms (Pushchino, Moscow region).
VKM is one of the largest Russian collections in the area of non-medical microbiology. It hosts nearly 20,000 cultures of bacteria (including actinobacteria), Archaea, filamentous fungi and yeasts, and contains many type and reference strains as well as strains of biotechnological interest. About 7,000 strains are currently listed in the on-line catalogue,
the other resources will be included after further validation (which is currently on-going). VKM offers services such as supply and deposition of cultures, including deposition for patent purposes according the requirements of the Budapest Treaty and deposition of newly described taxa. Scientific services mostly focus on identification, sharing expertise as well as training. The collection-related research at VKM emphasizes microbial taxonomy and studies of microbial diversity in various ecosystems, especially extreme ones (e.g. permafrost).
VKM maintains active communication with a network of professional organizations national as well as world-wide, including STRAININFO, MycoBank, GenBank, and the World Data Center for Microorganisms (WDCM) of the World Federation for Culture Collection (WFCC). The collection is a member of WFCC and the European Culture Collections’ Organization ECCO.

VKM is a partner of MIRRI, and participates in several national research projects. Its activity within MIRRI is focusing on the work package dealing with data resources management.

Recent activities of VKM and its Head, Dr. Lyudmila Evtushenko, emphasize the development of information resources at VKM, as well as integration of the currently dispersed microbial collections in Russia into a common virtual network. The future joining of this Russian collection's network to pan-European initiatives like MIRRI will extend access of scientific community to microbial resources and hopefully foster research and innovations world-wide.

The Marine Microbiology Group (MMG) belongs to the department of Ecology and Marine Resources of the Mediterranean Institute for Advanced Studies (IMEDEA) that is a joint institute between researchers of the Spanish Council (Consejo Superior de Investigaciones Científicas, CSIC) and the University of the Balearic Islands (UIB). The IMEDEA is an interdisciplinary institute that gathers researchers working in different areas that range from oceanography to ecology of plants and animals in oceanic and terrestrial environment.
The MMG is centring its research in microbial communities thriving in natural environments, especially extreme habitats as hypersaline ponds and salterns, as well as anaerobic marine sediments. The major research goal is advancing in the basic knowledge on microbial diversity by means of culturing and culture-independent methods. Besides, Ramon Rosselló-Móra (RRM), leader of the MMG, is also contributing to several theoretical aspects of taxonomy and classification, the most basic and necessary tools to organize the biological diversity observed. The participation in MIRRI is mostly related to the knowledge on taxonomy and taxonomic tools that can be important resources for culture collections. The expertise of RRM in taxonomy and his contacts with taxonomists through his editorial work in the Systematic and Applied Microbiology journal permit access to generate databases on the current expertise along the European Union. Recognizing the expertise in taxonomy and systematics in the frame of the EU is of paramount importance for further interactions among scientists and for the microbiological resources to have access to the knowledge and obtain proper training.

The CBS-KNAW Fungal Biodiversity Centre (Centraalbureau voor Schimmelcultures) is an institute of the Royal Netherlands Academy of Arts and Sciences (KNAW). Founded in 1904, it holds the world’s largest public service collection for filamentous fungi and yeasts (90,000 strains), and a collection of bacteria (NCCB; 10,000 strains). Supply of living cultures and DNA, and acceptance of safe deposits and patent deposits are ISO 9001:2008 certified. CBS also has an identification service, and provides a wide range of database services online, including polyphasic identification and information resources for special groups of important fungi. CBS is an active partner in numerous national and international collaborative projects such as Q-Bank, iBOL, EMbaRC, and aims to use these projects to broaden its scope to include functional fungal biodiversity. Six CBS research groups focus on food- and industrial mycology, yeast systematics, medical mycology, evolutionary phytopathology, fungal physiology and bioinformatics.
CBS leads MIRRI work package 9, which aims at creating a legal operational framework that will assure MIRRI complies with legal and regulatory requirements in the field of Access and Benefit Sharing (ABS, the Nagoya Protocol and EU Regulation 511/2014) and Biosecurity. MIRRI is developing ABS best practice and the partners are implementing the Code of Conduct on Biosecurity for BRCs. According to CBS Director Prof. Pedro W. Crous, the Nagoya Protocol could have serious negative consequences for mBRCs: “Since its implementation a year ago, we have seen numerous examples where researchers simply refrain from depositing strains in public collections, as they do not have all the paperwork in place as required by the Nagoya Protocol. Direct implications are that in years to come numerous new species of fungi will be described, and the isolates will effectively be unavailable to the international research community. MIRRI plays a crucial role in this regard, as it needs to facilitate a more practical implementation of the Nagoya Protocol, or the number of strain deposits in BRCs adhering to the Nagoya Protocol will see a drastic decline, which will not serve scientific progress.”


Beyond the microbe's world

BBMRI-ERIC aims at facilitating the fair access to quality-defined human disease relevant biological resources including associated data, in an efficient as well as ethically and legally compliant manner by reducing the fragmentation of the biomedical research landscape through harmonisation of procedures and by implementing common standards and by fostering high level collaboration.

Using a distributed governance structure and building on the ERIC status (a specific legal form is designed to facilitate the joint establishment and operation of research infrastructures of European interest on a non-economic basis), BBMRI-ERIC facilitates a gateway to access the biobanks and biomolecular resources of 17 Member States and one International organisation; Austria, Belgium, Czech Republic, Estonia, Finland, France, Germany, Greece, Italy, Malta, the Netherlands, Sweden and the United Kingdom as Members and Norway, Poland, Switzerland, Turkey, IARC/WHO as Observers. This makes BBMRI-ERIC one of the largest Research Infrastructures for health research in Europe.

