MIRRI - Microbial Resource Research Infrastructure


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MIRRI NEWS | Issue 3

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,


I hope all readers enjoyed the break over the Christmas time and relaxed sufficiently to tackle 2015 business.

For MIRRI, there is no time for contemplation; the New Year started as busy as the old one had ended: During a WP Leader meeting in Amsterdam at the beginning of September 2014 several issues raised in the Mid-term review were discussed, and the ERIC Statutes, the MIRRI Partner Charter, the Rules of Operations and the Terms of Use were drafted. This brings us one step closer in finalising the legal framework for the envisioned MIRRI-ERIC. In addition, the MIRRI Financial Plan was revised and a much better overview on costs and revenues is now outlined. These issues were also on the agenda during the 2nd mBRCs Heads Meeting (December, Amsterdam) to discuss the future operational structure of MIRRI. The strategies resulting from all these discussions shaped the 3rd Iteration Business Case (in print) and prepared the Steering Committee for the “easy” short assessment by ESFRI, just delivered on January 30th, 2015.

The implementation of the Nagoya Protocol in October 2014 kept many of us busy in attending stakeholder workshops in Paris and Brussels to influence the guidance papers for its implementation and to explain phrases used in some articles of the basic EU Regulation concerning ABS. MIRRI has been and will be involved in the discussions on the implementation of the EU Regulation 511/2014, raising its voice for the microbial community. Updates on this topic can be found on the MIRRI website.

The results of the Horizon2020 applications have been published and our thanks go to the team at the UMinho-MUM for involving MIRRI in the Training Programme Ritrain, and to the DSMZ, UGent, CRBIP and CAB International for participating in MBRIC. The CORBEL project (with Jacobs University, CAB International, DSMZ, MUT, CBS) is on the reserve list for Infradev-4. Unfortunately, the Europe-Africa joint project BrinA (CRBIP, DSMZ, CAB International) will not be funded. Thanks to all MIRRI Partners who contributed in ideas and text to the various funded and non-funded Horizon2020 projects for positioning MIRRI on the European landscape of research infrastructures.

2015 will be the last year of the MIRRI Preparatory Phase, and several workshops and many deliverables are still ahead of us. We all should have a positive attitude; partners engagement at the national level have been very successful and we are well on the way to reach the required number of signatories for the Memorandum of Understanding and governmental support to initiate the MIRRI-ERIC legal status in 2016. I am confident that the MIRRI consortium will work hard to assure a smooth transfer into the Implementation Phase.


Kind regards,

Erko Stackebrandt
MIRRI Coordinator


MIRRI Insights

During the last months MIRRI asked its stakeholders, especially the users of genetic resources, what they think MIRRI can improve:

MIRRI and its coordinated approach is important, because...

… Europe needs to increase facilities to store risk level 3 organisms”; participant of the MIRRI Biosecurity Workshop

mBRCs need to be better involved in processes and definition of guidelines/regulations, e.g. in the field of biosecurity/risk assessment”, participant of the MIRRI Biosecurity Workshop

through its interactions with other ESFRI Research Infrastructures such as EU-OPENSCREEN or Euro-BioImaging, MIRRI would be able to provide its users with the possibility to analyze an unprecedented choice of isolates using powerful analysis tools in a coordinated manner”, head of a public mBRC

it can provide the bio-industry with interoperable databases, searchable for important microbial properties, e.g. enzyme profiles or secondary metabolites”, participant of the MIRRI Workshop on Communication Approaches to Bio-industry

… via its web portal it can offer centralized and facilitated access to microorganisms, their properties and growth requirements”, customer from a public mBRC

… mBRCs must be able to increase their capacity and accept resources from endangered scientific collections”, University professor holding a scientific collection.

At the moment MIRRI is developing strategies for the implementation of mechanisms which will fulfill the users’ requests.


