Advertisement

Public Service Collections and Biological Resource Centers of Microorganisms

  • David Smith
  • Dagmar Fritze
  • Erko Stackebrandt

Abstract

From its very beginning in the second half of the nineteenth century, microbiology as a scientific discipline recognized the need to preserve microbial resources for scientific studies and as reference material by the establishment of research collections. To better serve the scientific public with the increasing number of strains of medical importance and physiological novelty, collections were established with the specific remit to support the research and user communities, the public service collections. A few of these early collections that continued to increase their holdings over the years and gained international recognition still exist today (e.g., ATCC, USA, CBS, the Netherlands; CIP, France (see Abbreviations). The number of research collections that were created during the past 140 years is unknown as is the total number of those collections that disappeared because of insecure funding and little recognition of their scientific importance. This chapter will highlight the importance of public service collections as the guardians of valuable microbial resources and as one of the cornerstones of research. It will explain the need for collections to improve all aspects of their mandate, namely, accessioning, long-term preservation and provision of microbial strains and their derivatives in order to meet the demands of their users in the era of the knowledge-based bio-economy.

Keywords

Global Biodiversity Information Facility Microbial Resource Public Collection Biological Resource Center Microbial Collection 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Abbreviations

ACM

The Asian Consortium for the Conservation and Sustainable Use of Microbial Resources (http://www.nbrc.nite.go.jp/e/project01-e.html), a network of Asian culture collections and BRCs (see Box 11.5).

ATCC™

American Type Culture Collection; Manassas; VA, USA.

BCC

Biotech culture collection, Bangkok, Thailand.

BCCM™/LMG

Belgian Co-Ordinated Collections of Micro-Organisms, Laboratorium voor Microbiologie, University Gent, Belgium.

BCCUSP

Brazilian Cyanobacteria Collection, University Sao Paulo, Brazil.

BRC

In the context of this chapter defined as a microbial Biological Resource Center (sensu OECD), a CC running under a defined quality management system which yet needs to be agreed upon by the stakeholders.

CABI

CAB International, Egham, UK

CABRI

Common Access to Biological Resources and Information (www.cabri.org), a EU-funded network of eight European Collections (1996–1999), (http://www.cabri.org).

CBD

Convention on Biological Diversity (http://www.cbd.int/), a global agreement addressing all aspects of biological diversity: genetic resources, species, and ecosystems. Their protection, sustainable use and access to including benefit sharing of the advantages arising from their use.

CBS

Centraalbureau voor Schimmelcultures, Utrecht, The Netherlands.

CC

In the context of this chapter defined as a microbial Culture Collection, a general term of a facility accessioning and maintaining microbial resources (prokaryotes, fungi, yeast), DNA, plasmids, phages, and material derived therefrom. Public Culture Collections provide this material to users. For a comprehensive list of abbreviations see WDCM and http://www.bacterio.cict.fr/collections.html.

CCAP

Culture Collection of Algae and Protozoa, Scottish Marine Institute, Oban, Argyll, UK.

CCMM

Moroccan Coordinated Collections of Micro-organisms, Morocco.

CCMP

Culture Collection of Marine Phytoplankton, Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, Maine USA.

CCTCC

Chinese Center for Type Cultures Collections, Wuhan University, Wuhan, Hubei, China.

CCUG

Culture Collection of the University of Göteborg, Institute of Clinical Bacteriology, Immunology, and Virology, Göteborg, Sweden.

CECT

Colección Española de Cultivos Tipo, Valencia, Spain.

CGMCC

China General Microbiological Culture Collection Center, Institute of Microbiology, Chinese Academy of Sciences, Beijing, PR China.

CIP

Collection of the Institut Pasteur, Paris, France

CPCC

Canadian Phycological Culture Center (formerly known as UTCC), University of Waterloo, Waterloo, ON, Canada.

DSMZ

Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.

EBRCN

European Biological Resource Centers Network (http://www.ebrcn.net), a EU-funded network of 15 European culture collections of microorganisms and cell cultures (2001–2004).

ECCO

European Culture Collection’s Organisation (http://www.eccosite.org), a network of European Culture Collections and BRCs (see Box 11.4).

