Research team
Expertise
My expertise focuses on exploring the potential of beneficial bacteria or probiotics for the upper respiratory tract. This includes the isolation and screening of potentially beneficial bacteria, microbiome analysis of the airways and bacteria-host interaction assays. I also have ample experience in organizing human clinical studies in relation to the microbiome.
Insights into the lifestyle and adaptation factors of Dolosigranlum pigrum as probiotic for the upper respiratory tract.
Abstract
The upper respiratory tract (URT) is a key habitat of the human microbiome, but it is currently underexplored compared to other body sites, especially at the functional level. URT diseases such as chronic rhinosinusitis (CRS) form leading causes for antibiotic prescription, while the functional role of bacteria in the disease pathology is still not clear. As such, CRS is a microbial disease needing new insights in functional biology and microbial ecology to design novel therapeutic strategies. Based on microbiome sequencing of the URT, the underexplored lactic acid bacterium Dolosigranulum pigrum is associated with URT health, highlighting its potential as URT probiotic. Nevertheless, fundamental and molecular research is lacking on its beneficial mechanisms of action, and on its ecological and adaptation mechanisms in the human nasal cavity. This project will therefore focus on exploring the biology and metabolic properties of D. pigrum strains isolated from healthy URT samples, using comparative genomics, phenotypic screening assays and fluorescent microscopy techniques. In addition, the barrier-enhancing and anti-inflammatory properties of D. pigrum isolates will be evaluated in complex in vitro cell culture systems. In parallel, molecular biology tools will be used for further molecular characterization of the isolated strains' mechanisms of action. Finally, the most promising D. pigrum strains will be evaluated in murine models relevant for CRS.Researcher(s)
- Promoter: Lebeer Sarah
- Co-promoter: Vanderveken Olivier
- Fellow: De Boeck Ilke
Research team(s)
Project type(s)
- Research Project
Functional insights into host-microbe interactions in the upper respiratory tract through metagenomic sequencing and fluorescence microscopy.
Abstract
Chronic rhinosinusitis (CRS) is a common upper respiratory tract (URT) disease with a major socioeconomical impact linked to URT microbiota perturbations. Current treatment options often fail so the need for alternative treatment options based on better insights into the URT microbiota is high. This is reflected by the widespread interest in this topic, not only by the scientific and medical world, but also by the patients themselves. During my PhD project and in the final of "De Vlaamse PhD Cup 2020", I have been very committed to actively engage CRS patients in my research and got to know the needs of many patients. Their willingness to test alternative microbiota-based treatment options convinced me of the urgency for generating insights leading to such novel treatments. In this project, I propose to implement novel state-of-the-art techniques that will enable in depth insights into the URT microbiota and its relation with the human host. In order to do this, I propose the optimization of shotgun metagenomic sequencing for low biomass URT samples to allow better taxonomic resolution and functional characterization of the microbial communities. In addition, I will use fluorescent in situ hybridization in combination with immunohistochemistry to gain insights into the human host-bacteria behavior, as well as bacterial interspecies interactions. These insights can contribute to overcome some of the limitations in the URT microbiome field. One important research gap is for instance that it remains very difficult to determine what defines a balanced microbiota and we still do not know whether a microbial imbalance is a cause or a consequence in CRS and associated inflammation. This is mainly because most 16S amplicon sequencing techniques remain descriptive. They don't allow functional characterization and identification up to microbial species or strain level, while pathogenicity and probiotic potential are expressed at strain level. Hence, in this project, the goal is to obtain new insights in the possible driving force of the microbiome in CRS. The implementation of these techniques can help to develop better treatment strategies based on beneficial microbiota members and can help to determine which patients might benefit the most from such therapy. In addition, the shotgun sequencing and microscopy pipelines developed in this project are an important stepping stone for my upcoming FWO junior postdoc proposal, and can also be implemented in the Centre of Excellence Microbial Systems Technology of the University of Antwerp.Researcher(s)
- Promoter: De Boeck Ilke
Research team(s)
Project type(s)
- Research Project
Study of the microbiota and the potential of probiotics in chronic rhinosinusitis
Abstract
Upper respiratory tract (URT) infections have a major impact on public and animal health with a high incidence in Flanders. Moreover, these infections predispose to lower respiratory tract and lung infections, which have a higher impact on health worldwide than all other infectious diseases combined. The study of the microbiome and the investigation of new possible bacterio- and probiotic therapies can deliver additional first in line solutions, which will eventually lead to lower antibiotics usage.Researcher(s)
- Promoter: Lebeer Sarah
- Co-promoter: Vanderveken Olivier
- Fellow: De Boeck Ilke
Research team(s)
Project type(s)
- Research Project