MIRRI - Microbial Resource Research Infrastructure


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MIRRI NEWS | Issue 1

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,


MIRRI, the Microbial Resource Research Infrastructure, was placed on the ESFRI roadmap in 2010. Starting our Preparatory Phase at the end of 2012 we are aiming at establishing the leading infrastructure for microbial resource centres in Europe.

MIRRI – or better the microbial domain Biological Resource Centres (mBRCs) building the MIRRI consortium – aim to coordinate the currently fragmented landscape of microbial resources within Europe. By doing so, researchers from industry and academia will benefit from a facilitated access to a significantly higher offer of microorganisms, their associated data and expertise in a wide spectrum of techniques, instrumentation and advice.

With this first issue of the MIRRI newsletter we would like to inform you, our stakeholders, about project news and upcoming events where you have the opportunity to meet MIRRI representatives. Each issue has a variety of sections in which MIRRI partner centres are introduced, stakeholders are interviewed, updates from the work packages are provided and much more.

Since this is the first issue of the MIRRI newsletter we distribute it to all those of you who have agreed to be informed about MIRRI and who are considered as partners of our stakeholder community. If you do not want to receive the MIRRI NEWS in the future, you have the opportunity to unsubscribe.

We would like to encourage our readers to forward this newsletter to interested colleagues and to invite them to subscribe. In order to foster communication we also encourage you to share your ideas about what you would like to be covered in the forthcoming issues.


We hope that you enjoy reading this newsletter.

Do not forget to deposit your published strains in public resource centres (see Publications).


Kind regards,


Erko Stackebrandt

MIRRI Coordinator


MIRRI Insights

MIRRI in Europe

Highlights from MIRRI activities demonstrating progress towards a better microbial resource offer to microbiological research and development.

During the current Preparatory Phase the MIRRI consortium consists of 16 Partners and 20 Collaborating Parties, representing 19 countries across Europe. This cross-border cooperation addresses the challenge to harmonise the fragmented landscape within the community of Biological Resource Centres and Culture Collections. The aim of the Preparatory Phase is to develop strategies to establish a service-orientated infrastructure meeting the users’ needs for microbial material and information. These strategies include the protection of investment by research funders, coordination and harmonisation of access to microbiological expertise, a holistic approach to data management to facilitate knowledge generation from microbial strain data to provide innovative solutions to scientific, technological and informatic problems. The envisioned infrastructure will be all inclusive with capacity building programmes to facilitate all European microbial resource collections to join. Knowledge and technology transfer is core to MIRRI’s operations and with appropriate partners it envisages training and education programmes to ensure the continuation of currently diminishing areas of expertise. MIRRI will endeavour to address key issues in microorganism use and is already examining with policy makers and the user community just how the new EU regulation on Access and Benefit Sharing to implement the Nagoya Protocol will impact on microbiology. Such interventions are crucial to get compliant practices that engender trust but that do not impede science and development. MIRRI’s interdisciplinary approach seeks improved support for research and development in both industry and academia, leading to valued innovations for the whole of society.

The MIRRI consortium had contact with the European parliament for the implementation of the Nagoya protocol and it will have an impact for the microbial researchers at the international level.

MIRRI has prepared a Memorandum of Understanding (MoU): each partner is going to discuss it with its national representatives to engage their help in designing a successful infrastructure, which is also a very important stage for the future implementation of MIRRI.

MIRRI invites input from its user community; so please do not hesitate to contact us to discuss participation, future MIRRI services or are interested in collaboration.


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? This section will answer these questions with a short presentation of MIRRI partners. The series starts by introducing the Colección Española de Cultivos Tipo (CECT; Spain), the Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures (Germany) and the Micoteca da Universidade do Minho (UMinho-MUM; Portugal).


The CECT is the only public culture collection in Spain that maintains and supplies Bacteria, Archaea, yeasts and filamentous fungi. Although it is a broad scope collection, it is currently focused on marine and food-related bacteria due to different in-house research projects. They hold about 8,000 strains that are supplied in different “user-friendly” formats. In addition, they offer microbiology-related services such as training, deposit, identification and characterization of strains.

