MIRRI - Microbial Resource Research Infrastructure


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MIRRI NEWS | Issue 6

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


Prof. Erko Stackebrandt

Dear all,

I hope all readers enjoyed the break over the Christmas time and relaxed sufficiently to tackle 2016 business. For MIRRI, there is no time for contemplation; the New Year started as busy as the old one had ended: in October 2015 the EC agreed to a cost-neutral 6-month prolongation of the MIRRI Preparatory Phase; the focus of the additional six months will be to develop a MIRRI Best Practice for ABS (for details see “MIRRI Insights”). Almost at the same time the first meeting of national representatives to discuss the future of MIRRI took place. During this meeting representatives of several countries discussed the documents necessary to initiate the ERIC application process. The feedback was positive, and some homework had been done for the next meeting in Berlin (Germany), February 3rd, 2016. Again, MIRRI received encouraging support from members of this second stakeholder meeting, which stressed the importance of the presence of a higher number of state representatives to proceed with the ERIC application.


The MIRRI consortium will use the still existing momentum to convince stakeholders to become operable as soon as possible.



Kind regards,

Erko Stackebrandt
MIRRI Coordinator


MIRRI Insights

Since the Nagoya Protocol entering into force in October 2014, researchers around the world face a broad spectrum of legal challenges before being allowed to work with a specific genetic resource. The implementation of the EU-Regulation 511/2014 and the very diverse national interpretation of this regulation make it even worse. MIRRI Partners have a long tradition working with genetic resources and possess a huge knowledge on ABS-related issues. Therefore, in its cost-neutral prolongation of the Preparatory Phase (11/2015-04/2016) MIRRI aims to support researchers around the world working with genetic resources in a legal compliant way.
The results elaborated in WP9 “Legal operational framework for access to microbial resources” provide a baseline for setting up a workflow system to guide mBRCs’ staff (curators) in their daily work to comply with the demanding task expected to be laid down in the EU guidance protocol and Implementation Act in particular for ‘Registered Collections’.
The principle of Access and Benefit Sharing (CBD, Nagoya Protocol, EU-Regulation 511/2014) will determine the curators’ daily workload of resource acquisition and resource provision which can be handled optimal by having in place a workflow system of document tracking and monitoring applicable to all MIRRI partners and associated parties.

To support mBRC staff in their daily work, MIRRI will develop the MIRRI Best Practice for ABS. After the evaluation of the EU guidance, Implementation Act and requirements for ‘Registered Collections’ for mBRCs and outline of a workflow manual scheme in harmony with the MIRRI ABS best practice, the lifecycle and value chain of microbial resources will be defined, including the various steps of passing resources through an mBRC and defining potential utilization of resources. In conclusion, the MIRRI Best Practice for ABS will include

- a policy statement on how MIRRI member mBRCs commit themselves to contributing to reaching the main objectives of the CBD while operating in compliance with all applicable national and international laws on ABS and regulatory requirements;
- sets of minimal requirements MIRRI regards necessary for compliant operation of the member mBRCs;
- MIRRI Best Practice to provide guidance for the mBRCs in implementing their ABS institutional policies and working procedures for
            (a) acquisition of material;
            (b) supply of material (including exchange);
            (c) delivery of other services;
            (d) research by the mBRCs on their own holdings and lawful utilization of genetic                          resources


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 Scandinavian Culture Collection for Algae and Protozoa (SCCAP) and the VTT Culture Collection.

