MIRRI - Microbial Resource Research Infrastructure


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MIRRI NEWS | Issue 7

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


Prof. Erko Stackebrandt

Dear all,

the end of April marked the official end of the MIRRI Preparatory Phase. What is left is the finalization of the paperwork needed to receive the final payment from the EU. Although now entering the often cited ‘Valley of Death’, the MIRRI consortium has been bound together and is sufficiently strong to pass the fund-less period. MIRRI Partners still believe in the importance and the beneficial impact of establishing a microbial resource research infrastructure in Europe and therefore the negotiations with national stakeholders will go on. A positive example, for which our Latvian Partner must be congratulated, has recently been the signed MoU of Latvia; this brings the total number of MIRRI-MoUs to five. 


With the support of all MIRRI Partners, I will continue to coordinate the consortium during the upcoming Interim Phase, leading in the end to a legal structure for MIRRI. For researchers it is important to know that already existing services and tools (for details see here will be continuously offered.

Published as the last project deliverable, MIRRI presented its Best Practice Manual on Access and Benefit Sharing (for more details see below). This ‘living’ document provides support for resource centres as well as researchers to act in legal compliance when working with microbial genetic resources. It is once more evidence of the bundled expertise of the MIRRI consortium and the necessity to make this knowledge available in a sustainable, fully operable research infrastructure.

The MIRRI journey continues and I would like to invite you to join this trip. We will keep you updated on recent developments on our website, in the social media and via this newsletter.


Kind regards,

Erko Stackebrandt
MIRRI Coordinator


MIRRI Insights

MIRRI Best Practice Manual on Access and Benefit Sharing (ABS)

In addition to the MIRRI Policy on Biological Diversity and the Nagoya Protocol the MIRRI consortium developed a Best Practice Manual on Access and Benefit Sharing. This manual was developed in response to Article 20 of the Nagoya Protocol and Article 8 of the Regulation (EU) No 511/2014. It provides guidance for the microbial domain Biological Resource Centres (mBRCs) in implementing their ABS institutional policies with regard to genetic resources and associated traditional knowledge, and working procedures for the acquisition of material, including accession, i.e., formal acceptance of new material in the public collections of the mBRCs, for transfer of material including supply to third parties and the delivery of other services. It also aims to increase transparency on how the mBRCs themselves conduct research on their holdings and lawfully utilize the genetic resources and associated traditional knowledge.

As the Nagoya Protocol applies to any kind of genetic resources, the MIRRI Best Practice Manual on Access and Benefit Sharing can be easily adopted by curators of mBRCs and the entire range of researchers from the academia and the bio-industry.



BioMicroCore project

Coordinated by the Institut Pasteur (France), some MIRRI partners in collaboration with other European research institutes and SMEs submitted a project proposal to the H2020-INFRAIA-2016-2017 call, topic INFRAIA-02-2017.

The BioMicroCore project aims to deliver added value knowledge and technology to the users of leading European public microbial domain Biological Resource Centres (mBRCs) to enhance implementation of ideas on innovation and to accelerate discovery by providing expanded access to key microbial expertise and tools. Strategies and policies for coordinated interactions among mBRCs and with their user clientele from the academic environment and the private sector were already developed within MIRRI. These strategies will be realized in the BioMicroCore project by a subset of MIRRI partners, one non-MIRRI partner collection and three SMEs to develop models and procedures that would tighten the links between them and address and implement topics of common interest. The approach outlined will offer access to a highly visible pool of high quality facilities, tools, improved databases and services to match ongoing activities in other European Research Infrastructures. The microbial component of this domain will include information about services, expert knowledge and facilities and will allow users to choose the appropriate research environment for their research. Integrated approaches and procedures across partner institutions will serve as a test-bed for implementation of MIRRI, in particular monitoring of the socio-economic impact of mBRCs. BioMicroCore will take steps to link microbial resource holders with researchers and innovators to facilitate cooperation and transfer of knowledge across Europe and beyond. The execution of the proposal elements will result in enhanced innovation in bio-industry through optimising the work of the microbiologist and efficiently extracting useful information to reduce redundancies, save time, and allow advances to be made in a timely manner.

