Mark Reed explores the evolving science of storage, archiving and retrieval of bacteria and fungi, examining how culture collections, regulatory frameworks and technological innovation have shaped contemporary practice and highlighting the operational, ethical and quality considerations that now define effective biobanking.
Biobanking has become a cornerstone of modern biomedical science, underpinning advances in diagnostics, epidemiology and personalised medicine. Alongside the rapid expansion of human tissue and serum banks, the long-term preservation of microorganisms has assumed growing importance, providing essential reference material for clinical laboratories, research institutions and public health services worldwide.
As the term biobanking suggests, the practice of storing material of a biological origin safely over short or long periods of time remains of paramount importance with respect to reliability, quality, safety, proven reliance and compliance. Essentially, a biobank is a ‘bank’, a safe, trusted and secure facility or equipment set up for valuable assets to science. Biobanking offers an ever-expanding resource for research, analysis, epidemiological and statistical analysis, and an educational application resource from large and diverse populations in numerous scientific applications in many areas and disciplines of science. The availability of diverse, high-quality samples and associated data is valuable for advancing personalised or precision medicine, where treatments are tailored to an individual’s unique genetic makeup and disease characteristics.
As an estimate there are currently over 570 Biobanks from 20 member states in Europe that form the Biobanking and Biomolecular Research Infrastructure BBMRI-ERIC Network.
Originally established in 2013 under EU legislation, enabling the development of innovative technology and processes as a cross-domain network that facilitates responsible access to high-quality samples, data and biomolecular resources. Members of the network can be classified in several ways depending on their controlling entity; be that government, commercial, private, or private research institution. It is interesting to note the majority are not for profit.
Biobanking is marked by evolution of biorepositories from small, university-based repositories to large, government and commercial biorepositories.
Of particular note and reputation is the biobanking practice established in Framingham, Massachusetts in 1948, the ‘Framingham Heart Study’, with a cardiovascular study that continues today. As we look at the number of biobanks or biorepositories today operating worldwide, the development of science worldwide would not be, and could not have become, what it is today without this important and essential practice. This includes research that led to the Human Genome Project in 1990and the complete publication of the human genome in 2003, and many breakthroughs of groundbreaking research for the understanding and management of critical diseases and health conditions.
These repositories also facilitate the discovery of biomarkers, which are measurable indicators of biological processes, disease states, or responses to treatment. Biobanks also play an important role in drug development by enabling pharmaceutical companies to test the safety and effectiveness of new therapies using stored samples.
To set up a biobank of organised samples of human, plant, animal or microbial biological material, accompanied by associated information, there are responsible biobanking practices that should be followed.
Responsible biobanking prioritises ethical considerations and operational standards to safeguard donor rights and maintain public trust. Informed consent is a primary aspect, ensuring individuals fully comprehend the purpose and potential implications of donating their biological samples and data. This consent process also informs donors of their right to withdraw participation at any time.
Protecting donor privacy and data security is another important practice, often achieved through de-identification techniques where personal identifiers are removed or replaced with codes. Biobanks adhere to legal and regulatory frameworks, along with internal governance structures, to manage sample access and data sharing.
The biobanking process begins with obtaining informed consent from individuals who agree to donate their biological materials for research. This step ensures donors understand how their samples and data will be used, stored, and shared. Following consent, samples are collected using standardised protocols to maintain their quality and integrity.
After collection, samples undergo various processing steps, including aliquoting, quality control checks, and the extraction of specific molecules like DNA or RNA. These processed samples are then stored long-term under controlled conditions, often in cryogenic freezers at ultra-low temperatures, such as −80°C or in liquid nitrogen at −196°C, to ensure preservation. Data management systems track each sample and its associated information from collection to distribution.
As we know, biobanks and their biospecimens are critical components for many areas of clinical and basic research. The quality of biospecimens and associated data must be consistent and collected according to standardised methods to prevent spurious analytical results that can lead to artifacts being interpreted as valid findings. A number of international institutions have taken the initiative to develop and publish best practices, which include technical recommendations for handling biospecimens as well as recommendations for ethical and regulatory practices in biobanking.
To offer accreditation, UKAS established a pilot programme to develop the assessment approach and offer accreditation to biobanking Conformity Assessment Bodies (CAB) operating biobanks in the areas of defined biological materials from human, animal, plant and microorganisms as well as related information and data.
The ISO 20387:2018 standard specifies general requirements for the competence, impartiality and consistent operation of biobanks, including quality control requirements to ensure biological material and data collections are produced and maintained appropriately.
