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Antarctic microbial biodiversity: the importance of geographical and ecological factors (AMBIO) (Belgian Science Policy Office)
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Coordinator : A. Wilmotte
Promotor(s) : A. Willems, W. Vyverman
Period : 15/12/2006 - 31/1/2011
Staff : Karolien Peeters (PhD student) & Natanael Denbaes (technician)
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Description : AMBIO will determine the microbial diversity, community composition and taxonomic turnover in permanently and seasonally wet habitats (lakes, cryoconites and seepages) across Antarctica, and assess the relative importance of ecological versus historical factors in explaining the geographical distribution of particular taxa and communities. To this end, we will study regions at a circum-Antarctic level and along a latitudinal gradient ranging from high-latitude continental sites in East and West Antarctica (including the site of the future Belgian Base near the Utsteinen nunatak), to the Sub-Antarctic islands.
The first two years will be devoted to a systematic inventory of the diversity and community composition as well as to the establishment of culture collections of focal groups. Focus will be on Proteobacteria, Bacteroidetes, Cyanobacteria, Chlorophyta and Bacillariophyta, all known to be well-represented in Antarctic microbial communities. A mid-term assessment will identify regions and taxa particularly important to test hypotheses about the driving factors behind Antarctic microbial diversity and its evolution. These will be the focus of the two following years of the project. |
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| last updated Wed 25 Jun 2008 09:32:00 |
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Bacterial species: from new concept to new definition (FWO-Vlaanderen)
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Promotor(s) : P. Vandamme, P. De Vos, A. Willems & N. Logan
Period : 01/01/2007 - 31/12/2010
Staff : Evie De Brandt (technician)
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| Description : The project aims to perform comparative studies of whole-genome sequences for model groups of bacteria representing different phylogenetic lineages, in order to design widely applicable sets of genes and primers which can be used to develop a multilocus sequence analysis-based approach for the delineation of species. The ultimate aim is to use the lessons from these model groups to design a generic approach for a general MLSA-based species definition. |
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| last updated Fri 20 Apr 2007 12:00:00 |
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BCCM/LMG Bacteria collection (Federal Office for Scientific Policy)
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Promotor(s) : P. De Vos
Period : since 1980
Staff : Postdocs, scientific collabotors, technical staff (total 20 persons)
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| Description : The BCCM/LMG bacteria collection aims at preserving and distributing bacterial strains amongst which type and reference strains. The culture collection functions under the ISO 9001 quality label and complies with the Budapest Treaty for Patent strains and safety deposits. The research activities of the BCCM/LMG bacteria collection are in close connection with the services of identification of bacteria that are provided for third parties, academic, non-profit as well as profit based customers. The BRC coincides with the OECD guidelines and overall the BBCM/LMG bacteria collection functions in close collaboration with the research groups of the host laboratory. |
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| last updated Mon 23 Jun 2008 14:32:57 |
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BELDIVA - Phase 1, Belgian Microbial Diversity Exploration near the Princess Elisabeth Station, Antarctica (Belgian Science Policy Office)
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Coordinator : W. Vyverman
Promotor(s) : A. Wilmotte, A. Willems, B. Van de Vijver, D. Ertz
Period : 1/01/2009 - 30/06/2011
Staff : None
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| Description : This project is aimed at sampling representative habitats (potentially) containing microorganisms in an area of 200 km around the Belgian Princess Elisabeth Base (PES), Dronning Maud Land, East Antarctica. In particular it will involve two exploratory field campaigns in an area of about 50 km around Utsteinen during the Austral summers of 2008-2009 and 2009-2010. This project will be integrated with the project AMBIO and ANTAR-IMPACT. |
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| last updated Thu 18 Aug 2011 10:37:30 |
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BELDIVA - Phase 2, Belgian Microbial Diversity Exploration near the Princess Elisabeth Station, Antarctica (Belgian Science Policy Office)
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Coordinator : W. Vyverman
Promotor(s) : A. Wilmotte, A. Willems, B. Van de Vijver, D. Ertz
Period : 01/01/2011 - 30/11/2012
Staff : Pia Clercx
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| Description : This project is aimed at sampling representative habitats (potentially) containing microorganisms in an area of 50 km around the Belgian Princess Elisabeth Base (PES), Dronning Maud Land, East Antarctica. It will involve an exploratory field campaign during the Austral summer of 2010-2011. This project will be integrated with the recently completed projects AMBIO and ANTAR-IMPACT. |
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| last updated Tue 24 Jan 2012 11:50:25 |
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Biotic interactions across size classes as structuring factors for marine benthic ecoystem functioning (FWO)
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Coordinator : M. Vincx
Promotor(s) : J. Vanaverbeke, A. Willems
Period : 01/01/2011 – 30/11/2014
Staff : Maryam Yazdani (PhD student, Biology Dept.)
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| Description : This project is a collaboration with the Marine Biology research group (Biology Dept.) and will focus on marine coastal sediment foodwebs. We will investigate how functional biodiversity at the level of the larger, habitat-engineering macrobenthos will cascade into levels of biodiversity of the microbial level
which is directly responsible for important ecosystem functions (e.g. nitrification/denitrification).