EMbaRC

European Consortium of Microbial Resource Centers (http://www.embarc.eu/) networking the BCCM™/LMG, Belgium

CECT

Spain

CIP

France

DSMZ

Germany and two French research collections INRA-CIRM-BP in Tours and CIRM-BIA, Rennes), aiming to improve, coordinate and validate microbial resource center (MRC) delivery to European and International researchers from both public and private sectors (Box 11.4).

ENBI

European Network of Biodiversity Information (www.enbi.org), an EU funded project established to include all European national nodes of the Global Biodiversity Information Facility (GBIF). (2003–2006).

ESFRI

European Strategy Forum for Research Infrastructures a strategic instrument to develop the scientific integration of Europe and to strengthen its international outreach (http://ec.europa.eu/research/infrastructures/index_en.cfm?pg=esfri)

FEMS

Federation of European Microbiological Societies (http://www.fems-microbiology.org).

GBIF

Global Biodiversity Information Facility (http://www.gbif.org/), an international government-initiated and funded initiative focused on making biodiversity data free and openly available online.

GBRCN

Global Biological Resource Center Network (http://www.gbrcn.org), a project following work in the OECD to improve access to high quality biological resources and information to support research and biotechnology as a platform for a knowledge-based bio-economy.

INRA CIRM-BIA

Center International de Ressources Microbiennes - Bacteries d'Interet Alimentaire, Institut National de la Recherche Agronomique, Rennes, France.

INRA CIRM-BP

Center International de Ressources Microbiennes – Bacteries Pathogenes, Institut National de la Recherche Agronomique, Nouzilly, France.

KACC

Korean Agricultural Culture Collection, National Institute of Agricultural Science and Technology, Suwon, Republic of Korea.

KTCT

Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, Taejon, Republic of Korea.

LMG

The Belgian Consortium of Collections of Microorganisms (BCCM™), represented by the Universiteit Gent, Belgium.

MINE

Microbial Information Network Europe, an EU-funded network of European culture collections, running between 1986–1989 and 1990–1993.

MIRRI

Microbial Resource Research Infrastructure (http://www.mirri.org/), a pan- European distributed research infrastructure established on the European Strategy Forum for Research Infrastructures (ESFRI) road map with the goal to improve access to the microbial resources and services that are needed to accelerate research and discovery processes.

MOSAICC

Micro-Organisms Sustainable use and Access regulation International Code of Conduct, an EU-funded project (1997–1999), a tool to support the implementation of CBD at the microbial level, in accordance with other relevant rules of international and national laws.

MUM

Microtheca do Universidade do Minho, Braga, Portugal.

NBRC

Biological Resource Center, National Institute of Technology and Evaluation, Chiba Pref., Japan.

NCAIM

National Collection of Agricultural and Industrial Microorganisms, Department of Microbiology and Biotechnology, University of Horticulture and Food Industry, Budapest, Hungary.

NCCB

Netherlands Culture Collection of Bacteria, Utrecht, The Netherlands.

NCIMB

National Collection of Industrial and Marine Bacteria, National Collections of Industrial, Food and Marine Bacteria, Aberdeen, UK.

NCTC

National Collection of Type Cultures, Central Public Health Laboratory, London, UK.

NRRL

Northern Regional Research Center, Agricultural Research Service Culture Collection, National Center for Agricultural Utilization Research, US Department of Agriculture, Peoria, Illinois, USA.

OECD

Organisation for Economic Co-operation and Development (http://www.oecd.org/).

SAG

Culture Collection of Algae Sammlung von Algenkulturen, University Göttingen, Göttingen, Germany.

UCL

The Belgian Consortium of Collections of Microorganisms (BCCM™), Université Catholique de Louvain, Belgium.

WDCM

World Data Center of Microorganisms, an activity of the WFCC, providing an electronic gateway to databases on microbes and cell lines and resources on biodiversity, molecular biology and genomes (see Box 11.3).

WFCC

World Federation for Culture Collections (http://www.wfcc.info/), a Federation within the International Union of Microbiological Societies (IUMS, http://www.iums.org) (see Box 11.2).

Notes

Acknowledgments

We wish to thank all contributing collections for sharing their data with us. Special thanks go to Dunja Martin, Hanover, for critically reading and for improving this chapter.

