NCIMB: A genetic resource for the 21st Century and beyond

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? As NCIMB celebrates its 30th anniversary, Deputy Curator Dr Samantha Law looks at the history of the National Collection of Industrial,  Food and Marine Bacteria, its role as a genetic resource and how changes in technology are shaping its development.Although NCIMB was established as a company in 1982, the history of the collection itself dates back to 1950, when the National Collection of Industrial Bacteria (NCIB) was established by the Department of Scientific and Industrial Research at the Chemical Research Laboratory, Teddington, starting with a core of 200 non-medical bacteria of industrial interest.  Seven years later, at the Ministry of Agriculture Fisheries and Food (MAFF) administered Torry Research Station in Aberdeen, an in-house collection of bacteria isolated mainly from marine fish and solar salts was established as the National Collection of Marine Bacteria (NCMB), and in 1959 the two collections were brought together when NCIB was moved to the Torry Research Station. For several years both collections existed independently, side by side but were subsequently merged to form NCIMB. The collection remained there until the Civil Service reforms of the 1980s resulted in the formation of NCIMB Ltd, which was initially created as a wholly owned subsidiary of Aberdeen University Industrial Services (AURIS).  In 1993, as a result of a government commissioned review of all UK culture collections, the National Collection of Food Bacteria (formerly the national Collection of Dairy Organisms) was moved to Aberdeen and became part of NCIMB thus further extending its remit as the UK’s premier collection of reference strains from environmental sources. Finally, in 2000, NCIMB Ltd was spun out to become an independent commercial company, and the only nationally designated genetic resource in the world to be privately owned.

Thirty years on, NCIMB has grown into a company that offers a range of microbiological and chemical analytical services, including secure storage and maintenance of bacterial strains belonging to industrial clients.  NCIMB is also an International Depository Authority (IDA) under the Budapest Treaty, and as such, maintains strains of microorganisms that are involved in patented processes.  This patent deposit service has been extended to include plant seeds, making NCIMB one of only a handful of global collections offering this facility.

Bacteria have a bit of an image problem due to their association with disease, but it should be emphasised the vast majority are harmless to humans

However, the core of NCIMB’s business remains the open or public collection of reference strains which now numbers approximately 8,000 strains.  These strains have been isolated from a wide variety of environmental sources both in the UK and overseas, including marine hydrothermal vents, the gills of fish and wallaby droppings.  What we are looking to include in the collection are type strains of newly discovered environmental bacteria and those that may be environmentally and/or commercially useful. Bacteria from the collection are regularly supplied to industry and used for teaching purposes or academic research.  A large proportion of the strains that have been taken into the collection since it was established are actinomycetes: this is perhaps predictable, as 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.

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, however, media attention is often focused on plant and animal species rather than bacteria. This is perhaps understandable as bacteria have a bit of an image problem due to their association with disease, but it should be emphasiszed the vast majority are harmless to humans and indeed the general public are often unaware of the essential roles that bacteria have in the environment and the array of products and industrial processes they are involved in. Examples include the production of industrial enzymes, the biodegradation of industrial effluents and the manufacture of many everyday foodstuffs.

[caption id="attachment_30018" align="alignright" width="200" caption="Cultures from the Rothamsted Research Station soil collection, preserved in soil alongside the ampoules of freeze dried cultures that NCIMB use today"][/caption]

There are over 600 recognised national culture collections within the World Federation of Culture Collections (WFCC), of which NCIMB is one, and there are probably thousands more privately owned collections in companies and research organisations around the world.  Culture collections play an important role in harnessing, describing and preserving microbial biodiversity for current and future generations of scientists, as well as being a means of making strains isolated through academic research available to industry and other researchers. For example, two of the most recent accessions to the NCIMB collection are a new genus isolated from the gut of a bee, and a new actinomycete that was isolated from a Norwegian fjord sediment.  The decline of bee populations is a topic of current concern, and strains of the rare actinomycete genus Verrucosispora are currently the focus of considerable interest as a source of new bioactive compounds and anti-cancer drugs. The accession of these new strains to an open culture collection makes them available to researchers studying bee health and ecology or drug discovery companies around the world respectively, and is therefore fundamental to the advancement of research.