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| last updated Thu 18 Aug 2011 11:32:54 |
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BRIO. Banking Rhizosphere Micro-Organisms. European - Russian initiative to set up a network of rhizosphere microbiological resources centres (EC-7FP)
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Coordinator : Philippe Desmeth (BelSPO)
Promotor(s) : Willems Anne (UGent-promotor), Stephane Declerck (MUCL), Marcel van der Heijden (ART, Switzerland), Giovanna Cristina Varese (UNITO, Italy), Lyudmila I. Evtushenko (VKM, Russia), Irina Ivshina (IEGM, Russia), Olga V. Turkovskaya (IBPPM RAS, Russia)
Period : 01/05/2011 - 20/04/2013
Staff : Technician
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| Description : The objectives of BRIO are:
I. to organize cooperation between specialised collections containing beneficial micro-organisms isolated from the rhizosphere,
II. to constitute a common wide-range pool of microbial diversity exploitable for research and industry: the Pan-European Rhizosphere resources Network (PERN).
Collaboration between culture collections having material from West-European ecosystems and Russian Biological Resources Centres having micro-organisms from East-European biotopes will create a coordinated network of combined collections offering a wide range of micro-organisms coming from a broad spectrum of ecological zones spread over an extensive geographical area to study and exploit. The network of combined collections will offer scientists facilitated access to geographically diverse microbiological material.
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| last updated Thu 18 Aug 2011 11:25:58 |
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Characterisation, ecology and epidemiology of plant pathogenic pseudomonads of leaf crops (lettuce and leek) (IWT- Landbouwkundig onderzoek)
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Coordinator : POVLT (Beitem); P. Bleyaert
Promotor(s) : P. De Vos
Period : 2005-2008
Staff : 1 technician
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| Description : The project aims at understanding and developing a sustainable controling strategy of the pseudomonas infections on leaf crops. Therefore (i) causative agent will be isolated from vastly developed rib rot and characterised; (ii) infection sources of the bacterial pathogens will be traced by newly developed real-time PCR-based detection method; (iii) pathogenicity factors and their role in plant-pathogen interactions will be studied; (iv) the effect of environmental factors (e.g. irrigation, compostion of soil fertilization etc.) on the pathogen development will be analysed. Two crops – lettuce in greenhouses and leek in open field - are studied as models. |
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| last updated Fri 20 Apr 2007 11:42:00 |
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Classification and source tracking of psychrotrophic bacteria isolated from packed food products (Bilateral collaboration in the frame of GOA project)
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Promotor(s) : F. Devlieghere & G. Huys
Period : 2010-2013
Staff : Vasileios Pothakos (PhD student)
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| Description : The aim of this project is to investigate cases of spoilage occurring on packed and stored under chilling temperatures food products, that show low microbial contamination according to the widely applied enumeration methods of the mesophilic microflora before the end of their shelf-life. |
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| last updated Fri 30 Sep 2011 10:40:00 |
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Democratic governance a reflexive theory of collective action
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Coordinator : J. Lenoble (UCL)
Promotor(s) : P. De Vos (twinned with B. De Baets)
Period : 01/01/07 - 31/12/11
Staff : 1 technician, 1 PhD
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| Description : The project aims at examining the exploration and exploitation of microbial research commons by bundling the contributions and intelectuazl property rights in sharing biological information. Further development of strainInfo.net bioportal that is regarded as a working model system to test the theoretical underpinnings of collective action in the IUAP network. Application of semantic web technologies for ‘incemental machine learning’ as hands-on excercise to control machine interpretation of vast amounts of research data, aiming at the combination of research outcomes in non-anticipated and non-traditional ways. |
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| last updated Fri 20 Apr 2007 11:44:00 |
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Development of a new diagnostic tool using DNA barcoding to identify quarantine organisms in support of plant health (QBOL) EU (Framework VII)
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Promotor(s) : P. De Vos
Period : 01/05/2009 - 31/04/2012
Staff : Joanna Zaluga
Website : http://www.pri.wur.nl/UK/research/projects/qbol
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| Description : The project “Phylogenetic study and identification of plant pathogenic clavibacters” is part of “QBOL-Quarantine Barcoding of Life” which is a European project that makes collections harboring plantpathogenic quarantine organisms available. The QBOL - consortium of 20 partners (universities, research institutes and phytosanitary organizations), has a long-term vision of developing a sustainable diagnostic resource to enable 'DNA-barcode identification' ultimately for all quarantine plant pests or pathogens of statutory importance. |
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| last updated Fri 2 Jul 2010 14:42:00 |
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Development of fingerprints as barcodes for industrial microbial populations
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Promotor(s) : P. Vandamme and A. Van Landschoot
Period : 1/1/2008 - 31/12/2013
Staff : Elisabeth Vercammen (Post-Doc)
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| Description : The projects aims to develop a mass-spectrometric fingerprint for a mixed microbial population which allow real-time microbiological assessment of the fermented product, but also of the production process. Aquakefir, a simple fermented beverage produced by 'kefir grains' upon fermentation of figs and lemons added to an aqueous culture, has a limited microbial diversity and will therefore be used as a model system |
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| last updated Mon 23 Jun 2008 00:00:00 |
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Development of public collections of diatoms, polar cyanobacteria, and mycobacteria in Belgium (Federal Office for Scientific Policy)
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Promotor(s) : P. De Vos
Period : 01/01/2005 - 31/12/2010
Staff : V. Storms (½ time Post Doc)
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| Description : |
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| last updated Fri 20 Apr 2007 11:49:00 |
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Diagnosis and prevention of Xanthomonas fragariae in strawberry crop (PROJECT IWT 070597)
