Microbiology throughout VIB

18 March 2018

​The Sofie Goormachtig group focuses on the fascinating world of plant-microbe interactions
Soil is extremely diverse in terms of microbial life, and it is fascinating that roots engage in mutualistic interactions with some of these, but repel others. We still have no clear idea how this discrimination works. In nutrient-poor environments, plants heavily rely on microorganisms for growth. A key example are legumes that grow as pioneer plants in poor soils but require symbioses with nitrogen-fixing rhizobia in order to do so. Plants even develop new organs: the nodules to host the microbes! Plant roots communicate with surrounding microbial life through chemical signal exchanges. We only know little about the language they speak.

Sofie Goormachtig (VIB-UGent Center for Plant Systems Biology): “Communication is the basis of life. Without excellent communication, you do not survive, or you stay very unhappy. Just look at humans… The same holds true for plant roots communicating with the surrounding microbial life.”

Crop protection via single domain antibodies
Chemical crop protection is still widely used to control plant diseases, despite its adverse effects on human health, and on environment and resistance development on the pathogen side. In that context, the Bruno Cammue Lab (KU Leuven and VIB-UGent Center for Plant Systems Biology) investigated, in a joint effort with the VIB spin-off company AgroSavfe, the potential of camelid single domain antibodies (VHHs) to control plant diseases. VHHs were generated that specifically bind to fungal glucosylceramides (fGlcCer), known through the Cammue lab’s research as specific binding sites for the antifungal plant peptides termed plant
defensins and important pathogenicity factors. In vitro these anti-fGlcCer VHHs were shown to inhibit the growth of one of the most devastating fungal plant pathogens, Botrytis cinerea, as well as reduce disease caused by this pathogen on tomato leaves. This data supports the potential of the VHH-based approach as an alternative strategy to combat plant diseases.
De Coninck et al., Front. Microbiol. 2017

First Belgian Germfree and Gnotobiotic mouse facility opened in Ghent
The VIB-UGent Center for Inflammation research (IRC) has successfully launched a germfree mouse facility, through the joint efforts of VIB, UGent and UZ Gent. The facility represents a great asset for studying physiological and immunological functions related to microbiota. Many inflammatory, metabolic and even neurological disorders are characterized by distinct shifts in microbiota composition (termed ‘dysbiosis’). Using germfree and gnotobiotic mouse technology, we are now able to perform functional causality studies
in a plethora of disease models. The facility is coordinated by Lars Vereecke. (VIB-UGent Center for Inflammation Research).

Stimulating root development and nutrient acquisition by interfering with the soil microbial community
In the Root Development Group of Tom Beeckman (VIB-UGent Center for Plant Systems Biology), one research topic focuses on the role of the plant root system in soil nutrient acquisition and its plasticity to
increase nutrient access. The microbial community in agricultural soils is being recognized as a major contributor to changing plant nutrient levels. Taking the microbiome contribution into account, the final goal is to identify new strategies to improve fertilization and nutrient use efficiency by plants. A more elaborate description of such strategies has recently been published in Current Opinion in Biotechnology.
Beeckman et al., Curr. Opin. Biotechnol. 2018

A link between the microbiome and neurological diseases
Over the last few years, the impact of the gut microbiome on our health, including neurological manifestations and referred to as gut-brain axis, has been increasingly recognized. Roosmarijn Vandenbroucke (VIB-UGent Center for Inflammation Research) reports that gastric Helicobacter suis colonization in mice is associated with behavioral changes, including cognitive decline. Analysis of the mechanisms revealed that this is due to breakdown of the gastrointestinal barrier, increased leakage of TLR4 ligands in the periphery and subsequent loss of brain barrier integrity, specifically at the blood-cerebrospinal
fluid (CSF) barrier.

Emerging evidence is pointing to a crucial role for the microbiome in Parkinson’s disease. PhD student Arnout Bruggeman will soon start a placebo-controlled randomized clinical trial of fecal microbiota transplantation in Parkinson’s disease patients in close collaboration with Debby Laukens (Gastroenterology, UZGent) and Patrick Santens (Neurology, UZGent). Microbiome analyses will be done in collaboration with the Jeroen Raes lab (VIBKU Leuven Center for Microbiology). The ultimate goal of this project is to address the impact of
microbiota on motor and non-motor Parkinson’s disease symptoms and progression.
Gorlé et al., Brain Behav. Immun. 2017

Structural molecular biology of bacterial cell surfaces
The Han Remaut Lab (VIB-VUB Center for Structural Biology) looks at bacterial cell surface components
and processes because of their prime role in bacterial physiology and host-pathogen interaction on the one hand, and as a source for new biomaterials and biotech applications on the other hand. “In the Structural & Molecular Microbiology group, protein structure and function studies are deeply rooted in their (micro) biological context, reflecting my dual interest and training in biology and biochemistry”, says Han. Main topics include chronic and inflammation-associated colonization by pathogenic Escherichia coli and Helicobacter pylori, and bacterial amyloid assembly and biotechnology.


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Germ free facility