The Scandinavian Culture Collection of Algae and Protozoa (SCCAP) has existed as a public service collection since 1986, but started as a research collection in the late 1940’s. It contains nearly 1,000 strains of primarily microalgae representing most taxonomic groups and from most parts of the world. It is the only of its kind in Denmark and the largest public collection of algae in Scandinavia. Services include sales of cultures, culture media, and consultancy for research, teaching for commercial purposes, e.g. a teaching kit for high schools. SCCAP is part of the Marine Biological Section at the Department of Biology, University of Copenhagen, which has a strong position in research on marine microbiology including autecology, molecular biology, taxonomy, and ultrastructure. The collection also collaborates with the IOC UNESCO Programme on Harmful Algal Blooms, which has its international programme office hosted by the Marine Biological Section. Thus, SCCAP supplies cultures to numerous IOC UNESCO courses on harmful algae and phytoplankton in general, e.g. the UNESCO Advanced Phytoplankton Course.
SCCAP has been member of ECCO since 2011 and collaborating party in MIRRI since 2014. For a small culture collection this has been very useful and inspiring and has provided invaluable insights on best practises running a culture collection, legal aspects etc., and illustrates MIRRI’s potential in assembling smaller microbial collections of the European landscape. Presently, Denmark has surprisingly few public microbial culture collections, implying that this area is presently not identified as an issue in the Danish Roadmap for Research Infrastructures. Until this might change, the SCCAP will be following MIRRI closely being ready to become a member should the opportunity arise.

VTT Culture Collection (VTTCC) was established by VTT Technical Research Centre of Finland in 1959 as a collection of microbial strains, with special emphasis on industrial strains and biotechnical applications. Today, the collection with its ca. 6,500 microbial strains and plant cell lines covers a wide biodiversity with over 800 bacterial species from 225 genera, over 600 fungal species from 255 genera, and ca. 50 plant cell lines. VTTCC also has a major collection of brewing yeasts of which many are in regular use in beer production. Many of the VTTCC strains are unique and available only at VTTCC. VTTCC provides strains and identification services for the food and biotechnological sectors worldwide. The VTT operating system is certified under ISO 9001:2008 and ISO 14001:2004 covering research, technology transfer, consultation services and development of new technology.
VTTCC offers deposit of strains for public access and for safe keeping, distribution of strains for research and for industrial partners, initiation of callus and cell suspension cultures from various plant species, and identification of bacteria and fungi by molecular tools. VTTCC has
long-standing Safe Deposit agreements with external customers. International Depositary Authority (IDA) status was granted to VTTCC in 2010, allowing the deposit of microorganisms for Patent Purposes under the Budapest Treaty. This is the only collection with IDA status in the Nordic countries.
VTTCC is a member in European Culture Collections' Organisation (ECCO) since 1984, having contributed also to its board work, and in World Federation for Culture Collections (WFCC) since 1985, registered in the World Data Centre for Microorganisms (WDCM number 139). VTTCC is a founding member of Finnish Microbial Resource Centre Organisation (MICCO), devoted to the preservation and use of the unique Finnish microbial diversity.

VTTCC is a collaborating party in MIRRI, especially interested in the development of services and interdisciplinary work programs. Prior to MIRRI, VTTCC was
participating in a demonstration project for a Global Biological Resource Centre Network (GBRCN) with participants from all continents, aiming at long-term availability of living biological material.


Beyond the microbe's world

CORBEL – Coordinated Research Infrastructures Building Enduring Life-science services

Biological and medical research that addresses the grand challenges of health and ageing span a broad range of scientific disciplines and user communities. The BMS RIs play a central, facilitating role in this ground-breaking research: inter-disciplinary biomedical and translational research requires resources from multiple research infrastructures such as biobank samples, and resources from multiple research infrastructures such as biobank samples, imaging facilities, molecular screening centres or animal models. Through a user-led approach CORBEL will develop the tools, services and data management required by cutting-edge European research projects: collectively the BMS RIs will establish a sustained foundation of collaborative scientific services for biomedical research in Europe and embed the combined infrastructure capabilities into the scientific workflow of advanced users. (Source: CORBEL website, www.corbel-project.eu).


EMBRIC -European Marine Biological Research Infrastructure Cluster

Marine biotechnology seeks to unlock the vast economic potential presented by living systems in the world’s oceans. Fragmentation has made it difficult to exploit this potential to its fullest – for example research services that operate in isolation, barriers (practical and cultural) between academic and commercial R&D, and a lack of harmony in regional innovation policies. EMBRIC seeks to overcome these barriers by linking biological and social science research infrastructures throughout Europe, and by joining up aligned efforts in science, industry and regions. EMBRIC will engage industry in multiple ways. The consortium involves three private companies. The joint development activities will interact with cognate private actors to identify and implement market pulled innovative projects, presenting a high potential for TT. Industry is also one of the main targets in the communication strategy of WP1 and dedicated dissemination tools and outreach events will be used to attract new industrial users and promote the cluster. (Source: EMBRIC website, www.embric.eu.


