Culture collections: an international genetic resource for the 21st century – and beyond

by Samantha Law

by Samantha Law

International Microorganism Day

International Microorganism Day aims not only to promote microbiology as a field of professional activities, but also to raise awareness of the essential role that microorganisms play in our health, environment and quality of life.  Although it is over 300 years since Robert Hooke and Antoni van Leeuenhoek first observed and described microorganisms, we are really just beginning to understand their contribution to our lives and unlock their potential. Bacteria represent a rich and industrially valuable source of genetic biodiversity, but when a new species or strain is discovered, how is it preserved and made available to the scientific community?

For International Microorganism Day, NCIMB’s culture collection curator Dr Samantha Law looks at the history of NCIMB’s collection and considers the importance of culture collections around the globe.

An international resource

NCIMB Ltd is custodian of the UK’s National Collection of Industrial, Food and Marine Bacteria. Historically, this collection was created from the merger of three smaller collections – the National Collection of Industrial Bacteria (NCIB), the National Collection of Marine Bacteria, and the National Collection of Food Bacteria (formerly the national Collection of Dairy Organisms). Together with the separately managed Public Health England Collections, the National collection of Industrial, Food and Marine Bacteria forms an important and comprehensive national resource. As a member of the European Culture Collections’ Organisation, NCIMB is also part of an international network of organisations that is essential in supporting the development and application of microbiological knowledge and understanding.

When I tell people who are not microbiologists about our culture collection, they are often surprised that such a thing exists – they struggle to think of reasons why people would need to purchase our strains. However, bacteria from our collection are regularly supplied to industry and used for teaching purposes or academic research.  For example, the collection includes a large number of actinomycetes: these filamentous bacteria have a major role in the production of antibiotics and have been the subject of a great deal of industrial and research interest. Other strains in the collection have been used to manufacture the enzymes added to biological washing detergents, degrade industrial wastes and produce yoghurt.

Preserving biodiversity

At NCIMB, what we look for when we decide to accept a new strain into our collection are type strains of newly discovered environmental bacteria and those that may be environmentally and/or commercially useful. These can come from all kinds of locations and the strains in our reference collection have been isolated from an eclectic range of environments around the world, including bathing water of a hippopotamus in a zoo, the skin of a cod, and medieval church murals.

In recent years much effort has gone in to raising awareness of the importance of biodiversity and the rate at which it is being diminished, with most public attention focused on plant and animal species rather than bacteria. However, with the recent reporting of topics such as antimicrobial resistance and microbiome research in the mainstream press, things may be beginning to change.  People are starting to understand the importance of microbial diversity to both human health, society and the wider ecosystem, and I believe culture collections around the world have an important role to play in developing mankind’s relationship with microbes.

The role of new technology

The availability of new technologies has revolutionised how we approach the study of microbes and culture collections have embraced the opportunities that these technologies present. For example, the development of next generation sequencing technology and bioinformatics analysis has opened to door to affordable whole genome sequencing. Whole genome sequencing is the ultimate in organism characterisation. It allows us to take a deep dive into individual strains, and at NCIMB one application we are very interested in – because of the nature of our collection- is screening strains for the production of industrially or clinically important compounds. We offer this as a service to customers and also work in collaboration with other researchers to explore the potential of our own cultures.

Another critical application of whole genome sequencing is in characterising probiotic products for human or animal use.  This is a rapidly developing area, and in addition to investigating strains for their probiotic qualities, it is essential that genomes are screened for the presence of anti-microbial resistance genes and virulence factors so that strains used do not facilitate the spread of resistance or pose other health risks.

Safeguarding strains 

Despite the vital role they play, financial pressures and continuity of funding are key challenges for culture collections, particularly in today’s harsh economic climate, and valuable collections in poorer countries can often be endangered because of the lack of something as simple as a freezer. In the past, our staff have become involved in supporting some of these endangered collections by helping to secure small grants to alleviate this kind of crisis.   In addition, our own collection has expanded not only as a result of individual new accessions, but also through the acquisition of whole collections.  If a key university researcher retires or funding for a particular area of work within a company stops, specialist collections may be put at risk, and over the years NCIMB has played an important role in ensuring that a lifetime’s work is not relegated to the autoclave.  Some interesting material has been acquired in this way, including cultures from the Rothamsted Research Station soil collection, which includes unsealed glass vials dating back to the 1920s, and also the world-famous Nathan Smith/Ruth Gordon Bacillus Collection which was saved from extinction and transferred from Virginia in the United States, to Aberdeen. This collection is comprised of around 1,700 strains which are currently preserved in their original state on sterilised soil.

A genetic resource for the future

A fundamental element of our remit at NCIMB, and one that I, and my colleagues, are very passionate about, is preservation of a genetic resource for future generations and it is important that we find the right balance between meeting commercial demands and maintaining a resource that will be of value to researchers in the future.

We have seen in the past how trends in research, developments in technology, and the needs of industry can increase demand for particular strains. For example, work done for the offshore oil and gas industry has at times increased demand for particular strains in a way that would have been quite difficult to predict in the 1950s.  Similarly, the huge advances in molecular biology since the collection was established are allowing us to learn so much more about the strains that we hold and may enable the discovery of valuable characteristics that were previously unknown.

If society is to benefit from the amazing resource that microorganisms offer, culture collections like NCIMB, along with other similar organizations around the globe therefore have a very important role – not only in safeguarding the physical resource of their collections but also in anticipating the need of future researchers.