According to its director, Prof. Rosa Aznar, the participation of the CECT in MIRRI can raise the awareness of the Spanish government on the importance of the mBRCs in the bioeconomy. The CECT leads one of the work packages (WP) in MIRRI, dedicated to the design of the Microbial Resource Research distributed Infrastructure. By means of different surveys, this WP has gathered important information about many resources that are maintained in research laboratories and are not accessible to the research community. Rosa believes that for the Spanish research environment “this information is crucial as it will help to build a Spanish network of microbial collections in view of the future construction of MIRRI”. Finally, Rosa highlights the importance of this kind of initiatives to boost and facilitate both basic and applied microbial research. “More and more we receive requests about the commercialization of our strains. MIRRI should establish the framework to provide high quality resources and expertise but also to guarantee that this is done according to international regulations including those implementing the Convention of Biological Diversity.”


The Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures is an institution of Leibniz Association. Offering comprehensive scientific services and a wide range of biological materials, it has been a partner for research and industry organizations worldwide for decades. DSMZ is one of the largest biological resource centres of its kind to be compliant with the internationally recognized quality norm ISO 9001:2008. As a patent depository, DSMZ currently offers the only facility in Germany of accepting biological materials according to the requirements of the Budapest Treaty.

The collection (based in Braunschweig, Germany) exists now for 42 years and hosts more than 48,000 cultures and biomaterials. It is the most diverse collection worldwide: in addition to fungi, yeasts, Bacteria and Archaea, it is home to human and animal cell cultures, plant viruses, and plant cell cultures that are archived and studied there. The second major function of DSMZ, in addition to its scientific services, is its collection-related research. It participates in several national and international (research) projects as well as in MIRRI – for which the coordination is located at the DSMZ. In addition to the coordinator and the project manager further employees are involved in MIRRI-relevant issues like communication, quality as well as data management and biosecurity.

For the Leibniz Institute DSMZ and its director, Prof. Jörg Overmann, it is absolutely necessary to overcome the current fragmentation in the Biological Resource Centre’s landscape by establishing an infrastructure like MIRRI. Only by joining forces the currently suboptimal exploitation of the wealth of microbial resources can be improved. A facilitated access to high-quality microbial resources, associated data and expertise – as planned by MIRRI – will foster innovations in industry as well as in academia and lead to added value not only for scientists but for the whole society.


Micoteca da Universidade do Minho - MUM is a filamentous fungi culture collection established in 1996 and is hosted by the Biological Engineering Centre. The Applied Mycology Group (AMG) is one of the working groups of this centre. The AMG works in the field of the Applied Mycology, aiming at developing new or improved applications of fungi in Biotechnology and Bioengineering. Furthermore, the AMG and their laboratories host MUM.

The mission of MUM is to be a resource centre for fungal biodiversity preservation and information creating solutions for sustainable development and human well-being. MUM intends to be a centre of knowledge, information and training in mycology, operating at a global level and under national and international regulations. In order to keep its high standards MUM has implemented a Quality Management System based on the normative reference ISO 9001:2008 for deposit, preservation and supply of filamentous fungal strains. MUM maintains holdings with the main focus on Aspergillus and Penicillium as well as other relevant reference strains providing expertise and information associated with them. MUM has a high performance on post-graduate training (MSc and PhD) in mycology.

The Mycology laboratory and other related laboratories of the Biological Engineering Research Centre are well equipped for the main actual research in Biotechnology, Food and Technology, Health and Life Sciences, Environmental and Management Sciences.

Currently, MUM is a partner of MIRRI, and three research projects in Brazil. It was also partner of previous EU projects like, EMbaRC, COMBOW, WINE-OCHRA RISK, and SAFER (supported by Quality of Life and Management of Living Resources programmes). MUM was the OECD Portuguese delegate for BRC’s task-force participating in the main work done to develop the OECD Best Practices Guidelines for BRC’s. Furthermore, MUM is a member of WFCC and ECCO and until 2013 was the node manager of GBIF-Portugal.


Beyond the microbe's world

Networking and collaboration with other initiatives is essential and MIRRI has already successfully started this work. In spring 2014 MIRRI joined the BioMedBridges initiative as associated partner. This joint effort of ten biomedical sciences research infrastructures on the ESFRI roadmap fosters the development of shared e-infrastructures which allow data integration and interoperability. This “bridging’” and combining of research data will lead to better insights in the biological and medical sciences. The MIRRI consortium is committed to support this vision as a part of this network.

MIRRI is also involved in the development of Horizon2020 cluster projects (e.g. INFRADEV-4). This call aims to implement cross-cutting services and solutions for clusters of ESFRI and other relevant research infrastructure initiatives to prevent fragmentation of the European research landscape. Coordinators of relevant infrastructures meet regularly to discuss project ideas and to elaborate appropriate grant applications (deadline for application: September 2, 2014).