RItrain - Research Infrastructure Training Programme

RItrain’s mission is to improve and professionalize the training of managerial and leadership staff in research infrastructures (RIs). This is vital for the future success of Europe because access to excellent RIs underpins the success of today’s research and innovation. The successful management and leadership of research infrastructure require a complex collection of competencies, especially for those working across national borders. We will develop a flexible, modular executive master’s degree for RI managers and leaders, including executive directors of RIs, heads of finance and administration, heads of HR and communication. We want to strengthen the human capital of RIs, stimulate their efficient management and promote their development and competitiveness at national, European and international level. (Source: RItrain website, ritrain.eu/).


Microbe Highlights

In this issue, the series continues with highlights from MIRRI Collaborating Parties Greek Coordinated Collections of Microorganisms-Agricultural College of Athens - Dairy Culture (ACA-DC) and the Culture Collection of Algae and Protozoa (CCAP):

Streptococcus macedonicus, a species demonstrating adaptation to the dairy environment

The Streptococcus bovis/Streptococcus equinus complex (SBSEC) consists of commensals found in the gastrointestinal tract of herbivores. Species of this complex, like Streptococcus gallolyticus and Streptococcus pasteurianus are known human pathogens involved in a range of diseases including endocarditis, meningitis, bacteremia, colon cancer etc. Nevertheless, certain members of the complex like Streptococcus macedonicus are frequently isolated from traditional fermented foods, mostly of dairy origin. Analysis of the complete genome sequence of S. macedonicus ACA-DC 198 isolated from traditional Greek Kasseri cheese revealed important traits of adaptation to the dairy environment (see figure, Papadimitriou et al. 2014). The strain contains a significant percentage of potential pseudogenes indicating that it may have evolved through genome decay processes, an evolutionary strategy also adopted by the dairy Streptococcus thermophilus. Streptococcus macedonicus has an extra gene cluster for lactose and galactose metabolism unique among the SBSEC members and a typical proteolytic system required for casein hydrolysis. Furthermore, we found evidence in the genome of S. macedonicus suggesting HGT (horizontal gene transfer) events with potential donors Lactococcus lactis and S. thermophilus. Perhaps the most pronounced among these HGT events is the presence in S. macedonicus of pSMA198, which belongs to the lactococcal pCI305/pWV02 family of plasmids. Our analysis suggests that pSMA198 may have been acquired by S. macedonicus from L. lactis (Papadimitriou et al. 2015). Finally, S. macedonicus misses some of the common virulence factors present in pathogenic SBSEC suggesting diminished pathogenicit for the strain analyzed. Further investigation of S. macedonicus may provide important evidence for the adaptation of a potential commensal microorganism to the dairy environment.

CCAP resources with biotech potential

Micro-algae photoautotrophically synthesize high levels of lipids, carbohydrates and proteins, thus attracting considerable interest for the biotechnological production of fuels, environmental remediation, functional foods and nutraceuticals.  An extensive screen of the major algal phyla was undertaken during the EU funded Biomara project that identified strains capable of fulfilling these goals. A strategy based on rapid Mass-Spectrophotometric analysis (MS) of nitrogen (N) and carbon (C) subsequently validated by Gas-Chromatography (GC), identified Chlorella vulgaris CCAP 211/21A (see picture) and Nannochloropsis oceanica CCAP 849/10 as the best oil producers. Dunaliella polymorpha CCAP 19/14 was found to be the most productive for carbohydrates. High retention of supplied N in biomass was observed in Monodopsis subterranea CCAP 848/1, suggesting potential applications in N-remediation. Overall, a subset of productive strains emerged that are likely to be robust and effective in large-scale low-cost cultivation scenarios utilizing salt water.
For more details see Slocombe S.P. et al. Unlocking nature’s treasure-chest: screening for oleaginous algae. (2015) Scientific Reports: 5:9844.