WP2: Design of the Microbial Resource Research distributed Infrastructure
WP6: Development of services, outputs and foster interdisciplinary work programs

WP2 and WP6 undertake the design, coordination and harmonization of the MIRRI offers and expertise:
In Europe there are a considerable number of well-established, mature microbial domain Biological Resource Centres (mBRCs) and Culture Collections (CCs) which differ in many aspects such as size, focus, quality assurance, information and communication technology (ICT) development, etc. At present, the European public mBRCs/CCs operate in a fragmented and isolated way. As a consequence, neither the European landscape nor the scope of holdings and services is obvious to users who search for specific resources or services offered. Also the visibility and the profile of individual mBRCs is low and needs to be raised to reach a sustainable perception for the users.
MIRRI aims to transform this situation into a coordinated and operational Research Infrastructure. To develop a strategy for designing such an infrastructure, resource providers and users have been consulted through four ad hoc surveys
. Based on the feedback a more coherent view on present needs and the MIRRI distributed offer concerning resources and services were deduced in order to meet users’ demands. In addition, the communication with users has been improved; potential users (e.g. from the bio-industry) were identified underpinning the further strategic development of MIRRI.
The first objective envisaged is a strategy to broaden a targeted coverage of holdings, considering the gaps but avoiding redundancy in combination with a coordinated offering of (innovative) services addressing academic and industrial needs. The second objective is to offer standard quality in resources and services through harmonization of best practices among providers. Coordination of the MIRRI offer will be carried out through the MIRRI web portal that will guide the user to access a wider range of resources and integrated data, and to identify centres of expertise which will provide the maximum information retrieval for scientific research and exploitation.
The design of the scope and coverage of the provision of resources and services to the user community by MIRRI in combination with integrated knowledge on characteristics of the resources, services and research in a sustainable multipurpose platform should place the mBRCs at the front of academic research and a bio-economy based community.


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 beanswered by the Culture Collection of Industrial Microorganisms at the Institute of Agricultural and Food Biotechnology (CCIM/IAFB), the Centre International de Ressources Microbiennes (INRA-CIRM) and the Jacobs University Bremen.

The Culture Collection of Industrial Microorganisms is a part of the Prof. Waclaw Dabrowski Institute of Agricultural and Food Industry and one of the oldest industrial culture collections in Europe. Provision of comprehensive microbiological services for Polish biotechnological industry is an essential goal of IAFB. In its 60 years plus history CCIM/IAFB has developed and published many numbers of patents including new microbiological strains or technology solutions. Nowadays, to provide users with a high quality service, CCIM/IAFB cooperates with the Microbiological Department (lab accreditation according to standard ISO 17025) which provides a small scale fermentation line.
CCIM/IAFB preserves over 3,000 microorganisms with unique industrial features. The holding comprises a variety of microbiological taxa such as yeast (applied in winery, brewery), bacteria including pathogenic food isolates, lactic acid bacteria (used in the dairy industry) and fungi (agricultural isolates); preserved by lyophilisation and liquid nitrogen. Microorganisms stored in CCIM/IAFB find application in research on metabolic biodiversity of specific groups in various biotechnological processes related with food production and agriculture. This is especially valuable in the production of pro-health organic food obtained by traditional technology.
Microorganisms are characterized by traditional, physiological techniques as well as by molecular techniques such as PCR or qPCR. This is the first step towards finding connections between technological features and the genetics of microorganisms.
CCIM/IAFB is a partner of MIRRI, member of WFCC (since 1982) and ECCO (since 1993); it was a partner in the European Biological Resource Centres Network (EBRCN). Furthermore, it has the status International Depository Authority, accepting biological materials according to the requirements of the Budapest Treaty (since 2000).

