Spring Conference 2011 - Society for General Microbiology

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Please note: Abstracts are published as received from the authors and are not subject to editing. 35 Spring Meeting 11–14 April 2011 Harrogate – www.sgmharrogate2011.org.uk SESSION AbSTrACTS ↑Contents HA06 Cont. (strains, mutants, viruses and so on) available is too weak to convince most authors to share their strains with colleagues, not to mention deposition in culture collections. To blame authors in general would be an injustice to those who actually deposit selected strains, there are also several other stakeholders involved in a complex network of interactions. At least five partners can be identified, i.e., authors, public collections, funding agencies for research and for collections, as well as editors; in addition, the emerging Global Biological resource Centre Network (GBrCN; http://www.gbrcn.org/), offering an electronic platform for communication between authors and collections, may be involved. The dimension of the task requires a concerted action, an intense dialog collecting a broad spectrum of opinions from all stakeholders involved. This strategy will be presented. Maintaining taxonomic and nomenclatural standards in the era of ‘omics’ – a future challenge or a lost battle? Peter Kämpfer Institut für Angewandte Mikrobiologie, Justus-Liebig-Universität Giessen, Henrich-Buff-Ring 26-32 (IFZ), D-35392 Giessen Germany Taxonomy has been circumscribed as ‘the art of biological classification’ but is consisting of more than just classification (the orderly arrangements of recognizable units). in addition to classification, nomenclature, i.e. labelling of these units defined by classification and also identification of these units, are of central importance for a stable, practical and predictable system in all disciplines of microbiology. An essential aspect in classification is the comparison of two or more elements, whether they are genes or genomes, proteins or proteomes, biochemical pathways or metabolomes or whole organisms and the most important part is the definition of the ‘taxonomic units’ to be classified. The development of high throughput sequencing techniques has led to an enormous amount of data (genomic and other ‘omic’ data) and have also revealed an extensive diversity behind these data. Based on these findings, there is a strong tendency to classify and name the taxonomic units preferably on the basis of sequence data which are sometimes contrary to other informations and the biological meaning behind. The criteria used for classifications may change in the future, when we have a full insight into the complexity of the genomes (and other ‘omes’) of micro-organisms. However, the maintance of stable and predictable taxonomic and nomenclatural standards is even more important in these ‘high-throughput’ times. Describing new microbial taxa: Quis custodiet ipsos custodes? iain C. Sutcliffe School of Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST (Email: iain.sutcliffe@northumbria.ac.uk; Tel: +44 (0)191 227 4071) Microbial taxonomy and systematics are vital in providing a sound framework for microbiology, particularly now that an explosion of molecular sequence-based approaches has revolutionised our understanding of microbial diversity. Formal descriptions of novel taxa remain the bedrock of taxonomy, along with the re-evaluation of established taxonomies. New descriptions face the challenge of proving genuine novelty in the face of an ever expanding catalogue of previously described taxa. The vast majority of descriptions of novel taxa are published in the International Journal of Systematic and Evolutionary Microbiology (iJSEM) and, furthermore, the valid publication of any new name (or combination) must be published in this journal. However, a small but significant number of descriptions of novel taxa appear in journals such as Antonie van Leeuwenhoek, which i represent as Editor-in-Chief. it is thus important that such studies conform to appropriate benchmarks that are upheld by rigourous peer review. Thus the guidelines for authors of the iJSEM rightly remain the gold standard for all descriptions of novel taxa. However, the future of taxonomy and our ability to attract young scientists into the field will depend on flexibility and pragmatism in defining minimal standards that are clear, open and not unnecessarily proscriptive. Thus Editors responsible for handling descriptions of novel taxa must remain encouraging custodians rather than zealous guards. reconstructing prokaryotes from diverse data sets – the importance of plausibility, predictability, correlation and verification Brian J. Tindall DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH. Inhoffenstrasse 7b, Braunschweig, 38124, Germany Biology is rapidly moving towards two major goals, the availability of vast arrays of data and the possibility of high throughput sequencing of a large number of genomes. Nowhere are these aspects more apparent than in prokaryotes research. However, amid the euphoria there are also serious problems to be solved. Among these is the administration of the data, the correct annotation of the individual components and the realization that one should be equally rapidly working towards understanding how organisms work at the cellular/whole organism level. At present the data associated with a particular organism is held in distributed formats, ranging from public databases to publications and lab note books. Only when one attempts to the put the data into context is it possible to see it makes sense. it is the last step that s o c i e t y f o r g e n e r a l Microbiology