In the future issues of this newsletter EU projects with relevance for MIRRI will be introduced and potential areas of collaboration will be highlighted.


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.

Within the first 18 months of the project the basics for the development of strategies have been defined:

- WP2 conducted surveys for users and providers of microbial material to identify the needs and expectations of these stakeholders

- WP3 explored the potential legal status of the future MIRRI infrastructure

- WP4 drafted the business case

- WP5 established communication and outreach

- WP6 analysed MRCs’ holdings and service offers for overlap and gaps

- WP7 identified the status quo regarding education and training, current tools and contents within and outside of MRCs

- WP8 determined the current data management and IT infrastructure in mBRCs

- WP9 determined gaps in biosecurity issues


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


Microbe Highlights

This section focuses on highlights from the MIRRI partners’ collections: a specific new strain constituting the first representative of a new phylogenetic group, an older strain of renewed interest (new patents, interesting features or applications, news from genome sequencing, etc.). In this issue, the series starts with highlights from three of the MIRRI partners:


Chromobacterium violaceum (CV026) CECT 5999, a biosensor to detect quorum sensing in Gram-negative bacteria

Quorum Sensing (QS) is a mechanism by which certain bacteria and other organisms can detect the population density by measuring the level of external signalling molecules. Through this system, bacteria can communicate and coordinate important microbial behaviour such as bioluminescence, antibiotic biosynthesis, symbiosis, conjugation, biofilm formation or virulence in response to environmental changes. There exist also several molecules, natural or synthetic, that are able to disrupt this QS mechanism and could help inhibiting strain pathogenicity. This process is known as Quorum Quenching (QQ) and has proved to have antimicrobial activity. Due to the continuous increase and spread of antibiotic resistance, this is becoming a relevant field of research.

N-Acyl homoserine lactones (AHLs) are the most common signal molecules that activate QS in Gram-negative bacteria. Chromobacterium violaceum (CV026) CECT 5999 is a white mutant unable to produce violacein by disruption of a QS mechanism due to the lack of AHL production. When colour-less CECT 5999 culture is incubated in the presence of AHLs the production of the pigment is restored and the colonies become violet. The picture shows C. violaceum CECT 5999 on the left, becoming violet when getting in contact with the AHLs produced by Aeromonas veronii CECT5761 (right side of the picture).

This strain can thus be used as a biosensor to screen for AHLs producing bacteria revealing the QS ability. It could also be applied in the screening of molecules that participate in QQ mechanisms.


Thermotoga thermarum strain LA3T (DSM 5069) gene sequence now available

This organism was chosen and sequenced as part of the Genomic Encyclopedia of Bacteria and Archae project (GEBA) project which aims to obtain reference genomes that more broadly cover the evolutionary diversity of prokaryotes. T. thermarum LA3T is the fourth sequenced genome of a type strain from the genus Thermotoga. The order of Thermotogales represents the deepest branch and the most slowly evolving lineage within the eubacteria (Huber, R. & Stetter, K., 1992). DSM 5069 is a Gram-negative, rod-shaped bacterium whose mobility is assured by flagella (photo credit Göker et al.). It was isolated from a hot continental solfataric spring in Lac Abbé (Djibouti). As a thermophilic microorganism its growth optimum is at 70 °C with a pH optimum at 7.0. Salinity range is tolerated between 0.2% and 0.55% NaCl. Several differences to the other Thermotoga genomes have been identified, e.g. regarding the cofactor metablism, the Fe-S cluster synthesis, the utilisation of precursors of cobalamin (vitamin B12) as well as of oligogalacuronides or the number of glycosyl hydrolases. Its metabolic characteristics make T. thermarum interesting for biogas production by anaerobic digestion of agriculturally produced/derived biomass as well as for the food industry. For more details see Göker, M. et al. Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring. (2014) Stand. Genomic Sci. 9:3.


Aspergillus parasiticus B strain (MUM 10.256), an atypical strain that produces aflatoxins B only

Aspergillus flavus and Aspergillus parasiticus remain the most important and representative species of Aspergillus section Flavi occurring naturally in food commodities. These species are responsible for the production of aflatoxins in a wide variety of foods all over the world. Since aflatoxins are highly toxic fungal secondary metabolites (aflatoxin B1 is regarded as the most potent naturally occurring carcinogen), considerable interest has been placed in inter- and intra-specific diversity, ecophysiology and toxigenic ability of Aspergillus section Flavi species.