CIRM (Centre International de Ressources Microbiennes) is a unique collection of microorganisms in France, run by INRA, one of the largest agricultural research agencies in the world. It is a network of five geographically distinct sites dedicated to food bacteria (CIRM-BIA), bacteria pathogens of humans and animals (CIRM-BP), plant associated bacteria (CIRM-CFBP), biotechnological yeasts (CIRM-Levures) and filamentous fungi (CIRM-CF), totalling over 20,000 isolates. The main mission of CIRM is to gather and preserve the microbial biodiversity of INRA to sustain research and innovation in the areas of agro-food, health, biotechnology and environment. These resources are made available to the international scientific community under high quality standards guaranteed by ISO 9001 certification. Each CIRM site is hosted by a research laboratory and therefore takes part in the ongoing research in its field of expertise. Indeed, CIRM participates in national and international research programs by making available their biological resources and their expertise resulting from up to 40 years of experience.
CIRM offers a wide array of services including safe deposit, identification and characterization of strains and high throughput screening for various phenotypic characteristics. CIRM has an efficient Information System which boasts three exhaustive taxonomy databases: lignocellulolytic fungi, plant associated bacteria and yeasts.
After coordinating the EU FP7 funded project EMbaRC (E
uropean Consortium of Microbial Resources Centres), CIRM now participates in the MIRRI project, being involved in several aspects such as the construction of the infrastructure, training, Information Technology and legal matters.
For CIRM and its coordinator, Serge Casaregola, MIRRI will facilitate the retrieval of the strains of interest by making available highly efficient tools allowing data mining of their constantly growing databases. In addition, MIRRI can facilitate collaborations with other ESFRI initiatives.

Jacobs University Bremen is a highly selective, private institution for the advancement of education and research. Its academic programs and cultural environment prepare graduates for international leadership and global citizenship. Research at the Jacobs University Bremen aims at key contributions in the following three areas: MOBILITY (of people, goods, and information), HEALTH (focus on bioactive substances) and DIVERSITY (of modern societies).
The expertise provided by Jacobs University into MIRRI is the management and integration of large, heterogeneous and complex data as well as the development of community standards for contextual (meta)data. With the envisioned MIRRI Information System designed as a “one-stop-shop” to serve the community with reliable data products, expertise and services, the European infrastructure MIRRI is a fascinating field of application, says Prof. Dr. Frank Oliver Glöckner, head of the Microbial Genomics and Bioinformatics Research Group.


Beyond the microbe's world

EU-OPENSCREEN is a pan-European research infrastructure initiative to academic Chemical Biology research. MIRRI’s sister initiative is listed on the roadmap of ESFRI, the European Strategy Forum on Research Infrastructures since 2008 and is currently in its Transition Phase aiming at the implementation of an ERIC in 2015.
As a joint effort of national networks in 16 European countries, EU-OPENSCREEN will collaboratively develop novel molecular tool compounds (i.e. chemical inhibitors or activators of biological targets) with users from various disciplines of the life sciences (e.g., microbiology, cell and molecular biology, early drug discovery). The use and study of these chemical tools is currently restrained by the fact that it requires significant resources and investment. EU-OPENSCREEN faces this challenge by integrating high-capacity screening platforms throughout Europe and offering access to unique shared resources and expertise to scientists. These include latest screening technologies, assay adaptation, follow-up chemistry services for “hit” optimization, and a unique compound collection composed of (up to 300,000) commercial and proprietary compounds collected from European chemists. By testing, systematically and repeatedly, this chemical collection in hundreds of assays originating from very different biological themes, the screening process generates enormous amounts of valuable information about the biological activities of the substances and thereby steadily enriches our understanding of how and where they act. All data collected during a screening
will be published in a central European Chemical Biology Database, being accessible for the whole scientific community.
From the very beginning the close relationship between MIRRI and EU-OPENSCREEN was apparent: the infrastructures share a specific user clientele that needs to obtain microbial resources (from MIRRI) for producing compounds (to be screened at EU-OPENSCREEN facilities). Both infrastructures can support each other by providing their specific expertise and collaboration will be reinforced in cluster projects subject to H2020 funding like e.g. MBRIC.


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 updated the future operational structure, based on discussions during the Steering Committee – Work Package Leader Meeting

- WP3 revised the ERIC Statues based on discussion results during the Steering Committee – Work Package Leader Meeting

- WP4 revised the Third Iteration Business Case of MIRRI; if you are interested in this document, please contact us

- WP5 analysed the first R&D expert group meeting and submitted the deliverable “Impact of MIRRI on society”

- WP6 submitted the deliverables “Report on strategies and incentives to improve accessibility of orphan cultures” and “Report on the main methods to be standardized”

- WP7 submitted the deliverable “Report on current E&T programmes”

- WP8 submitted the deliverables “Strategies for data evaluation and validation and on potential mechanisms and improvements for ICT” and “Report on workshop and surveys on current collection status”

- WP9 organised, back-to-back with WP3, the Workshop “Biosecurity Implementation Strategies and Compliance Management in mBRCs”