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Coordinator : Dr. Tine Maes (ILVO)
Promotor(s) : P. De Vos
Period : 01/09/2007 - 31/08/2012
Staff : Joke Buysse (technician)
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| Description : Bacterial leaf spot in strawberry occurs in open field cultures and is caused by the quarantine bacterium Xanthomonas fragariae. The disease is recently spreading in Flemish strawberry nurseries, in spite of its quarantine status. In 1997, the experimental station of Hoogstraten made the first observation in 15 different production companies, and in 2003-2004 already 20 to 25 % of the companies had infection. Not only the spread, but also the severity of the disease increases. In case of severe outbreak, also the petals show disease spots, which makes the fruit unmarketable. Open field cultivation in combination with a highly susceptible host, as the current CV Elsanta, is leading to a further spread of the disease and higher losses. In order to prevent this, we need clear identification of the Xf-problem in Flanders and development of effective measures to stop new pathogen introductions via latently infected planting material and to suppress existing contamination of field soils.
This projects focuses on the symptomless survival of the pathogen in plants and planting material and on reliable detection of these infections. It is a collaboration between the Institute for Agricultural and Fisheries Research (ILVO), Laboratory of Microbiology at Ghent University(LM-UGent), and the experimental stations of Hoogstraten and St-Truiden. Partner LM-UGent is involved in the isolation and typing of Xanthomonas fragariae isolates from strawberry plants to elucidate sources of contamination and unravel correlations between infection and cultivation variables (e.g. cultivar). |
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| last updated Tue 27 Jul 2010 13:03:00 |
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Diversity and nutritional modulation of fecal microbiota in the captive cheetah (BOF-UGent en MAF)
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Promotor(s) : G. Janssens, G. Huys & M. Hesta
Period : 10/2010-09/2014
Staff : Anne Becker (PhD student)
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| Description : This project aims to characterize the intestinal microbiota of captive cheetahs with specific focus on the influence of changes in the strict carnivorous diet on the fecal microbiota and its role in the digestive process. Based on the use of molecular techniques (PCR-DGGE, real-time PCR) and dedicated in-vitro and in-vivo studies, we will identify indicator organisms with beneficial fermentation profiles, and new insights in their role to maintain the normal intestinal health status will be obtained. |
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| last updated Fri 30 Sep 2011 10:40:00 |
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Diversity of lactic acid bacteria from traditional fermented food in northern Vietnam (Belgische Technische Coöperatie)
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Promotor(s) : P. Vandamme
Co-promotors: B. Le Tanh & K. Van Hoorde
Period : 01/09/2008-31/08/2012
Staff : Nguyen Thi Lam Doan
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| Description : Developing countries have very diverse food consumption patterns and agricultural production systems but miss food processing technologies that meet the challenges of food safety, food security and nutrition problems. The aim of the present project is to study and preserve the LAB biodiversity of nem chua and tom chua, and to select and characterize functional starter culture strains which are capable to produce bacteriocins and high amounts of lactic acid such that the safety and shelf-life of these food products can be enhanced. |
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| last updated Tue 4 May 2010 00:00:00 |
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Diversity of rhizobia from Belgian leguminous plants: a molecular inventory (Bijzonder Onderzoeksfonds UGent)
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Promotor(s) : A. Willems, P. Goetghebeur and P. Dawyndt
Period : 2007 - 2011
Staff : Sofie De Meyer (PhD student)
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| Description : A molecular inventory of rhizobia from Belgian leguminous plants will be made. A collection of local rhizobia will be assembled. After initial screening by RFLP, identification will be achieved by multi-locus sequence analysis of housekeeping genes. Reference organisms will be included and the data compiled in a database linked to software tools. Newly discovered species will be characterized and named. |
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| last updated Tue 13 Nov 2007 17:01:00 |
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Double Blind Study on the identification of pseudomonads (Health Canada)
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Coordinator : Health Canada & M. Krichevsky – M. Segal
Promotor(s) : P. De Vos
Period : 1998 - 2008
Staff : L. Lebbe (technician)
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| Description : In a double blind approach 600 named pseudomonas strains were distributed over 8 internationally (US-2-, Canada, Spain, Thailand, China, Sweden and Belgium) recognised laboratories for Microbiology for the identification of bacteria. The methodology applied complies with the in house methodology that is applied in each laboratory for the identification of pseudomonads. Data analysis is in the final phase. |
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| last updated Fri 20 Apr 2007 11:41:00 |
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Effect of preservation on the psychrophilic Pseudomonas microbiota in raw farm milk (IWT, landbouwkundig onderzoek)
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Coordinator : M. Heyndrickx
Promotor(s) : P. De Vos
Period : 01/09/07 - 31/08/2011
Staff : Emly Samyn (technician)
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| Description : The project aims at studying the effect of cooling on the development of psychrotrophic pseudomonads in raw milk and also the relation between enzyme excretion by this psychrophilic microbiota, and the milk quality. A culture-independent detection method for the follow up and the detection of the psychroptrophic microbiota will be developed. The project also aims at refining the guidelines for preservation of milk during the collection and transport phase between the farm and the dairy factory in order to obtain the optimal conditions for milk preservation. |
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| last updated Fri 20 Apr 2007 11:43:00 |
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Endosymbiotic bacteria in coenocytic green algae - exploration of a partnership (FWO-Vlaanderen)
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Promotor(s) : A. Willems, O. De Clerck
Period : 1/1/2008 – 31/12/2011
Staff : Joke Hollants (PhD student)
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| Description : Endosymbiotic bacteria are reported to be of common occurrence in coenocytic green algae and may be associated with various metabolic functions. In Bryopsis bacteria are present at every stage of development including the gametes, indicating that the endosymbionts are vertically transmitted.
