MIRRI - Microbial Resource Research Infrastructure


View this email in your browser

MIRRI NEWS | Issue 4

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,


six more months to go to finalize the MIRRI Preparatory Phase: needless to say that we now enter the most crucial phase of the project.

The past months brought some positive news for the MIRRI consortium: First of all, with Poland and Greece as third and fourth signatory of the Memorandum of Understanding the process of the MIRRI-ERIC application is about to start. Once all necessary underlying documents are finalised, this important step towards the Implementation Phase will be initiated. The second piece of good news is that the INFRADEV-4 application CORBEL (Coordinated Research Infrastructures Building Enduring Life-science services) has now been fully granted by the European Commission. The MIRRI Partners CAB International, CBS, DSMZ, and Jacobs University will closely collaborate with other ESFRI BMS infrastructures to guarantee the success of this project. It is envisaged to start CORBEL in September 2015.

As mentioned in previous issues of this newsletter, the implementation of the Nagoya Protocol and the EU Regulation No 511/2014 keeps us busy. Together with external experts, MIRRI will introduce recent developments of mBRC interest and react to expected needs of users of microbial material during two workshops. The first workshop will take place back-to-back with the annual ECCO meeting (27th of May in Paris), the second during the FEMS meeting (9th of June in Maastricht). Both workshops are free of charge. For more details please go to the Meet MIRRI section of this newsletter.


Kind regards,

Erko Stackebrandt
MIRRI Coordinator


MIRRI Insights

What is the added value of MIRRI from the perspective of our stakeholders? Here are some statements from MIRRI stakeholders, taken from their Letters of Support for the establishment of MIRRI-ERIC:

· MIRRI will help to develop innovative strategies and solve issues related to the microbial strain deposit and supply, data on resources and assistance with taxonomy (…), lead to benefits not only for research community but for the whole society – Academy of Sciences of Moldova (Romania)

· Member States can benefit from the added value that MIRRI can provide as individual mBRCs cannot present global solutions to microbial needs. (…) (MIRRI will) help the process for collections to collectively achieve “registered collection” status and therefore help users of genetic resources fulfill due diligence of the EU Regulation. – Department for Environment Food and Rural Affairs (UK)

· (MIRRI will) provide more efficient support for research, development and applications through the improved supply of high quality microbial resources, their derivatives and associated data – Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (Spain)

· We strongly support the challenge to build up such a pan-European microbial initiative which will serve the overall strategy to put Europe at the forefront of scientific development to support bioeconomy. – Unimore Microbial Culture Collection (Italy)

· A coordinated, but distributed infrastructure for the facilitated and legal access to living biological material and related information (…) would help to develop innovative strategies on key problems such as in healthcare, food security and new energy resources. – BIO Deutschland e.V. (Germany)

· It is clear that the provision of improved access to microbial resources such as reference strains, new collections and their rich accompanying meta data, through MIRRI, is a significant new opportunity in which Instruct has a prime interest. – INSTRUCT (International)

· Microbial taxonomy is complicated and got much enhanced by molecular studies in the past decades, however, still only a fraction of diversity is known. MIRRI will professionally organize the microbial community and promote broad collaboration and by doing so achieve clarity in the identification and classification of microorganisms, and the application of this knowledge. – Species 2000 (International)

· We are clearly convinced that the MIRRI Project is a highest class scientific project, and a fundamental element of success for a pan-European microbiological scientific research. - Aguas de Valencia (Spain)



WP7: Capacity building, education and training

In a European‑distributed infrastructure such as MIRRI, the available Education and training (E&T) opportunities are typically spatially dispersed and heterogeneous in terms of their learning materials, fees, certification, learning language, etc. Currently, the offer is still fragmented and largely dominated by classic content types and delivery. It is our aim to develop MIRRI’s E&T offer to include widely available course catalogues and to create a common Continuing Professional Development (CPD) plan for our mBRCs, which ensures a high Quality Control/Quality Assurance (QC/QA) system to the users.

