CABI scientists have outlined a series of recommendations in a new paper published in the CABI Agriculture & Bioscience journal which serve, as the research title suggests, to help strengthen mycology research through coordinated access to microbial culture collection strains.
Lead author Dr David Smith, along with co-authors Anthony Kermode, Dr Giovanni Cafa, Dr Alan Buddie, Thelma Caine and Dr Matthew Ryan, in the paper – published to coincide with 100 years of mycology at CABI – argue that ‘well-managed genetic resources and associated metadata are essential to underpin research addressing the challenges to food security, healthcare, climate change, biodiversity, environment, education and our bio-based economy.’
Indeed, they go on to suggest that ‘culture collections have supported microbiology research for over 100 years, whether they are collections belonging to individual scientists or institutional repositories. The 790 collections registered with the World Data Centre for Microorganisms (WDCM) together hold over three million strains representing a wide range of microbial diversity.’
Note – see the paper in full for list of abbreviations.
In the review paper’s recommendations, the scientists state:
In delivering current needs:
There are gaps in organism coverage and insufficient candidates for high throughput screening for new products for example antimicrobials. A global strategy is needed to ensure organisms that are critical to scientific discoveries are preserved for future use;
Research funding is scarce with resources and expertise fragmented currently: BRCs need to respond to local challenges and network to get value from investment of public funding;
The study of microbiomes is accelerating and the benefits of engaging microbial communities recognised. A coordinated effort is required to address storage and access to microbial communities making up the various host and environmental microbiomes and their associated data to support research to facilitate the release of the full potential of microorganisms;
Key outputs come from research and utilisation of current culture collection holdings continue but gaps remain. Output and value would be enhanced enormously and duplication of effort avoided through coordinated effort;
Global challenges require global responses, multidisciplinary approaches and a critical mass to resolve. A mechanism to engage the full potential of the microbial resource community (mBRC) in providing resources and solutions to global challenges is required;
Mycological taxonomy and the naming of organisms has become complex with mixed taxonomies utilised and genome sequence databases incomplete and including erroneous data. mBRCs need to coordinate efforts to play their part in ensuring a comprehensive set of reference strains is available, sharing the coverage rather than duplicating effort, to fill gaps and remove errors;
Changes in the regulatory environment such as the enactment of the Nagoya Protocol require common compliant approaches.
Developing the infrastructure:
Participating BRCs must operate to international standards to ensure quality and importantly, interoperability of service, function and data;
Provision of assistance for countries with no or limited infrastructure;
BRCs need to develop robust business models to secure their sustainability;
Build upon current initiatives to coordinate mBRC operations such as MIRRI in Europe, USCCN in the USA, the Asian BRC Network to establish a global effort that provides infrastructure to support the efforts of the WFCC;
Take steps to establish the GBRCN envisaged by the OECD utilising the outputs of the GBRCN demonstration project (Fritze et al. 2012).
Policy, community support and funding:
Research funders, science publishers, the research community and bioindustry need to work together to develop and implement strategies to make the most of the potential of the hidden microbiology resource and harness the outputs of microbial communities;
A coordinated approach is required to utilise the limited funding through a research infrastructure and sharing the delivery through its constituent partners as exemplified through the distributed ESFRI research infrastructures in Europe;
Mechanisms to share resources more openly, such as open access publications, that will allow development and equitable sharing of benefits from discoveries and that accelerates the pace of discovery and innovation to address our common global challenges.
Dr Smith, in the paper’s conclusion, said, “It is evident that BRCs, specifically microbial culture collections, provide resources that underpin research and many new products and uses of microorganisms have been enabled by the study of organisms from collections.
“However, this function can be made much more efficient and effective with better coordination and linkage with funders and the research community. Researchers can access the holdings of collections but there is not yet a single platform that holds the information on all strains held. The GCM holds information on only 14% of the available strains. Collection organisations do their best to coordinate access but more needs to be done to facilitate the uptake and use of organisms and their associated data.
“The greatest opportunity to be able to understand, harness and moderate the hidden resource of microbial communities (99% of the microorganisms in the environment) is to coordinate microbiome activities and use the networks of BRCs to achieve this. It is not only the organisms in mBRCs currently that can be provided. There is the potential for coordinating networks of depositors into the collections in targeted isolation programmes to provide access to the new organisms, the samples containing them and their potential novel chemistry. A global effort is needed.
“Most importantly, the establishment of the GBRCN to provide coordinated access and the microbiome research community via appropriate global infrastructures should be undertaken. It has begun in Europe with MIRRI, with further activities by the Asian BRC Network and the USCCN. The foundations for significant advances are in place. Researchers, funders, journal editors and collections need to work together to coordinate strategy and introduce mechanisms to accelerate access to microbial communities essential for our survival and the future of our planet.”
Full paper reference
Smith, D., Kermode, A., Cafà, G. et al. Strengthening mycology research through coordinated access to microbial culture collection strains. CABI Agric Biosci 1, 2 (2020). DOI: 10.1186/s43170-020-00004-9
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