In this project we aim to study the association between coenocytic algae and their bacterial endosymbionts to identify the bacterial partner(s) and assess possible co-evolution. We will study the role of the bacterial partner, the degree of inter-dependency and how bacteria are recruited from the environment.
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| last updated Tue 15 Jan 2008 15:10:00 |
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European Consortium of Microbial Resource Centers (EmbaRC), EU (Framework VII)
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Promotor(s) : P. De Vos; BCCM/LMG
Period :
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| Description : EMbaRC (http://www.embarc.eu//) brings together key microbial resource centers in Europe to improve, coordinate and validate microbial resource delivery to European and International researchers from both public and private sectors. The conservation and utilization of microorganisms aim to help deliver a knowledge-based bioeconomy. |
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| last updated Tue 27 Jul 2010 13:17:00 |
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Genomic detection of selected Bacillus s.l. representatives during gelatine production (IWT)
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Promotor(s) : P. De Vos
Industrial Promotor : T. Vervust (Rousselot)
Period : 1/4/2006 - 31/03/2008
Staff : Rieka Reekmans (Post-doc)
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| Description : Bacteria attributed to Bacillus and related genera contaminate and survive gelatine production processes and hereby negatively affect the quality and safety of the end product. This project aims at optimizing and extending a real-time PCR detection method for the most worrisome contaminants and implementing this method in the quality management of a gelatine production plant. |
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| last updated Fri 4 May 2007 10:23:00 |
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Improved genomic identification of lactic acid and acetic acid bacteria (Federal Office for Scientific Policy)
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Promotor(s) : P. De Vos
Period : 01/12/2005 - 31/03/2008
Staff :
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| Description : Identification databases for lactic acid and acetic acid bacteria currently rely on standardized, but non-automated and inter laboratory irreproducible fingerprints. For both bacterial groups, a robust multilocus sequence-based system will be set up and automated using a robotic system. Databases will be constructed for reliable, high-throughput identification of isolates and delineation of existing and new taxa. The methodology will be applied to study several ecosystems, including cocoa fermentation. |
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| last updated Fri 20 Apr 2007 11:59:00 |
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Improvement of the identification potential of fluorescent pseudomonads: a molecular approach (Federal Office for Scientific Policy)
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Promotor(s) : P. De Vos, P. Cornelis
Period : 01/12/2005 - 31/03/2008
Staff : 1 technician
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| Description : The genus Pseudomonas has been a dumping ground for Gram negative rods, motile by polar flagella. As a consequence of this vague definition, the genus encompassed a number of species groups that were phylogenetically very diverse. This project aims at improving the taxonomic frame of the genus Pseudomonas by applying molecular techniques in a comparative analysis of housekeeping genes. |
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| last updated Fri 20 Apr 2007 11:50:00 |
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Integration of high-throughput approaches to link culturable microbial diversity and metabolic potential in traditional fermented foods: a new screening strategy for functional starter cultures (FWO-Vlaanderen)
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Promotor(s) : P. Vandamme
Co-promotors: L. De Vuyst, G. Huys
Period : 01/01/2010 - 31/12/2013
Staff :
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| Description : Traditional fermented foods are appreciated by the consumer for their organoleptic and health promoting characteristics. In such products it is often unclear which microorganisms and metabolites are responsible for their characteristics. The present project aims to develop and validate a new strategy to analyse this microbiological and metabolic potential more efficently in order to develop functional starter cultures with applications in food industry. |
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| last updated Tue 4 May 2010 00:00:00 |
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Metaproteomics analysis of the distal intestional microbiotica of cystic fibrosis patients (FWO-Vlaanderen)
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Promotor(s) : P. Vandamme
Co-promotors: P. Dawyndt, B. Devreese
Period : 01/01/2010 - 31/12/2013
Staff : Debyser Griet
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| Description : The intestinal microbiota play an important role in health and disease of humans. Cystic fibrosis patients suffer from lung infections that require multiple antimicrobial therapies. In addition, their intestinal physiology and food digestion are severely disturbed. The present project will use metaproteomics analyses to study the composition, dynamics and other characteristics of the distal microbiota of a cohort of cystic fibrosis patients and of their healthy siblings. |
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| last updated Tue 4 May 2010 00:00:00 |