This standard is applicable to all organisations performing biobanking, including biobanking of biological material from multicellular organisms (e.g. human, animal, fungus and plant) and microorganisms for research and development. It does not apply to biological material intended for food/feed production, laboratories undertaking analysis for food/feed production, and/or therapeutic use.
At present there does appear to be some lack of international harmonisation, as is often the case in science; causing uneven adoption, and insufficient oversight of best practices. This could lead to the prevention of further improvements in biospecimen quality and coordination among collaborators and biobanking networks. In contrast to the more straightforward technical and management issues, ethical and regulatory practices often involve issues that are more controversial and difficult to standardise.
Access to biobanks for all should be a straightforward matter; unfortunately that is not always the case. As many readers will be aware, access to biological samples for the development and research of commercial products to combat disease is not always straightforward. There can be many hurdles with paperwork, approval, an application process, and unfortunately quite high costs involved for access to patient samples for commercial companies. With increasing demands for the development of accurate and rapid diagnostic tools for the laboratory, and satisfaction to regulatory compliance, this issue of access to patient samples continues to be a hurdle that many commercial companies struggle with, and it does slow down the development and approval of products to be used in laboratory-based diagnostics.
‘The availability of diverse, high-quality samples and associated data is valuable for advancing personalised or precision medicine, where treatments are tailored to an individual’s unique genetic makeup and disease characteristics.’
2020 did see a significant expansion of biobanking and the recognition of its importance by the Medical Research Council (MRC), the Wellcome Trust and the Department of Health, leading to support and comment from the then Prime Minister. We still have some way to go with this recognition, to further enable product development. Of note were issues that arose for access to biological samples during the COVID-19 pandemic to commercial IVD (In Vitro Diagnostic) manufacturing companies. Multiple positive and negative samples were required to be tested by companies introducing kits that were needed due to high demand, and testing had to be independent, in a UKAS approval laboratory, with a gold standard and comparison to kits already approved. Given the pressure that testing sites were under, be they NHS or commercial, this did lead to issues with availability of tests, and frustration for commercial companies looking for market access. Whilst the need to ensure the quality and performance of tests being introduced and marketed is fully understood and respected, there is the question, was CTDA restrictive or as supportive as it could have been? That is a debate that will continue for some time and the date of repeal of the CDTA for SARS-CoV-2 assays in the UK is welcomed.
Present indications are that it will be repealed as soon as the amendment becomes law.
The storage of serum samples represents a significant proportion of the biobanking undertaken internationally. Laboratory-based diagnostic tests using blood and serum samples account for almost 65% of the sample types submitted to pathology departments on a daily basis. Sample numbers can often run into thousands each day, depending on the population area served. Clinical laboratory testing is moving at a tremendous pace and the appropriate biobanking of the samples has to be very carefully considered and planned.
Consider now the storage of living cells in a biobank. The intention here is not to maintain the integrity of a measurable parameter in a biological sample, but to retain living cells with genotypic and phenotypic characteristics intact over a short or preferably long period of time at −20°C to −70°C. The storage of bacterial and fungal isolates presents its own challenges and is faced with all of those encountered with biological associated data on lifestyle, location, age, environmental and clinical information. Tissue biobanks are also common, particularly for transplantation research and as virtual biobanks that integrate epidemiological cohorts into a common accessible pool.
The most widely used systems for storage of bacterial and fungal cultures include cryopreservation and freeze-drying. Cryopreservation means that materials are stored at low (from −20°C to −80°C in freezers) or ultra-low temperatures (−150°C in liquid nitrogen containers); in the latter case, cryopreservation takes place in the liquid or in the vapour phase of nitrogen. Freeze drying can present practical hurdles and is not ideally suited to smaller, localised culture collections.
Feltham et al. developed a simple method for storage of bacteria at −70°C. Their work revolutionised the way bacteria and fungi could be stored with simple preparations of a glycerol broth using small carrier beads in a vial that could be prepared by individual laboratories.
This had a limited scale of application as the need for cultures to be stored for research, quality control and reference applications increased. The advent of International Organization for Standardizsation (ISO) regulatory requirements for diagnostics manufacturers and laboratories requires a far more sophisticated product.
Established collections of microorganisms permit the characterisation of microbial diversity and microbial evolution. As microorganisms are essential parts of the biosphere then secure and effective storage is essential. Microbial and fungal culture collections face a huge task: consider that there are potentially over 1.5 million fungal species estimated worldwide, and less than 20% have been described to date.