This chapter has been prepared under the EMbaRC project (EU Seventh Framework Programme Research Infrastructures (INFRA-2008-1.1.2.9: Biological Resources Centers (BRCs) for microorganisms (Grant agreement number: FP7- 228310) and for the GBRCN Demonstration Project, financed by the Bundesministerium für Bildung und Forschung (BMBF), the German Federal Ministry of Research and Education.

References

  1. Anon (2010) The WFCC Guidelines for the establishment and operation of culture collections. http://www.wfcc.info/guideline.html. Accessed 03 July 2011
  2. Arber W (2003) Elements for a theory of molecular evolution. Gene 317:3–11PubMedCrossRefGoogle Scholar
  3. CABRI (2002) Common Access to Biological Resources and Information http//:www.cabri.org
  4. Canhos VP, Sette LD, Cupolillo E, Tigano MS, Vazoller RF (2007) O papel da Sociedade Brasileira de Microbiologia no suporte à consolidação da Rede Brasileira de Coleções de Culturas de Microrganismos. Microbiologia in foco 2:40–48Google Scholar
  5. Canhos VP, Ferraz de Souza RD, Ávila JPC (2009) Avanços na implementação da Rede Brasileira de Centros de Recursos Biológicos. Microbiologia in foco 9:46–47Google Scholar
  6. CBD Nagoya Protocol (2011) https://www.cbd.int/abs/
  7. Cohan FM, Perry EB (2007) A systematics for discovering the fundamental. Units of bacterial diversity. Curr Biol 17:R373–R386PubMedCrossRefGoogle Scholar
  8. Danilova MV, Nadirova JM, Emtseva TV (1980) The viability’s dependence of lyophilized and longly stored bacteria on the quantity of residual humidity. Izv Akad Nauk SSSR, Ser Biol 3:449–451PubMedGoogle Scholar
  9. Dawyndt P, Dedeurwaerdere T, Swings J (2006) Explorating and exploiting microbiological commons: contributions of bioinformatics and intellectual property rights in sharing biological information. Int Soc Sci J 188:249–258CrossRefGoogle Scholar
  10. Day JD, Stacey G (eds) (2007) Cryopreservation and freeze-drying protocols. In: Series: methods in molecular biology, 368, 2nd edn. Humana Press, ISBN 1-58829-377-7Google Scholar
  11. DeLey J, De Smedt TJ (1975) Improvements of the membrane filter method for DNA: rRNA hybridization. Ant van Leeuwenh 41:287–307CrossRefGoogle Scholar
  12. Emerson D, Wilson W (2009) Giving microbial diversity a home. Nat Rev Microbiol 7:758PubMedCrossRefGoogle Scholar
  13. Farrant J (1969) Is there a common mechanism of protection of living cells by polyvinylpyrrolidone and glycerol during freezing? Nature 222:1175, LondonPubMedCrossRefGoogle Scholar
  14. Fischer A, Kroppenstedt RM, Stackebrandt E (1983) Molecular-genetic and chemotaxonomic studies on Actinomadura and Nocardiopsis. J Gen Microbiol 129:3433–3446PubMedGoogle Scholar
  15. Fritze D (2005) Digital imaging of prokaryotes for taxonomic purposes. In: Häuser CL, Steiner A, Holstein J, Scoble MJ (eds) Digital imaging of biological type specimens. A manual of best practice. Results from a study of the european network for biodiversity information. Staatliches Museum für Naturkunde, Stuttgart, viii + 304 pp, ISBN 3-00-017240-8, pp 153–171Google Scholar
  16. Fritze D (2010) A common basis for facilitated legitimate exchange of biological materials proposed by the European Culture Collections’ Organisation. Int J Commons 4:507–527Google Scholar
  17. Fritze D, Weihs V (2000) Systematics and legislation. In: Priest F, Goodfellow M (eds) Applied microbial systematics. Chapman and Hall, London, pp 447–469CrossRefGoogle Scholar
  18. Fry RM (1966) Freezing and drying of bacteria. In: Meryman HT (ed) Cryobiology. Academic, London/New York, pp 665–696Google Scholar
  19. Fuller BJ (2004) Cryoprotectants: the essential antifreezes to protect life in the frozen state. CryoLetters 25:375–388PubMedGoogle Scholar