BBMRI-ERIC is part of the ISO/TC 276 Biotechnology committee, whose currently developed norm will directly influence the working procedures of European biobanks, repositories and Expert Centers connected to BBMRI-ERIC. Moreover, BBMRI-ERIC relies on its Common Services, which consist of facilities that provide expertise and tools. The recently established Common Service ELSI, for instance, ensures the proper consideration of ethical, legal and societal aspects relevant to biobanking, especially in relation to cross-border exchange of human biological resources and data. Furthermore, BBMRI-ERIC will provide a one-stop access to the collections of the European biobanking community, expertise and services, ultimately facilitated by the Common Service IT. It is equally important to ensure the close collaboration and dialogue between not only researchers and biobankers but also the general public, patient advocacy groups and the biotech/pharmaceutical industry, which BBMRI-ERIC addresses through its Stakeholder's Forum, which shall pave the way for a new research culture in Europe.


Work Package Update

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.

- WP2 submitted their las two deliverables “Workshop to agree minimal-maximal function of MIRRI” and “Compilation report on outputs”
- WP3
submitted the deliverables “Development of a MoU” and “An internal operational policy for MIRRI”
- WP4
started to finalise the MIRRI Financial Plan
- WP5
started preparation of the deliverable “Report on linkages to governing bodies and policy makers at national and European levels and common wok programmes with other infrastructures both in and outside Europe”
- WP6
held a workshop to set-up a working plan for interdisciplinary activities for the MIRRI construction phase and started preparation of the remaining deliverables
- WP7
submitted the deliverable “Report on a strategic concept for innovative learning programmes and tools”
- WP8
submitted the deliverable “Report on human and programmatic access and on documentation development and contents annotation”
- WP9
organised three international workshops on Access and Benefit Sharing (@ the ECCO2015, FEMS2015 and MIRRI Workshop on ABS)

Further information about the WPs can be obtained by the WP leaders


Microbe Highlights

In this issue, the series continues with highlights from MIRRI partner BCCM-LMG (UGent):

Burkholderia cepacia complex strain panels

The Burkholderia cepacia complex is a versatile group of closely related bacteria that are ubiquitous in nature. Some B. cepacia complex strains show biotechnological potential for bio-control, bioremediation and plant growth promotion, whereas others are pathogens for plants and immunocompromised individuals such as those with cystic fibrosis. Most of these bacteria are normal inhabitants of soil and water, and are of no or limited concern to the general population. However, the 1990s witnessed the emergence of infections in these patients caused by B. cepacia complex and a range of uncommon or novel bacteria, many of which are naturally resistant to a wide range of antimicrobial agents. Accurate diagnosis of these infectious agents in cystic fibrosis patients is important for infection control and patient management.
B. cepacia complex now comprises 20 validly named species but a considerable number of other nonfermenting Gram-negative bacteria are commonly misidentified as B. cepacia complex. Distinguishing all these microorganisms represents a major diagnostic challenge in cystic fibrosis microbiology. To support diagnostic laboratories with the identification of these micro-organisms, a strain panel that is representative of the large variety of clinical infections, environments and geographic locations from which B. cepacia complex strains may be recovered was deposited in the BCCM/LMG Bacteria Collection to make them available to the scientific community [1 , 2]. In addition, in the frame of the EU FP6 project EuroCareCF (LSHM-CT-2005-018932) a similar strain panel but extended with several other nonfermenting Gram-negative bacteria has been composed to support the identification of these cystic fibrosis pathogens.


News & Events


Meet MIRRI @

  • ESBB 2015 Annual Conference, September 30 – October 2, 2015 in London (UK); talk by D. Smith (CABI), poster by R. Hurtado-Ortiz (CRBIP)
  • BioMedBridges Open Symposium: Building the bio-connectome – open data infrastructure to accelerate innovation, November 17-18, 2015, Hinxton (UK); exhibition (M. Schüngel, DSMZ)
  • CORBEL Kick-Off meeting, November 19, 2015 in Hinxton (UK), subsequent to the BioMedBridges symposium


Rosselló-Móra R., Amann R. (2015) Past and future species definitions for Bacteria and Archea. Syst. Appl. Microbiol. 38(4):209-216

Viver T., Cifuentes A., Díaz S., Rodrígue-Valdecantos G., González B., Antón J., Rosselló-Móra R. (2015) Diversity of extremely halophilic cultivable prokaryotes in Mediterranean, Atlantic and Pacific solar salters: Evidence that unexplored sites constitute sources of cultivable novelty. Syst. Appl. Microbiol. 38(4): 266-275 

Konstantinidis K., Rosselló-Móra R. (2015) Classifying the uncultivated microbial majority: A place for metagenomic data in the Candidatus proposal. Syst. Appl. Microbiol. 38(4):223-230 

Overmann J. (2015) Significance and future role of microbial resource centers. Syst. Appl. Microbiol. 38(4):258-265



  • MIRRI exhibited at the 6th congress of European Microbiologists (7-11 June, 2015) in Maastricht, The Netherlands. With more than 2,000 participants from over 70 countries participating in the last FEMS congresses it was expected that the 2015 congress would also be well attended by scientists from a broad range of microbial applications. Raquel Hurtado-Ortiz (IP) and Manuela Schüngel (DSMZ) represented MIRRI during the exhibition. Visitors to the booth covered a broad range from students to senior researchers, representing both academia and industry. There were lots of vivid discussions about the MIRRI project and our mission and vision – everybody agreed on the need of such an infrastructure.

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.

European Strategy Forum on Research Infrastructures

This project has received funding from the European Union’s Seventh Framework Programme for research, technological development and demonstration under grant agreement no 312251.