Partners from academia and industry (in alphabetical order) are Biopolis SL (Spain), CAB International (CABI, UK), Culture Collection of Switzerland AG (CCOS, Switzerland), Gruppo Ricerche Avanzate Per l’Enologia (Italy), Institut National de la Recherche Agronomique (INRA, France), Leibniz-Institut DSMZ – Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH (DSMZ, Germany), Masarykova Univerzita (CCM, Czech Republic), Universita degli Studi di Torino (MUT, Italy), Universitat de Valencia (CECT, Spain), Université Pierre et Marie Curie – Paris 6 (EMBRC, France), Zürcher Hochschule für Angewandte Wissenschaften (Switzerland).


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 Culture Collection of Industrial Importance Microorganisms (CMII), the Microbial Strain Collection of Latvia (MSCL) and the National Collection of Type Cultures (NCTC).

The Culture Collection of Industrial Importance Microorganisms (CMII) is an in-house collection, which currently holds approx. 500 microbial strains (bacteria, fungi and yeasts), belonging to the biohazard groups 1 and 2 (60 strains are protected by patents in innovative biotechnologies and culture media).
The collection was established in the National Institute of Chemical Pharmaceutical Research and Development – ICCF, Romania, in 1952 and, since then, it has grown in the frame of projects financed by public authorities and companies. Our main directions are focusing on bioactive substances and biomaterials synthesis, R&D upstream and downstream processes, mostly with pharmaceutical applications. They are further developed to medicines or similar health products by pharmaceutical technology, analytical and pharmacological characterization studies in the institute.
The main function of CMII is to maintain strains of research interest, most of them having potential industrial application in amino acids, enzymes, probiotics, biopolymers SCP, food and fodder additives production, green chemistry.

The CMII is affiliated to the World Federation of Culture Collections (WFCC-232) since 1981. In addition, CMII is a collaborating party of MIRRI since 2014. Having a common aim and a close relationship with other culture collection centers in Europe will offer an important background information about microbial resources and collaboration in the field. For the ICCF and its director, Dr. Misu Moscovici, as a benefit derived from an international cooperation, MIRRI offers a reliable source of strain data and easily accessible information about cultures, professional training, which will promote microbial research and industrial innovation.



The Microbial Strain Collection of Latvia (MSCL) is one of the structural units of the University of Latvia. During the last decade MSCL has become an essential infrastructure for the Life sciences and biotechnology in Latvia. MSCL holds more than 1,600 strains of bacteria, filamentous fungi and yeasts. A considerable part of them have been isolated in Latvia and are single samples in the world. MSCL is the only microbial service collection in Latvia that performs isolation and purification of microbial cultures, identification, cultivation and characterisation of strains, distribution of pure cultures, etc. It is recognized as an IDA for patent purposes under the Budapest Treaty since 1997. In addition to service functions, MSCL staff participates in the teaching process of students Faculty of Biology University of Latvia. Several Master and Bachelor papers in the environmental microbiology, food microbiology and safety, in biotechnology each year have been elaborated or have been consulted at MSCL.

Through the partnerships and collaborations with research institutions and private companies MSCL has been involved in several joint research projects funded by EC and by National Research programme in priority scientific areas approved by the Cabinet of Ministers Republic of Latvia.
MSCL is a member of WFCC (since 1996), of ECCO (since 1997), it is registered at WDCM.
Participation in MIRRI facilitates current and will promote further development of MSCL as National research infrastructure of the knowledge triangle (research, education and innovations).



The National Collection of Type Cultures (NCTC), operated by the UK’s Public Health England (PHE), has been a trustworthy source of type and reference strains of bacteria of clinical and veterinary importance since 1920. It is the longest established collection in the world dedicated to preserving authentic bacteria for use in biomedical science. More than 5,000 strains are available in freeze-dried (lyophilised) format with associated data including the organisms’ characteristics, source and date of isolation, some of which refers back to the 19th century, as well as many recent isolates associated with current clinical challenges such as antibiotic resistance. Long read (PacBio) whole genome sequences are provided for more than 1,000 strains and can be accessed freely from the NCTC website or via the European Nuceleotode Archive (ENA). The historical strains and associated genomic data are proving invaluable for helping the understanding of the evolutionary history and population structures of bacteria that cause infections in humans.