Typical A. parasiticus strains are extremely uniform in their ability to produce aflatoxins: they are strongly aflatoxigenic, consistently producing both aflatoxins B (AFB), and G (AFG), while non-aflatoxigenic strains seem to be extremely rare. Recently, a new strain was isolated from Portuguese almonds (Prunus dulcis) and described. Although morphologically and genetically identical to A. parasiticus, it had the distinctive feature of producing AFB only (Arita et al. 2014). This strain has been named Aspergillus parasiticus B strain (MUM 10.256, photo credit Paula Rodrigues) and, to our knowledge, is the first reported A. parasiticus strain showing this atypical feature. Furhermore, strain B seems to be better adapted to lower temperatures than the typical A. parasiticus strain. The B strain produces the highest amounts of AFB at 25 °C, whereas typical A. parasiticus and other strong aflatoxin producing species (including A. flavus, A. arachidicola and A. nomius) do it mostly at 30 °C. Given this particular ecophysiological adaptation, the atypical A. parasiticus B strain can thus become a major food safety concern in colder regions where the typical A. parasiticus strains are not well adapted. MUM accepted the deposit of this key-strain in line with criteria defined by Stackebrandt et al. (2014).


News & Events

WP2 designed a survey on innovative services required from mBRCs in support of R&D in Europe. The survey is addressed to all kind of end-users of microbial material and shall provide input from our main stakeholders regarding the future service output of MIRRI. We invite all stakeholders to answer this questionnaire which is accessible here.


A second survey, elaborated by WP7 to draw a general picture of current microbiology education and training programs across the EU is open until June 11, 2014. Providing feedback to this survey will help MIRRI to develop a tailored training and education program.


The Intermediate Review takes place on June 18, 2014 in Amsterdam (The Netherlands). Subsequent to this evaluation by the European Commission the 3rd MIRRI General Meeting, the Mid-Term Review Meeting, takes place on June 19-20, 2014.


Partner Update: During the first 18 month MIRRI received several requests for joining the consortium. Currently, the process of including three new Collaborating Parties, i.e. European culture collections, has been completed. The new Collaborating Parties are CMII (Romania) , PHE (UK) and SCCAP (Denmark).


Meet MIRRI @

Core Technologies for Life Science (CTLS), June 2-5, 2014 in Paris (France), exhibition, lecture, poster


ECCO XXXIII, June 11-13, 2014 in Valencia (Spain), lectures by MIRRI representatives


16th European Congress on Biotechnology, July 13-16, 2014 in Edinburgh (Scotland), exhibition


IUMS 2014, July 27 – August 1, 2014 in Montreal (Canada), poster


Food Micro 2014, September 1-4, 2014 in Nantes (France) poster and lecture


1st International Conference on Quality Engineering and Management, September 14-16, 2014 in Guimarães (Portugal)



D. Smith, K. McCluskey, E. Stackebrandt (2014) Investment into the future of microbial resources: culture collection funding models and BRC business plans for biological resource centres. SpringerPlus 3:81


E. Stackebrandt; D. Smith, S. Casaregola, G.C. Varese, G. Verkleij, N. Lima, P. Bridges (2014) Deposit of microbial strains in public service collections as part of the publication process to underpin good practice in science. SpringerPlus 3:208



Participants of the MRC Head's Meeting


1st MIRRI mBRC Head’s Meeting

Initiated by the MIRRI coordinator Erko Stackebrandt, it was the first time that directors of leading European mBRCs met to discuss the future landscape of microbial holdings. The participants debated what kind of impact MIRRI will have on the daily mBRC business with respect to the envisaged concepts of data offer (interoperability to facilitate data mining), broader access to materials, business models for operations, legal certainty on use, security of strains for future use and protection of public funding investment and quality. The outcome of this event was very positive; and we expect to turn this into a regular event. A survey of the foreseen individual mBRC medium-term developments of holding’s emphasis is in preparation.


BioMedBridges Meeting

MIRRI was represented at the BioMedBridges 2nd Annual Meeting by David Smith (CABI). The event was used to make new contacts and continue on-going discussions (e.g. INFRA-DEV 4). In the course of the meeting MIRRI was accepted, alongside with the ESFRI BMS project ISBE, as new associated partner of the BioMedBridges initiative.


ICRI 2014

Raquel Hurtado and Dominique Clermont (CRBIP) attended the 2nd International Conference on Research Infrastructures on behalf of MIRRI. This event was used to establish new contacts to related research infrastructures and foster collaborations. The next conference, ICRI 2016, will take place in South Africa.

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.