Public Microbial Resource Centers: Key Hubs for Findable, Accessible, Interoperable, and Reusable (FAIR) Microorganisms and Genetic Materials

Abstract

In the context of open science, the availability of research materials is essential for knowledge accumulation and to maximize the impact of scientific research. In microbiology, microbial domain biological resource centers (mBRCs) have long-standing experience in preserving and distributing authenticated microbial strains and genetic materials (e.g., recombinant plasmids and DNA libraries) to support new discoveries and follow-on studies. These culture collections play a central role in the conservation of microbial biodiversity and have expertise in cultivation, characterization, and taxonomy of microorganisms. Information associated with preserved biological resources is recorded in databases and is accessible through online catalogues. Legal expertise developed by mBRCs guarantees end users the traceability and legality of the acquired material, notably with respect to the Nagoya Protocol. However, awareness of the advantages of depositing biological materials in professional repositories remains low, and the necessity of securing strains and genetic resources for future research must be emphasized. This review describes the unique position of mBRCs in microbiology and molecular biology through their history, evolving roles, expertise, services, challenges, and international collaborations. It also calls for an increased deposit of strains and genetic resources, a responsibility shared by scientists, funding agencies, and publishers. Journal policies requesting a deposit during submission of a manuscript represent one of the measures to make more biological materials available to the broader community, hence fully releasing their potential and improving openness and reproducibility in scientific research.

Strengthening mycology research through coordinated access to microbial culture collection strains

“…This is a huge missed opportunity for the scientific community as a whole, it is crucial for the benefit of science, future study and the confirmation of published research that the strains on which the published science hinges are maintained in a stable condition for future use. Stackebrandt et al (2014) went on to provide a sound case for journal editors to reinforce good practice, the requirement that strains cited in published research should be deposited in recognised public service collections and thus be available for scientific study (Becker et al 2019). This apparent lack of understanding of the value of depositing organisms for future study is exemplified by the fact that the strains that have been deposited, to date, in the WDCM collections represent less than 25% of the species currently described and represents a very small proportion of the number of taxa estimated to occur in nature e.g.…”

Streamlining Data-Intensive Biology With Workflow Systems

“…Most journals now require data for all manuscripts to be made accessible, either at publication or after a short moratorium. Further, the FAIR (findable, accessible, interoperable, reusable) data movement has improved the data sharing ecosystem for data-intensive biology [59,60,61,62,63,64,64,65]. You can find relevant sequencing data either by starting from the “data accessibility” sections of papers relevant to your research or by directly searching for your organism, environment, or treatment of choice in public data portals and repositories.…”

Preserving US microbe collections sparks future discoveries

“…Major public repositories such as the ATCC have grown through deposits ranging from a single culture cited in a publication or patent to large sets deposited by retiring professors. Analogous to FAIR (Findable, Accessible, Interoperable and Reusable) guiding principles for scientific data, and to open access journals and open source software, Becker et al (2019) recently proposed that scientific materials including microbes and genetic materials should be made more freely available to the research community. Preservation of micro-organisms continues to be important to ensure that research can be replicated, to allow future discoveries, and to avoid the costs of re-isolating microbes.…”