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 IPBM-VKM and CRBIP:

Coming in from the cold – a “cool” collection

A large set of strains (fungi, bacteria and Archaea) is kept in All-Russian Collection of Microorganisms (VKM), which have been isolated from permafrost samples kindly provided by the late Dr. David Gilichinsky. More than 200 subsurface samples (deeper than 50 m) were analysed at VKM by culturing and molecular approaches within frameworks of several international and national projects (including recent RFBR grants №12-04-01730 and №13-04-02082). The samples were aseptically collected in low-temperature regions of Arctic, dry and very cold valleys of Antarctica, and also in Kamchatka, Russia. The age of permafrost sediments was estimated to reach up to 3 million years; the samples were allocated to Holocene, Pleistocene and late Pliocene epochs. Microbes in such habitats apparently survive for a long time near the physico-chemical boundary for life.
The VKM sub-collection of fungi is the largest one among those “coming in from the cold” and currently includes nearly 750 strains belonging to more than 60 genera and 140 species. The strains mainly originate from samples of permafrost soil/sediments of different age and geography (550 strains), and also from ancient plant seeds and fragments of fossil animals, both found in permafrost (26 strains). Almost 100 strains are from the non-frozen sodium-chloride water brines (cryopegs) located in ancient permafrost sediments of marine origin, and about 70 strains are from frozen volcano ashes. Dominant (90%) among fungi from low-temperature habitats are anamorphic Ascomycetes (light, dark and pycnidial forms). Teleomorphic Ascomycetes and Basidiomycetes make up 8%, while zygomycetous fungi compose 2%. Overwhelming majority of the strains belong to the most frequently encountered genera Penicillium, Geomyces and Cladosporium, many species of which are known to possess high adaptive capabilities and some (Geomyces) were shown to grow at ‑2 °C, at high salt concentration (20%) and under low oxygen tension.

Screening conducted among Penicillium isolates revealed several strains of potential biotechnological and medical interest. For instance, production of new quinoline alkaloids and quinocitrinines A and B, was demonstrated. Many data on specific metabolites of the fungal strains from low-temperature habitats enriched the Microbial Application properties DataBase (MADB) under development at VKM.



Bacillus cereus (CIP 104568) a carbonatogenic bacterium used for producing superficial protecting coating on limestone buildings

Certain bacteria form crystals from the solutes in their aqueous environment and some authors have associated this activity with the extensive deposits of CaCO3. Some of these bacteria belong to the genus Bacillus, such as Bacillus cereus, which can form carbonate crystals even in their growth media. The ability of the so-called carbonatogenic bacteria may be used for producing superficial protecting coatings (biocalcin) on limestone buildings, monuments and statuary. This is the concept of bio-mineralisation.
The first life-size experimentation on bio-mineralisation was carried out in Thouars (Deux Sévres, France) on the south-east tower of Saint-Médard Church (Le Métayer-Levrel et al., 1999)
. This church (upper picture, ©Wikipedia) was built during the 12th century with Tuffeau limestone and, since that date, has been restored several times. The treatment was applied on an area of 50 m2. The evolution of the bacterially produced biocalcin while exposed to weather variations was evaluated twice and the last measurement confirmed the good quality and consistency of the biocalcin. Furthermore, the abundant development of carbonatogenic bacterial populations prevented the development of autochthonous acidifying bacterial consortia. The biocalcin provides the stone with a protective surface that reduces its absorption of water (with a 1/5 ratio) yet retains its permeability for gas, without detracting from its aesthetic appearance.
Compared to the more traditional methods, the bio-mineralisation differs mainly in their natural and ecological character and in the fact that the protection acquired tends to increase with age and tends to recreate a naturally produced material in a way that is similar to the limestone substrate.
The Bacillus cereus CIP 104568 strain (lower picture
, ©Institut Pasteur) was deposited in the Collection of Institut Pasteur in 1995.