In WP7, we have gathered and interpreted survey data on the E&T offer and demand within MIRRI and among its stakeholders. These datasets have formed the basis to identify gaps and needs for improvement not only of the training content itself, but also for its delivery. Having collected data on innovative learning tools, built on outputs from previous and ongoing projects such as EMbaRC, and discussions on this topic with our colleagues in EMTrain, we are now designing a conceptual strategy for E&T that makes use of innovative learning tools, including e‑learning and virtual labs.

By following a common CPD plan and having easy and cost-effective access to a wide course catalogue, scientists will assemble an ever-updated portfolio of potentially transferrable skills and competences. The course catalogue will be offered to a wider community of MIRRI stakeholders and industrial partners. A strategy is being designed based on existing mechanisms and parallel projects to promote the essential harmonization of E&T standards and practices across MIRRI and to ensure proper accreditation of each course. A strategy for capacity building will be discussed in an upcoming workshop to address the needs for expertise, facilities and technologies for new services within MIRRI.

Finally, on behalf of MIRRI, MUM-UMinho is participating in the new H2020 project RItrain (Research Infrastructures Training Programme), recently approved by the European Commission. This project aims to develop a flagship training programme enabling RIs across all domains to gain expertise on governance, organisation, financial and staff management, funding, IP, service provision and outreach in an international context.


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 IRCCS Azienda Ospedaliera Universitaria San Martino – IST Istituto Nazionale per la Ricerca sul Cancro (USMI), the Service Public Fédéral de Programmation – Politique Scientifique (SPP-PS) and the Universiteit Gent (UGent – BCCM/LMG).

The IRCCS AOU San Martino IST (USMI) is a Scientific Institute for Research, Hospitalization and Health Care of National interest. Its Technological Platform includes the core facility Biological Resource Centre, aimed at coordinating institutional biobank facilities. Among these, the Interlab Cell Line Collection (ICLC), was established in 1994. ICLC is a point of reference for biomedical researchers to whom it supplies: human and animal cell lines, STR profiling of human cell lines, safe and patent deposit of cell lines and hybridomas. The catalogue of services is on-line, and the cell lines are distributed all over the world. ICLC has contributed to the definition of the OECD Guidelines for the management of Biological Resource Centers, participates in the European Infrastructure of Biobanks and Biomolecular Resources (BBMRI-ERIC) and in MIRRI.
USMI is maintaining the CABRI web site. CABRI (Common Access to Biological Resources and Information
) project was funded by the EU from 1996 to 1999. The project implemented a unified access to culture collection catalogues of partners, an online 'one-stop-shop' for biological resources where researchers can search, identify and pre-order strains. The CABRI web site currently includes 28 catalogues from height distinct European mBRCs. Overall, more than 130,000 resources are described. The majority of these are microbial strains, but there also are plasmids, phages, cell lines, plant cells and plant viruses. The CABRI web site is a pioneer model for an integrated, while distributed, database, which is searchable through a common gate.

The Service Public Fédéral de Programmation – Politique Scientifique or Belgian Science Policy Office (Belspo) has a longstanding engagement towards research on and preservation of biological diversity. This commitment is demonstrated through the support of the federal natural science museums, the establishment of an interface function between biodiversity researchers and policymakers, the realisation of dedicated research programmes as well as through the funding and coordination of the Belgian Coordinated Collections of Micro-organisms, BCCM.
Belspo has initiated the BCCM consortium in the early eighties. Since then the BCCM collections have developed from individual, research-based collections to a consortium of 7 public, service-oriented collections. Each collection forms a binomial with its host laboratory to exchange scientific expertise. The cooperation within the consortium ensures a harmonised approach to tackle issues of common interest. In this regard, a special role is set aside for the BCCM coordination cell that makes part of Belspo. This cell coordinates the ISO 9001 quality management system, information technology (e.g. LIMS), external and internal communication, international cooperation and legal aspects of the consortium.