Culture collections range from localised research projects to laboratory quality control collections, to national and international resource collections. Regardless of the size of microbial and fungal cultures, biobanks are an invaluable tool for accelerated discovery and characterisation of microorganisms and for promoting their beneficial use.
Culture collections must be maintained reliably with minimal deterioration over time, and they must be protected from physical damage, both accidental and intentional, and the registration of each sample should be stored centrally, usually on a computer-based system that can be backed up frequently. There are over 700 culture collections in more than 70 countries registered in the World Data Centre for Microorganisms (https://wdcm.org) set up as a data centre for the World Federation for Culture Collections. The WDCM catalogues many millions of microbial strains across these collections, encompassing bacteria, fungi, viruses, cell lines and other biological agents.
Familiar members include the National Collection of Type Cultures (NCTC), founded in 1920 and recognised as the longest-established collection of its type in the world. NCTC also serves as a United Nations Educational, Scientific and Cultural Organization Microbial Resource Centre. Another major repository is the Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures in Germany, which now holds more than 91,000 bioresources, including over 32,000 bacterial strains, around 690 archaeal strains and more than 7,000 fungal strains, making it one of the largest and most diverse biological resource centres worldwide. In the United States, the American Type Culture Collection similarly plays a pivotal role in the preservation and global distribution of authenticated microbial strains and cell cultures for research, industry and education.
All of these organisations offer invaluable service to the science community, providing resources of reference microorganisms and cell lines for research and diagnostic purposes.
Microbank™, developed and manufactured by Pro-Lab Diagnostics, has offered a solution to laboratories for the efficient storage of bacterial cultures for over 35 years. It is an advanced platform that utilises specially etched porous glass beads and a uniquely formulated cryopreservative.
Ongoing independent laboratory trials have accumulated up to 30 years of successful storage data for both bacterial and fungal cultures, including fastidious bacteria such as Neisseria gonorrhoeae, Campylobacter spp. and anaerobes. Each vial contains approximately 25 sterile coloured beads (single colour) and the unique cryopreservative. The specially treated beads are of a porous nature allowing microorganisms to readily adhere to the bead surface. After inoculation, the vials are kept at −20°C to −70°C for extended storage. When a fresh culture is required, a single bead is removed from the vial and used directly to inoculate a suitable culture medium. The 2D barcodes on the box and vials provide a freezer-safe, non-erasable (hyphen inserted) label that can be scanned.
The Microbank™ Worldwide Performance Portfolio (“MWWPP”) is an essential reference guide including data from many international bacterial and fungal culture collections. Since its launch in 1991 it has gathered real-world performance data, peer-reviewed studies and long-term storage outcomes from renowned culture collection centres, demonstrating the Microbank™ system’s durability, consistency and ease of use. In collaboration with many international users in clinical, reference and research settings, we continue to build a deeper evidence base to support sample viability, traceability (via 2D-barcoding) and simplified retrieval workflows.
At Pro-Lab Diagnostics, we believe that robust culture preservation is foundational to microbiology excellence, whether that’s diagnostics, research, reference collections or industry applications. By contributing data to the Microbank™ Worldwide Performance Portfolio, laboratories become a part of a shared mission to raise standards, increase traceability and safeguard microbial assets for the long term.
In particular, the original work done at the UK Anaerobe Reference Unit (UKARU) in Cardiff is currently being revisited and updated for all original strains included. We have worked closely with the team at the UKARU, Trefor Morris, Michael Perry, and Sarah Copsey-Mawer for many years, and are grateful for their guidance and support. The unit are currently preparing for a full update on survival times for the Sixth Edition of the Microbank Worldwide Performance Portfolio.
The UKARU provides an identification and antimicrobial resistance reference service for anaerobic bacteria for the UK, offering reference standard antimicrobial susceptibility testing (AST) by agar dilution and molecular detection of resistance mechanisms. UKARU acts as the central laboratory for Wales for culture and full characterisation by WGS of Clostridioides difficile and provides UK wide clinical guidance for all anaerobic infections.
The research interests of the UKARU include commercial evaluations of AST products and C. difficile detection methods. The unit also provides reference level support for collaborations with the European Committee for Antimicrobial susceptibility testing (EUCAST) and the Clinical Laboratory Standards Institute (CLSI).
