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EC-sponsored Research on Safety of Genetically Modified Organisms - A Review of Results
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image High resolution of automated microbial identification: improvement of nucleic acid probe techniques

Background and objectives

The ability to identify bacteria is important to a variety of activities and disciplines including medicine, ecology, biotechnology and food hygiene, and when considering the safety of genetically modified organisms. There are numerous ways to classify bacteria and to assess how related two or more bacterial isolates or populations are to each other. They include genetic analysis, analysis of protein content, or of the similarities between particular proteins in the different bacteria, testing the biochemical activities of the isolates and analysis of immunological properties. However, different methods do not necessarily give exactly the same findings, as when one trait is studied bacteria may appear to be very similar whereas when a second trait is studied they may appear very different. Furthermore, different methods are differently suited to different purposes. This project developed improved technology for the rapid and accurate identification of bacteria, and assessed and compared the utility of various methods.

Approach and methodology

The approach was largely methodological, and included the development of automated systems. The project developed technology in diverse fields including nucleic acid sequence analysis, immunology, analytical chemistry, instrumentation and separation techniques. First, ribosomal RNA (rRNA) sequences, chemical biomarkers, macromolecular profiles and stable antigens of a large panel of commercially and environmentally relevant groups of micro-organisms were analysed. These data were then used to establish taxonomic relationships at the genus level and above and thereby a framework microbial taxonomy. The different approaches were then compared and analysed with respect to their utility, and the most useful used to expand existing taxonomic databases. Finally, nucleotide probes, in particular for rRNA, were developed for sensitive and specific identification for taxonomic purposes, and automated systems using these probes designed for handling large numbers of samples.

Main findings and outcome

The progress made by this project was both substantial and diverse. For example, the sequence and diversity of Pseudomonas rRNA was thoroughly investigated and exploited for nucleotide probe development. Species specific probes were obtained, and automated ribotyping based on restriction fragment size was validated for the first time. The associated software was developed and made available for industrial applications. The project also made significant advances in the use of low molecular weight RNA (tRNA) for taxonomic purposes and established a low molecular weight RNA database. Various other types of technique were also developed, including: PCR assays; supercritical fluid chromatographic analysis; and ELISA. With the wealth of data generated, extensive phenotypic and chemotaxonomic databases were established.

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Contract number

October 1991 - September 1993

K.N. Timmis
National Research Centre for Biotechnology (GBF)
Braunschweig (DE)

Follow-up of the project
This project was continued in EC project BIO2-CT94–3098.


A. Akkermans
Wageningen Agricultural University (NL)

D. Bitter-Suermann
Med. Univ. Hannover (DE)

D. Collins
AFRC Institute of Food Research
Reading (UK)

K. Schleifer
Technical University of Munich (DE)

P. Grimont
Institut Pasteur
Paris (FR)

M. Höfle
National Research Centre for Biotechnology (GBF)
Braunschweig (DE)

K. Kesters
Rijksuniversiteit Gent (BE)

R. de Wachter
University of Antwerp (BE)

N. Kennedy
CAPTEC - Computer Applied Technologies
Dublin (IE)

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