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Microstructural and sensorial effects of the functional components milk fat globule membrane-fragments and natural antioxidants in fermented milk products (BOF-UGent)
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Promotor(s) : K. Dewettinck & G. Huys
Period : 10/2010-09/2014
Staff : Mohammad Mozidul Islam (PhD student)
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| Description : The overall aim of this project is to obtain a more profound insight in the interactions between functional components, namely the milk fat globule membrane (MFGM) fragments and the natural antioxidants (AOX), and the bacterial starter and probiotic cultures in model systems of functional yoghurt formulations, and how the potential effects of these interactions are translated through the microstructure into the sensory properties of the fermented milk product. |
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| last updated Fri 30 Sep 2011 10:40:00 |
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Mining of (micro)biological profiles: going beyond cluster analysis… (Baekeland fonds)
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Promotor(s) : P. Vandamme
Co-promotors: P. Dawyndt
Period : 01/10/2009 - 30/09/2012
Staff : Koen Janssens
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| Description : The scientific objectives of this research project are to develop new methods for the detection of patterns and/or relationships within or between modern typing techniques, trying to converge the (biologically) most relevant information from each technique, while maintaining as long as possible an overall coherent view of the total, combined data content. In order to recover additional information from the combination of techniques, it will be important to filter out noise and unreliable data content. Finally, new data processing techniques for the separation of mixed profiles derived from microbial communities or populations, as generated by techniques such as e.g. DGGE, MALDI-TOF MS, and ESI MS will be designed and developed. |
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| last updated Tue 4 May 2010 00:00:00 |
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Molecular dissection of integrons and gene cassettes involved in the evolution and distribution of multiple antimicrobial resistance genes in Gram-negative opportunistic bacteria (FWO-Vlaanderen)
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Promotor(s) : P. Vandamme
Period : 01/10/2004 - 30/09/2007
Staff : Geert Huys (postdoctoral fellow)
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| Description : Molecular ecological studies demonstrated that antimicrobial resistance is not confined to the nosocomial environment and that a range of aquatic and terrestrial niches and the bacteria therein, represent important reservoirs for resistance genes, which may be localized on mobile genetic elements. The project aims to detect and characterize class 1 integrons and associated gene cassettes as one of the potential mechanisms of environmental bacteria to contribute to the evolution and distribution of multiple antimicrobial resistance. The target bacteria are members of the genera Acinetobacter and Aeromonas. |
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| last updated Fri 20 Apr 2007 11:59:00 |
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New tools for the unraveling of the importance of the gut microbiota
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Promotor(s) : A. Van Landschoot, P. Vandamme, W. Verstraete
Period : 01/09/2009 - 31/08/2015
Staff : Koenraad Van Hoorde (Post-Doc)
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| Description : In order to monitor the possible effect of (functional) foods, medication, toxic compounds, etc… on the microbial composition of the gastro-intestinal tract or to link (predispositions to) disease with the gut microbiota, fast powerful identification tools are essential. Nowadays, several sequencing and molecular fingerprinting tools (e.g. clone libraries and DGGE) are at hand to try to identify the different members of such complex microbial communities, however, all with their respective advantages and unfortunately also disadvantages. The aim of this project, is to set up MALDI-TOF-MS approach as a reliable and fast high-throughput analysis tool to study microbial communities associated with the gastro-intestinal tract. To this, samples retrieved from the SHIME, a simulator of the human intestinal microbial ecosystem, will be analyzed as a leg up to the subsequent implementation on animals and humans. |
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| last updated Tue 4 May 2010 00:00:00 |
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Onderzoek en ontwikkeling van metabolische processen
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Promotor(s) : P. De Vos (aanvrager)
Co-promotors: N. Boon, N. Callewaert, B. Devreese, G. Huys, P. Vandamme, A. Van Landschoot
Period : 01/01/2008 - 31/12/2010
Staff :
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Description : De associatieonderzoeksgroep heeft tot doel de bestaande onderzoeks- en onderwijssamenwerking een officiële vorm te geven en verder uit te bouwen, zodat het gemeenschappelijke onderzoekspotentieel kan versterkt worden. De onderzoekslijnen zijn te situeren in het domein van de industriële biotechnologie. Specifieke onderzoekslijnen houden verband met:
Microbiologie: detectie, identificatie, kwantificering, leefbaarheid, vitaliteit, effect antibacteriële agentia, propagatie en fermentatie van industrieel belangrijke organismen.
Glycobiologie en enzymologie: detectie, zuivering, identificatie, karakterisering en structuur-functie onderzoek van sacchariden en enzymen in industriële processen.