News & Events

  • The MIRRI consortium welcomes its 28th Collaborating Party, the UNIMORE Microbial Culture Collection (UMCC) in Italy. The collection holds about 2,700 strains including yeasts, lactic acid bacteria and acetic acid bacteria. The UMCC harbours competences on functional starter cultures for industrial fermentation processes and offers a useful service for several purposes such as research, teaching, screening assay and biotechnological applications. The strains in the collection are characterized by a polyphasic approach.
  • On February 16-18, 2016 CORBEL and RItrain co-organise two workshops about the skills gab in research infrastructure management and operation. Details about the participation can be accessed via the RItrain website.


Meet MIRRI @

  • the ECCO XXXV Meeting, this year taking place back-to-back with ICCC14 on November 1-2, 2016 in Antalya (Turkey)


Del Rocío Mora-Ruiz M., Font-Verdera F., Díaz-Gil C., Urdiain M., Rodríguez-Valdecantos G., González B., Orfila A., Rosselló-Móra R. (2015) Moderate halophilic bacteria colonizing the phylloplane of halophytes of the subfamily Salicornioideae (Amaranthaceae). Syst. Appl. Microbiol. 38(6): 406-416 

Vidal R., Ginard D., Khorrami S., Mora-Ruiz M., Munoz R., Hermoso M., Díaz S., Cifuentes A., Orfila A., Rosselló-Móra R. (2015) Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean. Syst. Appl. Microbiol. 38(7): 442-452 

Cortés-Lara S., Urdiain M., Mora-Ruiz M., Prieto L., Rosselló-Móra R. (2015) Prokaryotic microbiota in the digestive cavity of the jellyfish Cotylorhiza tuberculata. Syst. Appl. Microbiol. 38(7): 494-500 

Martin D., Stackebrandt, E., Smith, D. (2015) MIRRI promoting quality management systems for microbiology. EC Microbiology 2(2): 278-287

Stackebrandt E., Schüngel M., Martin D., Smith D. (2015) The Microbial Resource Research Infrastructure MIRRI: strength through coordination. Microorganisms 3(4): 890-902 

Antunes A., Stackebrandt, E., Lima, N. (2016) Fueling the Bio-economy: European Culture Collections and Microbiology Education and Training. Trends Microbiol. 24(2): 77-79 



  • In October 2015 the fourth and last MIRRI General Meeting of the Preparatory Phase took place in the Netherlands. Work package leaders presented the results of their work and outlined ways for implementing the developed strategies; i.e. how to translate the MIRRI offer into user-requested services. Invited speakers from Brazil, Japan and the USA provided insights into their experience of the implementation of the Nagoya Protocol.
    Highlight of this meeting was the first meeting of national representatives from countries interested in founding the MIRRI-ERIC. During the closed meeting premises for a participation were discussed and documents necessary for the ERIC application, prepared by the MIRRI consortium, were presented. A follow-up meeting was scheduled for early 2016.
  • BioMedBridges, a cluster project of several BioMedical Sciences Research Infrastructures (BMS RIs), to which MIRRI is Associate Partner, held its final meeting on November 17-18, 2015 in Hinxton (UK). During this Symposium on Open Bridges for Life-Science Data participants learned about the latest advances in the technical infrastructure behind large-scale data sharing and discussed the interoperability of data resources supporting biological, medical, translational and clinical research. MIRRI used this opportunity for a small exhibition and a poster presentation.

  • Back-to-back with the BioMedBridges Symposium, the CORBEL Kick-Off Meeting took place November 19, 2015 in Hinxton (UK). The work package leaders presented their working plans and strategies for the upcoming four years of work; special break-out sessions were used to discuss the different biological and medical use cases in more detail. Project updates can be obtained from the website or the CORBEL Twitter account (@CORBEL_eu).

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.