For a small country like Belgium the integration of its researchers in international activities is a must. The BCCM collections work together with colleagues from other countries in the frame associations such as ECCO and WFCC. Belspo believes that close cooperation between European culture collections will benefit the many users and help stimulate the further development of biotechnology and life sciences. For this reason, they have participated in consecutive European projects like MINE, CABRI, EMBRC and EMbaRC. Within the MIRRI Preparatory Phase, Belspo is the only participating research funding organisation, clearly demonstrating its interest in the MIRRI infrastructure.

The LMG Bacteria Collection was one of the founding partners of the Belgian Coordinated Collections of Microorganisms (BCCM) in 1983 and has since then developed into a well-known Microbial Biological Resource Centre (mBRC) specialized in bacteria, holding and offering over 25,000 well-characterized bacterial strains. It receives an excellent international recognition as repository of important groups of bacteria and for its strong expertise in bacterial characterization. The strain holdings are very diverse and serve the needs of both academia and various R&D sectors, including green, red, blue and white biotechnology. The strategic acquisition policy of BCCM/LMG is supported by an ISO 9001 certification for accession, control, preservation, storage and supply of biological material and related information in the frame of public deposits, safe deposits and patent deposits.
A glimpse on the BCCM/LMG EU project track record (MINE, CABRI, EBRCN, EmBaRC) clearly illustrates that BCCM/LMG supports the establishment of a pan-European Research Infrastructure for supporting both academia and bio-industry. In MIRRI, BCCM/LMG focusses on strategies for the reduction of gaps in holdings, development of services and outputs, and it also actively contributes to the data resources management work package.


Beyond the microbe's world

ELIXIR is the ESFRI Research Infrastructure for life science data. It aims to coordinate, sustain and integrate Europe’s bioinformatics resources by linking major bioinformatics institutes such as EMBL-EBI with the national bioinformatics infrastructures developed within each country. The volume and diversity of data being generated now in life sciences is too big for any one country to handle alone and researchers increasingly require access to data from several resources to be able to conduct their research.
There are over 1,800 life science databases and analysis tools in Europe, which range from major data archives such as the European Nucleotide Archive (ENA), to widely used knowledge bases such as Ensembl through to niche databases and analysis tools used by smaller communities of researchers. ELIXIR works to coordinate these resources by operating a series of service platforms for ‘data’, ‘tools’, ‘standards’, ‘compute’ and ‘training’. ELIXIR’s Innovation and SME programme provides direct support to research-intensive companies in accessing and using ELIXIR’s resources.

ELIXIR shares many synergies with MIRRI and there are several existing and future avenues for collaboration. ELIXIR will work closely with MIRRI on the EUR 14.5 million CORBEL grant, awarded by the European Commission, which will officially kick off later in 2015. This grant will ensure that common data bridges, shared access, ELSI services and innovation activities are developed between partnering organisations. This will allow for direct ELIXIR – MIRRI collaboration. On issues such as predictive systems for pharmacology for safer drugs and chemical products, ELIXIR will build curated reference datasets and annotations, tools for big data and literature mining and data storage, whilst MIRRI will provide world-class access to cell cultures, microbes and genomes. ELIXIR has also funded a Pilot Action on ‘Marine metagenomics: towards user centric services’. MIRRI is seen as a key infrastructure in this field, and as the Pilot Action expands, partners will seek to engage MIRRI’s experts closely in the development of new databases. Equally, MIRRI’s expertise in aspects such as the Nagoya Protocol is invaluable to ELIXIR’s partners.
Some of ELIXIR’s services may also be of interest to MIRRI’s users. The ELIXIR Tools and Data Services registry allows researchers to search for the right database and tool including those for microbial data. The emerging ELIXIR TeSS portal will allow users to identify and access relevant training courses and e-learning content run by ELIXIR partners, and again many of these will be of relevance to experts in microbial resources.