Microbiële ecologie: isolatie, karakterisering en applicatie van polluent-degraderende bacteriële stammen voor bioaugmentatie; toepassen van slow-release technieken voor microbiële inocula. |
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| last updated Wed 21 Nov 2007 10:37:00 |
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Ontwikkeling en toepassing van MALDI-TOF massaspectrometrie voor snelle identificatie van bierbedervers en brouwerijcontaminanten
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Promotor(s) : P. Vandamme, A. Van Landschoot, E. Vercammen
Period : 2009 - 2013
Staff : Anneleen Wieme
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| Description : Beer is a beverage with high microbiological stability because it contains insufficient amounts of oxygen and nutrients for the growth of many microorganisms. Low pH, high CO2-content, the presence of alcohol and antibacterial hop compounds ensure microbial stability. Nevertheless, beer spoilage bacteria are a common problem in the brewing industry and typically cause visible turbidity, acidity and off-flavours. Hence, spoilage microorganisms are a source of concern for the brewing industry worldwide. When performing quality control of beer products it is important to rapidly detect these microorganisms and determine their spoilage capacity. Currently, spoilage organisms are detected by ATP-measurements and culture-dependent methods using selective media. These approaches are notoriously laborious and time-consuming. Furthermore, faster detection methods such as immunological assays with PAb and MAb, DNA-typing, ribotyping and PCR based techniques are not specific or not sensitive enough. Therefore, the present study aims to develop a quick, specific and inexpensive technique to identify contaminants and spoilage bacteria in brewery intermediates and beer. Using MALDI-TOF MS specific biomarkers present in the MALDI-TOF MS profile will be identified for each beer spoiling species, in order to achieve a complete database. This will enable to characterize spoiled beer samples by performing MALDI-TOF analysis and comparing the MS profiles with the ones present in the database. This way breweries will be able to quickly anticipate to contamination and to avoid possible spoilage. |
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| last updated Mon 31 May 2010 00:00:00 |
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Probiotic administration as add-on therapy in ulcerative colitis and pouchitis (IWT-TBM)
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Promotor(s) : G. Huys
Period : 1/10/2007 - 31/12/2011
Staff : Margo Cnockaert (technician)
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| Description : A probiotic strain (Bifidobacterium breve UCP0911) was selected with anti-inflammatory properties and hence, important potential in the treatment of inflammatory bowel disease (IBD). During well-designed clinical trials, the potential of the selected probiotic in IBD patients (ulcerative colitis and pouchitis) will be fully explored. These clinical trials will aim at unravelling the basic interaction between microbial, immunological and genetic parameters in correlation with the clinical outcome, based on a rational multidisciplinary approach. |
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| last updated Fri 30 Sep 2011 10:34:00 |
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Prototype of a distributed FAME information system for improved identifications of Prokaryotes (Federal Office for Scientific Policy)
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Promotor(s) : B. De Baets, P. De Vos
Period : 01/12/2005 - 31/03/2008
Staff : B. Slabbinck (PhD)
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| Description : The project focuses on the integration of the fatty acid databases from several European microbiological research institutes. It demonstrates how previously unseen patterns can be learned from the information network, resulting in improved discriminatory power of fatty acid analysis for recognizing bacterial species. These findings will endorse the applicability of knowledge discovery in databases with the field of microbiology. |
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| last updated Fri 20 Apr 2007 11:51:00 |
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Quantification and management of the microbial diversity in ecosystems (GOA-BOF, University Ghent)
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Promotor(s) : P. De Vos & W. Verstraete
Period : 01/01/2002 - 01/01/2009
Staff :
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| Description : In this study a number of techniques that will evaluate bacterial diversity in ecosystems, both qualitatively and quantitatively, will be developed. The evolution of the bacterial diversity will be studied after introduction of biotic (pathogens, nitrifiers, etc.) and/or abiotic (pH, temperature, toxic substrates, and natural season-linked changes) factors. The activated sludge ecosystem has been chosen as first target for the study because it is well known at the one hand from the process operational point and from mathematical model building point, but hardly known at the other hand from the technical-microbial point. Because oxidation of ammonia and C-1 molecules is of great importance in the activated sludge and because the metabolic processes allow to be approached by molecular techniques, we will focus on these metabolic activities. Ammonia can only be removed from water by nitrification. During denitrification, which is the second step in the biological nitrogen removal, C-1 molecules (mostly methanol but also methane) are used as electron donor. 'In-depth' studies of both processes are based on new denitrifying and nitrifying isolates obtained via new approaches of isolation campaigns. |
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| last updated Fri 20 Apr 2007 11:10:00 |
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Renforcement des capacités institutionnelles du réseau des Collections Coordonnées Marocaines de Micro-organismes (CCMM) par valorisation des micro-organismes à potentiel biotechnologique (Belgian Technical Cooperation - Morocco)
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Promotor(s) : A. Willems & M. Amar
PI : P. Vandamme (Lactic Acid Bacteria in Moroccan dairy products)
PI : P. De Vos (Pathogenic pseudomonads)
Period : 5/2006 - 12/2012
Staff : Moroccan visiting scientists and students (M. Ouadghiri, PhD student - P. Vandamme, promotor)
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| Description : The aim is to reinforce and develop the CCMM network of Moroccan research groups by transfer of know-how with the Laboratory of Microbiology and the BCCM/LMG bacteria collection. In particular by valorisation of deposited strains en by elaboration of the collections through prospection in Moroccan ecosystems in the areas of health, agriculture and the evironment. |
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| last updated Thu 18 Aug 2011 10:53:18 |
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Roadmap towards a prokaryotic genomic taxonomy (FWO post-Doc)
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Promotor(s) : P. De Vos en Y. Van De Peer
Period : 1/10/2006 - 31/09/2009
Staff : Dirk Gevers (Post-Doc FWO)