News & Events

  • The MIRRI consortium welcomes the HAMBI Culture Collection from Finland as its 21st Collaborating Party. The holdings of this collection are in great extent sampled from Finnish nature and are not available anywhere else.
  • On October 12th, 2014 the Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits Arising from their Utilization to the Convention on Biological Diversity (short: Nagoya Protocol) entered into force. In parallel, Europe enacted its ABS regulation (Regulation (EU) No 511/2014). Users of microbial resources are provided with a summary of useful information on this topic on the MIRRI website.
  • In December the WP3-WP9 Workshop “Biosecurity Implementation Strategies and Compliance Management in mBRCs” took place in Braunschweig (Germany). MIRRI participants as well as invited international experts discussed challenges and developed solutions for implementation of biosecurity strategies in mBRCs.
  • A second workshop, “Communication approaches to the bio-industry”, was held in Amsterdam (Netherlands) in December. MIRRI participants as well as invited stakeholders discussed potential bottlenecks and strategies for a successful involvement of the bio-industry in MIRRI.
  • In March 2015 work package 2 will organise a workshop to define minimal-maximal function of MIRRI, partnership criteria and the MIRRI offer.
  • The MIRRI Partner CIRM has launched its revised website.
  • The annual event HandsOn: Biobanks (HOBB), organised by BBMRI-ERIC, will take place from July 29-31, 2015 in Milan (Italy). It is entitled “The EXPOnential relevance of Biobanking. Clinical Biobanks for personalized medicine”.

Meet MIRRI @

3rd Annual General Meeting of BioMedBridges, February 17-18, 2015 in Munich (Germany); poster by A. Vasilenko (VKM), lecture by E. Stackebrandt (DSMZ)

Knowledge Exchange Workshop: Data strategies for research infrastructures, organised by BioMedBridges, February 19, 2015 in Garching (Germany); A. Vasilenko (VKM), P. Romano (USMI)

Annual Conference 2015 of the Association for General and Applied Microbiology (VAAM), March 1-4, 2015 in Marburg (Germany); presentation of MIRRI at the exhibition stand of the DSMZ (M. Schüngel)

4th LifeTrain Workshop, March 2-3, 2015 in Brussels (Belgium); poster by S. Costa (UMinho-MUM)

BIT's 6th Annual Symposium of Enzyme & Biocatalysis 2015 "Catalyzing Green Chemistry for Huge Business", April 25-28, 2015 in Nanjing (China); lecture by E. Stackebrandt (DSMZ)



Schüngel M., Smith D., Bizet, C., Stackebrandt, E., The MIRRI Consortium (2014) The Role of the European Microbial Resource Research Infrastructure Project. Enliven: Microb Microbial Tech 1(1):001



The International Union of Microbiological Societies congress (IUMS 2014) aimed to promote international sharing, cooperation and open discussions on recent advances and perspectives in microbiology research. The congress brought together the largest, most comprehensive group of microbiology researchers at a single gathering.
MIRRI was represented by a poster exhibition (R. Hurtado-Ortiz; IP). In addition, the MIRRI poster was presented at the Scientific Symposium of the Institut Pasteur International Network (IPIN) which took place during the last day of IUMS 2014 congress.

At the 24th International ICFMH (International Committee on Food Microbiology and Hygiene) Conference (Food Micro 2014) about 800 attendees from around the world were informed about MIRRI during the lecture given by R. Hurtado-Ortiz (IP). In addition, a poster of MIRRI was displayed.

The MIRRI exhibition at the 2014 CARNOT Meeting in Paris was organised by the MIRRI Partner Institut Pasteur (R. Hurtado-Ortiz and D. Clermont). During this event lively discussions with stakeholders from the industrial sector took place at the MIRRI booth.

In December 2014 the directors of the MIRRI Partner mBRCs met for the second time to discuss the future impact of MIRRI on their collections. The drafted MIRRI ERIC Statutes, expected national costs for the establishment of National Nodes as well as the Nagoya Protocol which has entered into force in October 2014 were on the agenda of this meeting.

On December 16-17, 2014 the Italian Embassy in Berlin (Germany) hosted the Workshop on “Italian-German Workshop in Biological and Medical Research Infrastructures”. The aim of this workshop was to foster a bilateral Italian-German strategy towards research infrastructures in Europe. MIRRI was represented by E. Stackebrandt (MIRRI coordinator; DSMZ) and C. Varese (MUT).

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.