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 organised the “Workshop to agree minimal-maximal function of MIRRI”

- WP3 started to finalise, based on the outputs of the WP2 workshop, the documents necessary for ERIC application

- WP4 submitted the deliverables “Financial Plan” and “Final draft of business plan content"

- WP5 supports the other WPs by providing information relevant for the preparation of strategies, e.g. WP2 to define the operational structure of MIRRI by providing information on stakeholders’ feedback and continues outreach activities

- WP6 submitted the deliverable “Workshop to identify improved services, the priority actions and implementation mechanisms”

- WP7 is preparing the “Workshop on strategies for capacity building”

- WP8 finalised the ‘demonstrators’, a first proof of concept of mobilisation of metadata available from different mBRCs

- WP9 submitted the deliverable “Organise an international workshop on Biorisk assessment and Biosecurity measures”

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


Microbe Highlights

In this issue, the series continues with highlights from MIRRI partners CABI and MUT:

Fungi as tools in Agriculture - Fungal pathogens for research in plant pathology and insect biocontrol

The CABI culture collection continues to strengthen its holdings related to CABI’s global interests in crop health (www.plantwise.org) and management of invasive species. Recent new strains added to the CABI collection catalogue include several phytopathogen reference strains useful to researchers studying the prevalence of microbial pathogens in plant systems and for determining mechanisms of disease epidemiology and control. These include Fusarium incarnatum (IMI 500392) isolated from rice, Fusarium decemcellulare (IMI 395827, see picture with macroconidia from this species) and Cylindrocarpon destructans (IMI 500165) isolated from beetroot. Worthy of note is a new species of Cordana mercadiana (IMI 502221) (ex Type) a dematiaceous hyphomycete isolate from plant debris.
Entomopathogenic fungi have potential usage as biological control agents against insect pests. The use of entomopathogens as biopesticides provide a ‘greener’ alternative to chemical methods of insect control. New additions to CABI’s significant holdings of entomopathogens include Metarhizium acridum (IMI 501155) and Beauveria pseudobassiana (IMI 501988).



Mucor circinelloides MUT44, an effective biocatalyst for C=C double bonds and carboxylic acids/esters reduction

In the framework of the modern bioeconomy, the reduction of waste and by-product formation as process costs and energy requirements is a central goal and an actual challenge. The deficiencies shown by chemical synthesis are indeed overcoming by the focused development of biocatalytic processes based on fungi. Mucor circinelloides (picture shows sporangium of M. circinelloides MUT44) belongs to Zygomycota, and recently raised biotechnological attention due to its capability to accumulate poly-unsaturated fatty acids (Carvalho et al. 2015) and carotenoids (Torres-Martínez et al. 2012). Several strains of M. circinelloides efficiently reduce C=C double bonds, carboxylic acids and esters, carrying out crucial reactions of organic chemistry industry on both conventional and unconventional (i.e. not transformed by bacterial and yeast enzymes) substrates (Romagnolo et al. 2015). Many compounds with different electron-withdrawing groups and substituents nearby the C=C or COOR bounds can be efficiently transformed. The enoate reductase (EC1.3.1.31) and carboxylate reductase (EC1.2.99.6) activity, putatively expressed by those strains, have been rarely reported in filamentous fungi and, to our knowledge, this is the first report on M. circinelloides. Given its high reduction yields towards not conventional substrates, the expressed enoate reductase activity pattern by M. circinelloides MUT44 was investigated by RT-PCR. Ten putative genes were found; the expression of three of them was strongly and rapidly activated in presence of cyclohexanone, concurrently to its actual biotransformation, highlighting the active role of these enzymes. These reactions enrich the enzymatic toolbox available to organic synthetic chemistry for the development of green processes aimed to produce natural flavours and fragrances, satisfying the EU requisite for the natural labelling of the corresponding products.