  20. Gams W, Hennebert GL, Stalpers JA, Jansens D, Schipper MAA, Smith J, Yarrow D, Hawksworth DL (1988) Structuring strain data for the storage and retrieval of information on fungi and yeasts in MINE, Microbial Information Network Europe. J Gen Microbiol 134:1667–1689PubMedGoogle Scholar
  21. Grimont F, Grimont PAD (1986) Ribosomal ribonucleic acid gene restriction patterns as potential taxonomic tools. Ann Inst Pasteur/Microbiol 137B:165–175CrossRefGoogle Scholar
  22. Hawksworth DL, Schipper MAA (1989) Criteria for consideration in the accreditation of culture collections participating in MINE, the Microbial Information Network Europe. MIRCEN J 5:277–281CrossRefGoogle Scholar
  23. Heckly RJ (1978) Preservation of microorganisms. Adv Appl Microbiol 24:1–53PubMedCrossRefGoogle Scholar
  24. Hippe H (1991) Maintenance of methanogenic bacteria. In: Kirsop BE, Doyle A (eds) Maintenance of microorganisms and cultures cells, 2nd edn. Academic, London, pp 101–113Google Scholar
  25. Johnson JL, Ordal EJ (1968) Deoxyribonucleic acid homology in bacterial taxonomy: effect of incubation temperature on reaction specificity. J Bacteriol 95:893–900PubMedGoogle Scholar
  26. Kersters K, De Ley J (1975) Identification and grouping of bacteria by numerical analysis of their electrophoretic patterns. J Gen Microbiol 87:333–342PubMedCrossRefGoogle Scholar
  27. Kirsop BE, Doyle A (eds) (1991) Maintenance of microorganisms and cultured cells: a manual of laboratory methods. Academic, London, 308 ppGoogle Scholar
  28. Konstantinidis K, Stackebrandt E (2011) Defining taxonomic ranks. In: Rosenberg E, DeLong EF, Thompson F, Lory S, Stackebrandt E (eds) The prokaryotes: a handbook on the biology of bacteria, 4th edn. Springer, New YorkGoogle Scholar
  29. Lenski RE, Travisano M (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc Natl Acad Sci USA 91:6808–6814PubMedCrossRefGoogle Scholar
  30. Lion MB, Bergmann ED (1961) The effect of oxygen on freeze-dried Escherichia coli. J Gen Microbiol 24:191–200PubMedCrossRefGoogle Scholar
  31. Lovelock JE, Bishop MWH (1959) Prevention of freezing damage to living cells by dimethyl sulfoxide. Nature 183:1394–1395PubMedCrossRefGoogle Scholar
  32. Morichi T (1970) Nature and action of protective solutes in freeze-drying of bacteria. In: Iizuka H, Hasegawa T (eds) Culture collections of microorganisms. University Park Press, Baltimore, pp 351–361Google Scholar
  33. Morris GJ (1981) Cryopreservation: an introduction to cryopreservation in culture collections. Culture Centre of Algae and Protozoa, CumbriaGoogle Scholar
  34. Nei T (1974) Some aspects of freezing and drying of microorganisms on the basis of cellular water. Cryobiology 10:403–408CrossRefGoogle Scholar
  35. OECD (2001) Biological resource centres – underpinning the future of life sciences and biotechnology. (http://oecdpublications.gfi-nb.com/cgi-bin/oecdbookshop.storefront)
  36. OECD (2007) Best practice guidelines for biological resource centres (Online), http://www.oecd.org/dataoecd/7/13/GGTSPU-styx2.bba.de-7664-3281383-DAT/38777417.pdf Accessed 20 Jan 2011
  37. OECD (2011) The bio-economy to 2030: designing a policy agenda. The Organization for Economic Cooperation and Development (OECD), ParisGoogle Scholar
  38. Olive DM, Bean P (1999) Principles and applications of methods for DNA-based typing of microbial organisms. J Clin Microbiol 37:1661–1669PubMedGoogle Scholar
  39. Polge C, Smith AU, Parkes S (1949) Revival of spermatozoa after dehydration at low temperatures. Nature 164:666PubMedCrossRefGoogle Scholar