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. Our staff have often become involved in supporting some of these endangered collections by helping to secure small grants to alleviate this kind of crisis.   In the UK, NCIMB is continuously expanding not only as a result of individual new accessions, which are mainly deposited by academic researchers, 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.

As in the early days of the collection, we still rely heavily on phenotypic characteristics when working with cultures, however the identification of strains within our collection has been made so much easier by the use of genetic methods like 16s ribosomal DNA sequencing.  Looking forward, I predict that the use of genomics and proteomics will greatly enhance the collection by allowing us to discover the unique properties and commercial potential of the strains we hold. NCIMB meanwhile continues to operate a polyphasic approach to taxonomy and species identification which we consider a more rounded and inclusive approach to best characterise, and/or identify strains and to circumscribe new taxa.

Some strains in the collection may have potential applications that were not identified at the time they were isolated, and so we are looking at working with partners to investigate ways of determining the genetic maps of our strains, to look for novel properties and processes which may lead to new therapeutics or industrial applications.  With 8,000 strains in the collection there have to be some ‘hidden gems’ in there with great, but as yet undiscovered, industrial or medical importance.

With 8,000 strains in the collection there have to be some ‘hidden gems’ in there with great, but as yet undiscovered, industrial or medical importance

One approach to tackling this could be to establish a screening programme that involves looking for genetic cassettes for particular functions or properties, or in other words, looking for the DNA sequences that are known to be associated with useful biochemical functions and characteristics such as production of antibiotics or particular classes of enzymes.  This approach may enable a relatively quick and efficient screening of a large number of strains, but would still be a major undertaking, and consequently we have been investigating the availability of funding for such a programme as well as the possibility of partnering with other companies in order to continue to develop the collection for the next generation of researchers.

I am very excited about the future for NCIMB and looking forward to the next 30 years of working with researchers to preserve new strains of bacteria they have discovered, as well as serving our customers across the globe. The interaction with our customers, learning what is important to them and adapting our services and products to suit their changing needs is what I find most satisfying and is essential to ensuring the continued relevance of the culture collection.  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.

[caption id="attachment_30022" align="alignleft" width="200" caption="Dr Samantha Law, Deputy Curator examining ampoules from the collection"][/caption]

We have seen in the past how trends in research, developments in technology, and the needs of industry can increase demand for particular strains – so 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, as would the huge advances in molecular biology. Today, our strains are not only used by microbiologists, but researchers from other disciplines such as molecular biologists, bioinformaticists and chemists, and we need to adapt and provide information and products using our strains that can cater for these new users. For example, for many users, information on the genetics of the microorganisms is now of as much value as the ability to grow the organisms themselves, and so we have introduced a line of DNA from particular strains.

I have learnt many things from my colleagues at NCIMB, especially the curator Dr Peter Green who has a wealth of experience, having started his career with the NCMB in 1970; perhaps the most important is not to neglect the fundamental principles of microbiology and the importance of taxonomy. In the face of new and powerful technologies it is easy to overlook these essential basics and this is where I think culture collections like NCIMB have a very important role for the future - – in not only maintaining the physical resource of the collection but also the knowledge, understanding and capabilities required to preserve it for future generations. I am proud that I will be following in the footsteps of many excellent curators and I look forward to making my own contribution on this exciting journey.

The author: Dr Samantha Law Dr Samantha Law is deputy curator of NCIMB, working alongside Dr Peter Green who has been curator of the collection since 1995. Peter is currently winding down as curator and will be handing over to Dr Law when he fully retires.

Contact For more information about NCIMB Ltd and the culture collection contact  Dr Samantha Law or Dr Peter Green 01224 711100

s.law@ncimb.com p.green@ncimb.com www.ncimb.com