Please note: Abstracts are published as received from the authors and are not subject to editing. 36 Spring Meeting 11–14 April 2011 Harrogate – www.sgmharrogate2011.org.uk SESSION AbSTrACTS ↑Contents HA06 Cont. is the most difficult and requires putting individual data sets into context and attempting to determine whether it makes sense. it is at this point that a good working knowledge of prokaryote biology comes into play, and the elements of plausibility, predictability, correlation and verification take on central significance. unfortunately it is also the point at which one realises the pitfalls, flaws and errors that abound. The future of taxonomy A.l. Jones 1Dept of Biology, Food and Nutritional Sciences, School of Life Sciences, Northumbria University, Newcastle upon Tyne NE1 8ST Microbial systematics is a misunderstood scientific discipline. it is thought systematists use antiquated techniques to examine the molecular, morphological, physiological, and biochemical properties of micro-organisms. it is also thought that circumscribing novel taxa is not required and because of this, systematics has become a dying art. in truth this discipline is essential to all sciences, without the use of current techniques, descriptions of known and novel taxa cannot be correctly identified. Since the first publication on the use of 16S as a molecular tool, phylogenetic analysis of 16S rrNA genes has become an essential technique in microbial systematics. However this technique has limitations and it is becoming more apparent that full genome comparison is required for the full circumscription of novel taxa. The next generation of sequencing technology, is enabling more information to be incorporated into the full systematic picture. However the start of this era has shown that genomic data, via high throughput sequencing will compliment, rather than throwing a different light on the polyphasic data obtained. High-throughput sequencing is a cost effective method of genomic sequencing; however it is still years away from becoming one of the minimal standards. Culture collection federalization Pippa Bracegirdle CAMR, Porton Down, Salisbury, Wiltshire SP4 0JG The establishment of the Health Protection Agency in 2003 brought four of the existing uK national culture collections – the European Collection of Cell Cultures (ECACC), the National Collection of Type Cultures (NCTC), the National Collection of Pathogenic Viruses (NCPV) and the National Collection of Pathogenic Fungi (NCPF) – together within a single organization. The Health Protection Agency Culture Collections (HPACC) was established as an integrated, not-for-profit strategic business unit within the Health Protection Agency in 2005, with a mission to support and underpin laboratory healthcare science in the uK and worldwide. The HPACC is funded mainly by income from commercial sales supplemented by grant funding from the MrC, Wellcome Trust and Eu. The fundamental requirements of a Biological resource Centre apply to all four sister collections; however the specific technologies and processes can vary considerably. The commonalities and major divergences, and how the HPACC reconciles these, will be briefly reviewed. This presentation will also describe the ongoing process of integration and co-ordination of the four culture collections as a single unit, and as part of a large government health organization. A way forward? David Smith Curator of Genetic Resources Collection, CABI Bioscience UK Centre, Bakeham Lane, Egham, Surrey TW20 9TY Culture collections secure the microbial genetic pool for research and to support the continued search for properties and novel products. The diminishing resource of specialist taxonomists makes ensuring correct identity of strains difficult and discovery of new diversity slow and haphazard. Collections strive to find ways to survive, not unlike the organisms they hold and supply. Harnessing the power of networking provides some of the answers. The World Federation for Culture Collections has been fighting the cause for over 4 decades (http://www.wfcc.info). in Europe, the European Culture Collection’s Organisation (http://www.eccosite.org) has been providing an incubator for pan-European initiatives. However, a lot of work and investment is still needed, by collections, Governments and bioindustry, if the power of microbial diversity is to be harnessed effectively. A recent European project, the European Consortium of Microbial resource Centres (http://www.embarc.eu) is addressing collection sustainability. However, project funding is itself not enough. The Global Biological resources Centres Network (GBrCN) (http://www.gbrcn.org) and the Microbial resources research infrastructure are investigating new strategies. Bringing together collections with stakeholders (users, policy makers, funders and microbial research efforts) to improve access and deliver scientific and technological and managerial excellence for research, education and technology. s o c i e t y f o r g e n e r a l Microbiology
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