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| Description : Basic questions on bacterial genome organization and evolution could not be addressed before the complete sequencing of two bacterial genomes. Today’s opportunities from the large number of available genomes reach much further and puts comparative genomics central in deducing patterns in genome evolution. Within this project we suggest building a bioinformatics toolbox that will allow us to formulate models on prokaryotic genome evolution on the one hand and to create a genomic taxonomy for prokaryotes in collaboration with the Centre for Molecular Phylogeny & Evolution on the other hand. |
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| last updated Fri 20 Apr 2007 11:45:00 |
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State-of-the-art techniques for the study of microbial biodiversity patterns in East Antarctica (BOF)
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Promotor(s) : A. Willems
Period : 16/03/2011 - 15/03/2013
Staff : Bjorn Tytgat (PhD student)
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| Description : Two state-of-the-art methods for the study of microbial communities will be implemented for use on Antarctic environmental samples: Automated Ribosomal Spacer Analysis (ARISA) and parallel-tagged pyrosequencing of ribosomal RNA genes. ARISA permits a thorough comparison of the microbial community in a large number of samples along a gradient of humidity and allows a well-founded selection of samples for pyrosequencing. |
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| last updated Thu 18 Aug 2011 11:00:01 |
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Study of the dominant colon microbiota with cystic fibrosis patients (BOF-UGent)
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Promotor(s) : P. Vandamme & G. Huys
Period : 01/01/2008-31/01/2012
Staff : Gwen Duytschaever (PhD student)
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| Description : This study aims to characterize the predominant members of the intestinal flora of a group of cystic fibrosis patients and to compare these with the microbiota of siblings without the cystic fibrosis phenotype. The effect of frequent and combined antibiotic use on the develoment of antibiotic resistances in the commensal colonmicrobiota of a group of cystic fibrosis patients will also be studied. |
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| last updated Fri 30 Sep 2011 10:30:00 |
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Sustainable methanotrophs: from ecology to microbial resource management (BOF-GOA)
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Promotor(s) : P. De Vos
Period : 01/01/2009 - 31/12/2014
Staff : Sven Hoefman (PhD student)
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Description : Methanotrophic bacteria play a vital role in reducing emissions of the greenhouse gas methane. These organisms are ubiquitous in nature and can use methane as sole carbon and energy source. This project focuses on the “microbial resource management” of methanotrophic communities. An interdisciplinary work strategy is followed, in which both LM-UGent and LabMET are involved.
In a first phase natural methane-oxidizing inocula are used to develop “high speed” and “high affinity” methanotrophic reactors. The methanotrophs will be isolated into pure culture from these reactors and from natural samples. The isolation of these fastidious organisms into pure culture has proven difficult and laborious. Therefore, new cultivation techniques will be explored. The isolates and communities form the basis of this research project.
Most of the knowledge known to date is limited to low affinity aerobic methane-oxidizers. However anaerobic and high affinity aerobic methane oxidation also occurs. These different processes will be explored. A combination of Stabile Isotope Probing (SIP), flow cytometry with phylogenetic probes and 16S rRNA gene sequencing will be utilized to identify and quantify the key players involved in methane oxidation in the communities. The isolated methanotrophs will be characterized polyphasically.
Once purified, the majority of methanotrophic isolates cannot be maintained using the standard long-term preservation techniques. Therefore, this project also explores the protective capabilities of different agents during preservation in combination with varying resuscitation media and preservation methodologies. These findings and the development of quality control tools could form the basis for preserving other fastidious organisms and methanotrophic consortia.
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| last updated Thu 20 Aug 2009 14:45:00 |
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The relationship between microbial diversity and the unique characteristics of Flemish 'Oud Bruin' beers
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Promotor(s) : P. Vandamme, A. Van Landschoot
Period : 01/09/2011 - 31/08/2015
Staff : Isabel Snauwaert
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| Description : Currently, the microbiota in 'Oud Bruin' beer fermentations is largely unknown. Therefore, it is impossible to describe and protect these beers. The aim of this project is to characterize the microbiota and metabolites of these beers through new high-throughput technologies. This will allow to develop generic and specific criteria for these beers and to deliver a quality control tool. |
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| last updated Tue 3 Jul 2012 00:00:00 |
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The role of photoheterotrophic and chemoautotrophic prokaryotes in the microbial food web in terrestrial Antarctica: a cultivation approach combined with functional analysis (FWO)
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Promotor(s) : A. Willems, K. Heylen, G. Huys, P. De Vos
Period : 01/01/2012 - 31/12/2015
Staff : Guillaume Tahon (phd student)
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| Description : In continental Antarctica, where ecosystems are dominated by microorganisms and the food webs are relatively simple, the main primary source of organic carbon (and energy) and fixed nitrogen for microbial communities is generally thought to be photosynthesis by cyanobacteria. In this project we will investigate the hypothesis that in such situations, alternative mechanisms for CO2 fixation and mechanisms for exploiting solar energy may exist and these will provide the energy required for nitrogen fixation. We will explore the diversity of several alternative mechanisms by studying the diversity of key genes for these processes. We will also perform a large-scale isolation campaign from selected terrestrial Antarctic samples to obtain bacterial cultures that harbour these alternative mechanisms. |
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| last updated Tue 27 Mar 2012 10:58:32 |
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Top-down and bottom-up controls in benthic food webs and their importance for the dynamics and functioning of meiobenthos and bacteria. (FWO)
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Coordinator : T. Moens
Promotor(s) : M. De Troch, A. Willems, R. Danovaro
Period : 1/01/2009 - 31/12/2012
Staff : Tania Nara Bezerra (PhD student, Biology Dept.)