News & Events

  • The MIRRI consortium welcomes six new Collaborating Parties:
    Banco Espa
    ol de Algas, BEA (Spain),
    BRC Toxoplasma
    Culture Collection of Algae and Protozoa
    , CCAP 
    National Collection of Plant Pathogenic Bacteria
    , NCPPB
    National Collection of Yeast Cultures
    , NCYC
    National Institute for Biological Standards and Control
    , NIBSC

  • After France and Spain, Poland and Greece have signed the MIRRI Memorandum of Understanding for the MIRRI-ERIC.
  • The INFRADEV-4 project CORBEL (Coordinated Research Infrastructures Building Enduring Life-science services) has been granted for funding. MIRRI partners from CAB International, CBS, DSMZ, and Jacobs University will participate in this pan-European project.
  • The INFRADEV-4 project EMBRIC (European Marine Biological Resource Infrastructure Cluster), granted for funding, will officially start in June 2015. The MIRRI partners DSMZ, UGent, CRBIP and CAB International will participate in this pan-European project.
  • REDESMI, the Spanish Network of Microorganisms, has been constituted thanks to the INIA AC2013-00028 grant awarded to the MIRRI partner CECT. This network has been constituted to add value to the microbial strains isolated by Spanish research groups by different means: mapping the Spanish microbial resources, sharing good managing & preservation & characterization practices, increasing the visibility of both resources and expertise and generating a database of highly characterized resources with added value. It will help developing the Spanish National Node of MIRRI in the upcoming Construction Phase.
  • Amongst others, MIRRI has the patronage of ISSY32 the International Specialized Symposium on Yeasts, taking place September 13-17, 2015 in Perugia (Italy)
  • MIRRI organises two workshops on Access and Benefit Sharing; for details see below. Both workshops are public and free of charge.

Meet MIRRI @

  • ECCO XXXIV congress – European Culture Collections as tools in research and biotechnology, May 27-29, 2015 in Paris (France); lectures by C. Bizet (IP), S. Casaregola (CIRM), D. Martin (DSMZ), D. Smith (CABI), E. Stackebrandt (DSMZ) , G. Verkley (CBS)
  • On May 27, 2015 MIRRI organises a workshop entitled “The new EU Regulation for the use of genetic resources– the impact of the actual regulatory development on science and research in the European Union”, back-to-back with ECCO XXXIV. MIRRI experts as well as external speakers will present case studies and discuss important issues with the audience. For details, please visit the ECCO conference website.
  • 6th Congress of European Microbiologists - FEMS 2015, June 7‑11, 2015 in Maastricht (Netherlands); MIRRI exhibition booth with M. Schüngel (DSMZ), R. Hurtado-Ortiz (IP), several MIRRI posters will be presented.


Schüngel M. and Stackebrandt E. (2015) Microbial Resource Research Infrastructure (MIRRI): Infrastructure to foster academic research and biotechnological innovation. Biotechnol. J., 10:17-19



  • 4th LifeTrain Workshop: Achievements and challenges in lifelong learning for the biomedical sciences (02.-03.03.2015, Brussels): Sofia Costa (MUM) attended this workshop on behalf of MIRRI and presented a poster ‘Towards a strategic concept for innovative learning programmes and tools in the Microbial Resource Research Infrastructure (MIRRI)’. The workshop included oral and poster presentations, but was based mainly on discussion groups, that provided an excellent interchange of experiences. Knowledge gained during this event will be translated into the WP7 strategy on capacity building, education and training.
  • Techinnov 2015 (12.02.2015, Paris) and Bio-Europe Spring 2015 (09.-11.03.2015, Paris): Chantal Bizet and Raquel Hurtado (CRBIP) participated in these two meetings. Both events were used for lively discussions with stakeholders from the industrial sector. The received inputs will be used for the further development of the MIRRI strategies.

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.