PHE operates three other collections, the National Collection of Pathogenic Fungi (NCPF), the National Collection of Pathogenic Viruses (NCPV) and the European Collection of Authenticated Cell Cultures (ECACC). Together these four collections form a valuable Biological Resouce Centre (BRC) that is an internationally-recognised patent repository and provides safe storage and freeze-drying services. Our training courses and public engagement work streams focus on the importance of authentic biological materials in biomedical research and diagnostic testing. The PHE collections are part of the UK Biological Resource Centre Network (UKBRCN), ECCO, WFCC and are collabortaing partners in MIRRI.

Julie E. Russell, Head of PHE’s Culture Collections, believes it is important for BRCs to collaborate in order to enable researchers to access authentic biological resources and that MIRRI facilitates this for the wider scientific community and beyond.


Beyond the microbe's world

Euro-BioImaging (EuBI) is the pan-European Research Infrastructure project on the ESFRI roadmap, which will provide access to state-of-the-art imaging technologies for life scientists. Innovative imaging technologies are revolutionizing biology and medicine by allowing researchers to visualize, characterize and measure molecular and cellular function with a precision never reached before. Through EuBI researchers can have access to imaging instruments and expertise that they do not find at their home institutions or among their collaboration partners. As a EuBI user, a researcher will have the possibility to use the instruments needed for her/his own research and receive in addition expert technical assistance and support both with project planning and during project execution. Euro-BioImaging will also regularly provide training courses for current and future users as well as for staff of the imaging facilities across Europe. The training offerings span from basic hands-on-training on instruments to advanced training for imaging facilities’ staff. In addition, EuBI will provide support with image data processing, image data storage and access to a common data repository as well as cloud compute services.

Enjoying the support from 15 European countries and EMBL, Euro-BioImaging is foreseen to become a European Research Infrastructure Consortium (the EuBI-ERIC) in 2017. What is more, EuBI will open its doors to the scientific community already in May 2016 with the start of Interim Operations. This means that researchers at any stage of their career can request access to imaging technologies hosted at the 29 EuBI Node Candidates (specialized imaging facilities hosting the technology and expertise) by submitting a proposal for a project via the EuBI Interim Web Access Portal. Access will be granted based on the scientific merit and technical feasibility of the submitted research proposal with the only restriction that it will be subject to the available capacity at Euro-BioImaging in the time frame for the execution of the project.

For many researchers working with microbial resources, access to high-end imaging technologies is a big plus and provides substantial advantage for their research. Many questions can only be answered with the help of imaging technologies and therefore we anticipate that MIRRI users might be highly interested in the services provided by EuBI. Life-cell imaging, electron microscopy and CLEM, high-throughput or super-resolution microscopy – there are plenty of technologies at Euro-BioImaging that can be exploited in projects that are aiming for a better characterization and understanding of microorganisms.


Microbe Highlights

In this issue, the series continues with highlights from MIRRI Collaborating Parties Culture Collection of Fungi (CCF), National Collection of Industrial, Food and Marine Bacteria (NCIMB) and HAMBI Culture Collection (HAMBI):

Biatriospora sp. strain CCF 4378, a fungus with highly diverse spectrum of secondary metabolites including antibiotics

Biatriospora genus is a microscopic fungus (Dothideomycetes, Ascomycota), until recently known from marine environment (B. marina, mangrove roots) and from clinical material (B. mackinnonii, eumycetomes).
During a mycological survey of phloem endophytes of Ulmus laevis (European white elm) in the Czech Republic, an undescribed species related to B. marina was discovered which showed a unique antifungal effect against Pyronema domesticum, a highly competitive and rapidly growing fungus that overgrows other endophytic fungi.
The strain CCF 4378 is dark pigmented sterile fungus which unlike B. marina was not observed to form ascocarps. It was identified using DNA sequencing (ITS, LSU, SSU, ß-tubulin, and EF1α). Its species identity is now in the process of publication (Kolařík et al.). So far, eleven secondary metabolites were discovered as products of the strain CCF 4378: ascomycone A and B, 6-deoxyfusarubine, 6-deoxyanhydrofusarubine, herbarin, balticol A, 6-deoxybostrycoidine, pleorubrin A, B, C, and D. Structure of these naphthoquinone derivatives was elucidated by NMR spectrometry (Stodůlková et al. 2015).Testing of crude naphthoquinone mixture on adenocarcinoma HeLa cells and primary human skin fibroblasts revealed obvious bioactivity and toxicity. Surprisingly, compounds with similarities in chemical structure elicited different bioactivities ranging from no effect (6-deoxybostrycoidin, pleorubrin B – up to 100 μg/mL) to dramatic changes of the cellular content and cell death (6-deoxyfusarubin, ascomycone B). The effect was rapid (in minutes) in both cell types tested. For more details, see Stodůlková et al. 2015. The presented fungal isolate belongs to the rarely isolated and little known fungus with a great biotechnological potential.