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| Description : In this project processes structuring complex meiobenthic communities are studied, particularly, the role of the trophic (predator-prey) relationships and indirect interactions between species. Focus is on the role of predatory nematodes and copepods as possibly selective grazers of bacteria.
The trophic position of the most abundant nematode and harpacticoïd copepod species in selected marine and estuarine sediments, particularly from the intertidal zone, will be studied using natural stable isotopes of C and N and taking into account seasonal fluctuations. Food composition and preferences will be determined to elucidate trophic cascades in benthic food webs and to assess the impact of feeding on production, species composition and diversity of prey communities.
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| last updated Thu 18 Aug 2011 10:54:55 |
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Top-down and bottom-up controls in benthic food webs: effects of bacterivores and their predators on bacterial communities and implications for ecosystem functions (BOF)
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Coordinator : T. Moens
Promotor(s) : M. De Troch, A. Willems
Period : 1/01/2009 - 31/12/2012
Staff : Tania Nara Bezerra (PhD student, Biology Dept.)
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| Description : In this project processes structuring complex meiobenthic communities are studied, particularly, the role of the trophic (predator-prey) relationships and indirect interactions between species. Focus is on the role of predatory nematodes and copepods as possibly selective grazers of bacteria.
The trophic position of the most abundant nematode and harpacticoïd copepod species in selected marine and estuarine sediments, particularly from the intertidal zone, will be studied using natural stable isotopes of C and N and taking into account seasonal fluctuations. Food composition and preferences will be determined to elucidate trophic cascades in benthic food webs and to assess the impact of feeding on production, species composition and diversity of prey communities.
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| last updated Thu 18 Aug 2011 10:55:51 |
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Understanding biodiversity effects on the functioning of marine benthic ecosystems (GOA)
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Coordinator : M. Vincx
Promotor(s) : K. Sabbe, T. Moens, A. Willems, A. Vanreusel
Period : 01/01/2011 - 30/11/2016
Staff : Helen Decleyre (PhD student), Evie De Brandt (Technician)
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Description : The combination of high biodiversity in complex, multilevel food webs and pronounced small-scale heterogeneity in abiotic, biotic and functional features makes marine sediments ideal model systems for studying biodiversity-ecosystem function relations in both in situ and laboratory experimental conditions.
In this project we will investigate how small-scale heterogeneity on the one hand and horizontal and vertical, multilevel interactions on the other affect biodiversity ecosystem-function relations. We will target several important functional properties of marine sediments and their diverse inhabitants and combine field studies and micro- and mesocosm experiments using functionally well-characterized, naturally co-occurring groups of organisms. |
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| last updated Tue 24 Jan 2012 11:50:59 |
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VALORizing Andean Microbial Diversity through sustainable intensification of potato-based farming systems (VALORAM) EU (Framework VII)
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Coordinator : Université catholique de Louvain (UCL)
Promotor(s) : P. De Vos
Period : 01/02/2009-31/01/2014
Staff : Jonas Ghyselinck (PhD student)
Website : http://valoram.ucc.ie/
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Description : The objectives of this project meet the call goals of exploring and valorizing Andean soil microbial diversity for the development of alternative eco-efficient technologies and crop management knowledge in order to improve the sustainability and productivity of Andean cropping systems benefiting poor rural farming households. The participants will use state of the art methods including metagenomic, genomic, proteomic and metabolomic analysis to identify novel traits of microorganisms, and characterize beneficial soil microbial communities, which can be exploited to achieve the call goals. While the aims are to exploit the potential of Andean microorganisms and microbial communities for the benefit of subsistence farmers in the Andean region, the methodology and findings will also have potential for application to sustainable (organic/biological) production in the EU.
Main contributions for LM-UGent are
- Isolation and identification of indigenous potato endophytes and rhizosphere bacteria in traditional potato fields.
- Long-term maintenance of isolated bacteria in reputed EU germplasm collections and duplicates in local repositories.
- Isolation, screening and characterization of the isolates for beneficial traits such as plant growth promotion and disease alleviation under ex-situ controlled conditions.
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| last updated Tue 27 Jul 2010 13:03:00 |
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