  40. Pukall R, Brambilla E, Stackebrandt E (1998) Automated fragment length analysis of fluorescently-labeled 16S rDNA after digestion with 4-base cutting restriction enzymes. J Microbiol Meth 32:55–64CrossRefGoogle Scholar
  41. Rainey PB, Travisano M (1998) Adaptive radiation in a heterogeneous environment. Nature 394:69–72PubMedCrossRefGoogle Scholar
  42. Reed BM (2008) Plant cryopreservation – a practical guide. Springer, Heidelberg. ISBN 978-0-387-72275-7CrossRefGoogle Scholar
  43. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, DC, pp 607–655Google Scholar
  44. Smith D, Rohde C (2007) Biological resource centres compliance with law. Society for Microbiology, UK. http://www.sgm.ac.uk/pubs/micro_today/pdf/0299brc.pdf
  45. Smith D, Rohde C (2008) Safety in microbiology. Laboratory Manager Issue, vol 125. Croner, UK, pp 4–6Google Scholar
  46. Smith D, Ryan MJ, Day JG (2001) The UKNCC biological resource: properties, maintenance and management. UKNCC Secretariat, Egham. ISBN 0954028503Google Scholar
  47. Smith D, Ryan MJ, Stackebrandt E (2008) The ex situ conservation of microorganisms: aiming at a certified quality management. In: Doelle HW, DaSilva EJ (eds) Biotechnology. Encyclopedia of Life Support Systems (EOLSS). Developed under the Auspices of the UNESCO, Eolss, Oxford, UK. http://wwweolss.net
  48. Stackebrandt E (2010) Diversification and focusing: strategies of microbial culture collections. Trends Microbiol 18:283–287PubMedCrossRefGoogle Scholar
  49. Stackebrandt E (2011) Letter to the editor. Int J Syst Evol Microbiol 61:479–481PubMedCrossRefGoogle Scholar
  50. Stackebrandt E, Frederiksen W, Garrity GM, Grimont PAD, Kämpfer P, Maiden MCJ, Nesme X, Rossello-Mora R, Swings J, Trüper HG, Vauterin L, Ward AC, Whitman WB (2002) Report of the ad hoc committee for the re-evaluation of the species definition in bacteriology. Int J Syst Evol Microbiol 52:1043–1047PubMedCrossRefGoogle Scholar
  51. Stalpers JA, Kracht M, Jansens D, De Ley J, Van der Toorn J, Smith J, Claus D, Hippe H (1990) Structuring strain data for storage and retrieval of information on bacteria in MINE, Microbial Information Network Europe. Syst Appl Microbiol 13:92–103CrossRefGoogle Scholar
  52. Stamp TC (1947) The preservation of bacteria by drying. J Gen Microbiol 1:251–265PubMedCrossRefGoogle Scholar
  53. Stromberg PM, Dedeurwaerdere T, Pascual U (2012) The contribution of public networks to knowledge accumulation: ex situ collections in microbial research (in press)Google Scholar
  54. Suggett A (1975) Water-carbohydrate interactions. In: Duckworth RB (ed) Water relations of food. Food Science and Technology, a series of monographs. Academic Press, London, pp 573–586Google Scholar
  55. Tindall P, Kämpfer P, Euzéby J, Oren A (2006) Valid publication of names of prokaryotes according to the rules of nomenclature: past history and current practice. Int J Syst Evol Microbiol 56:2715–2720PubMedCrossRefGoogle Scholar
  56. Tindall BJ, Rosselló-Móra R, Busse HJ, Ludwig W, Kämpfer P (2010) Notes on the characterization of prokaryote strains for taxonomic purposes. Int J Syst Evol Microbiol 60:249–266PubMedCrossRefGoogle Scholar
  57. Verslyppe B, Kottmann R, De Smet W, De Baets B, De Vos P, Dawyndt P (2010) Microbiological common language (MCL): a standard for electronic information exchange in the microbial commons. Res Microbiol 161:439–445PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2013

Authors and Affiliations

  1. 1.CABIEghamUK
  2. 2.German Collection of Microorganisms and Cell Cultures GmbHBraunschweigGermany
  3. 3.Leibniz Institute DSMZ-German Collection of Microorganisms and Cell CulturesBraunschweigGermany

Personalised recommendations