Two novel strains isolated from bees deposited at NCIMB

Bees play a major role in agriculture through the pollination of many crops. Despite the substantial concerns about bee health and disease, and the potential impact on food production, little is known about the normal microbial flora in bees. Some possible roles of these species may be protection against parasites, or helping with digestion of pollen.
The unique bee microbiota consists of eight bacterial phylotypes. Some culturing of these bacteria has been reported, however most of the phylotypes remain undescribed. Two novel genera of bacteria isolated from Apis mellifera (Western honey bee) and Bombus sp. (bumble bee) were deposited at NCIMB by Waldan Kwong, a researcher at Nancy Moran’s Laboratory at Yale University, and have been named Snodgrassella alvi gen. nov., sp. nov., a member of the Neisseriaceae family of the Betaproteobacteria; and Gilliamella apicola gen. nov., sp. nov., a member of Orbaceae fam. nov., Orbales ord. nov.

It is hoped that the isolation of these new strains will contribute towards a better understanding their roles and functions within these ecologically important insects. Moreover, the bee gut microbiota presents an opportunity to investigate host-microbe interaction dynamics in a simple, tractable system (http://web.biosci.utexas.edu/moran/kwong.html).



The Obba genome project: The genome of a fungus isolated in Finland will be launched soon

Most of the microbial strains of HAMBI, including our cyanobacterial culture collection UHCC (University of Helsinki Cyanobacteria Collection) and the fungal biotechnology culture collection (FBCC), were isolated in Finland, and these strains represent uniquely Finnish biodiversity and are not deposited to other microbial culture collections.
Hundreds of fungi of FBCC were screened in a large research project aiming to find suitable fungi for spruce biopulping (i.e. fungal treatment of wood chips prior to pulping to save energy in refining), and the white-rot fungus Obba rivulosa FBCC 939 (syn. Physisporinus rivulosus T241i) appeared to be the most promising fungus. During wood degradation O. rivulosa degrades lignin selectively, which makes it suitable for many biotechnological applications. This strain is the first fungus isolated from Finland the whole genome of which was sequenced (June 2014).
The Obba genome project is coordinated by and most work is conducted in the University of Helsinki. Research partners include also USDA FPL (U.S. Department of Agriculture, Forest Products Laboratory) and the Clark University, USA. This project is part of the ‘1000 fungal genomes project’ in US DOE JGI (U.S. Department of Energy, Joint Genome Institute). O. rivulosa and other wood and litter degrading fungi of HAMBI have been in key position in many EU funded and national research consortia, and in the national Microbial Resources Center of Excellence.


News & Events

  • The ECCO XXXV meeting, originally intended to take place with the ICCC 14 in November 2016, is also postponed. The new date will be announced via the ECCO website.
  • Many of the project outputs developed during the Preparatory Phase (e.g. the MIRRI Partner Charter, the MIRRI Policies) have been uploaded to ZENODO, making them publicly available for stakeholders. In addition, the given DOI allows a proper citation of these documents. Search for “MIRRI” and find all uploads!
  • In April the CORBEL project launched its Innovation Office. It is intended to provide advice and assistance to streamline research collaboration among Europe’s BioMedical Research Infrastructures (RIs) and the industry. In addition to real-time advice on partnership issues the Innovation Office provides free access to essential collaboration tools such as guidelines, e.g. on intellectual property rights, as well as legal templates. For more information please visit the website of the CORBEL Innovation Office.

Meet MIRRI @

  • CTLS 2016 – Core Technologies for Life Science, June 12-15, 2016 in Heidelberg (Germany), poster by R. Hurtado-Ortiz (CRBIP) 
  • MaCuMBA conference “The Marine Microbiome – Discovery & Innovation”, June 27-30, 2016 in Berlin (Germany), poster by M. Schüngel (DSMZ) 

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.