The continuous evaluation at the Anaerobic Reference Centre (Cardiff) has demonstrated that the Microbank™ can offer a long-term solution. Vials were inoculated with clinical isolates of obligatory anaerobic bacteria referred to the Anaerobe Reference Unit for confirmation of identity, and were frozen at −80°C. A total of 100 isolates were selected to represent the range of species commonly isolated from clinical material.
All 100 strains of anaerobic bacteria of clinical origin were viable after storage in Microbank™ vials at −80°C for 10 years. Most strains yielded moderate to heavy growth from a single bead after 48 hours’ incubation, but three strains yielded only light growth after five days’ incubation. These comprised one of the two strains of Prevotella denticola examined, one of four Fusobacterium nucleatum strains and one strain of Fusobacterium varium.
The same 100 vials were sampled previously for viability after five and seven years’ storage. However, 34 of those 100 isolates had changed names since their original identification. These changes reflect advances in taxonomy and identification methods over the decade.
Additional reference studies for the Microbank™ for numerous isolates are available in the Microbank™ Worldwide Performance Portfolio.
Some species have simply been placed in novel genera and, in some cases, have changed gender in the process (e.g. Eubacterium lentum became Eggerthella lenta). The Gram-positive taxonomic review, resulting in the removal of most former Peptostreptococcus species to novel genera (e.g. Finegoldia, Anaerococcus, Peptoniphilus). Additionally, several novel species of anaerobic cocci have been described (e.g. Peptoniphilus harei, Peptoniphilus ivorii
Several novel species have been described in other genera (e.g. Prevotella, Porphyromonas, Actinomyces). The identification methods used in laboratories have also been revised to accommodate such taxonomic changes.
In addition, novel molecular methods have been developed, such as amplified 16S ribosomal DNA restriction analysis (ARDRA) for identification of Bacteroides, Prevotella and Porphyromonas, and for Actinomyces and other non-sporing Gram-positive bacilli. Consequently, some strains examined in the Microbank storage trial have been redesignated as a result of retrospective identification. By chance, two strains previously included in the Microbank™ storage trial as Actinomyces species subsequently have been identified as members of these novel species.
In summary, the evaluation demonstrated that Microbank™ vials are easy to use, compact, maintain viability and, therefore, are convenient for the long-term storage of anaerobic bacteria. The vials are particularly practical for repeated retrieval of strains as they ensure that the same strain is subcultured on each occasion with minimal effort.
The UKARU holds a collection of approximately 85,000 referred isolates dating back to the early 1980s. Isolates received in the past three decades have been stored in Microbank™ vials. This collection is a valuable resource for retrospective research in fields such as the evaluation of novel identification methods, monitoring of antimicrobial susceptibilities, and development of molecular typing schemes.
Baker M, Jeffries P. Use of commercially available cryogenic vials for long-term preservation of dermatophyte fungi. J Clin Microbiol. 2006;44(2):617-618. doi:10.1128/JCM.44.2.617-618.2006
Feltham RK, Power AK, Pell PA, Sneath PA. A simple method for storage of bacteria at -76 degrees C. J Appl Bacteriol. 1978;44(2):313-316. doi:10.1111/j.1365-2672.1978.tb00804.x
Seidel KE, Gareis M. Efficiency of microbank systems for the conservation of microorganisms relevant to veterinary medicine and others which are not easy to cultivate (in German). Berl Munch Tierarztl Wochenschr. 1995;108(6):215-220.
Microbank World Wide Performance Portfolio – 5th edition. (Pro-Lab Diagnostics, 2023) https://pro-lab.co.uk/wp-content/uploads/2019/08/Microbank-World-Wide-Performance-Portfolio-2024-small.pdf
Veguilla W, Peak KK, Luna VA, et al. Two-year study evaluating the potential loss of methicillin resistance in a methicillin-resistant Staphylococcus aureus culture collection. J Clin Microbiol. 2008;46(10):3494-3497. doi:10.1128/JCM.00654-08
United Kingdom Accreditation Service. Accreditation of Biobanking. (UKAS, 2025) www.ukas.com/accreditation/about/developing-new-programmes/development-programmes/biobanking/
Moyes A, Young H. Storage and repeated recovery of Neisseria gonorrhoeae using cryovials. Br J Biomed Sci. 1995;52(1):19-21.
Espinel-Ingroff A, Montero D, Martin-Mazuelos E. Long-term preservation of fungal isolates in commercially prepared cryogenic microbank vials. J Clin Microbiol. 2004;42(3):1257-1259.
