Urogenital tract

Women’s health, including the health of newborns and children, is closely linked to the female urogenital microbiome. These microbes play a role in vaginal disease prevention, successful fertilisation, and healthy pregnancies. Lactobacilli are keystone beneficial bacteria in the vagina, but we know little about their molecular modes of action and the variety of species and strains that can occur in this human body site. Therefore, we aim at benchmarking the vaginal microbiome and its influencing factors in Flanders, and collect microbiome data that can be applicable in areas from diagnostics, therapeutics, to forensics. Furthermore, beneficial lactobacilli are isolated and functionally characterised for future probiotic purposes, based on their anti-pathogenic, adhesive, and immunomodulatory properties (Isala).


Respiratory tract

The presence of beneficial microbes in the upper respiratory tract has been an early research focus of the LebeerLab (Procure). Many microorganisms can help to maintain a healthy homeostasis in different parts of our respiratory tract. We focus on the development of probiotics to target multiple respiratory tract diseases, including chronic rhinosinusitis, viral infections, otitis media, airway allergies, and cystic fibrosis. By sequencing and analyzing microbial communities in healthy and diseased human airways, we aim to unravel the niche-specific role and health-promoting potential of beneficial bacteria, such as lactobacilli and streptococci. Anti-pathogenic, barrier-promoting, and immunomodulatory mechanisms of probiotics for the respiratory tract are explored in vitro and in vivo, in animal models and clinical studies.



Evidence is growing that many common inflammatory skin conditions, such as acne vulgaris and atopic dermatitis, are associated with an altered skin microbiome. We focus on the analysis of microbial communities on healthy and diseased skin. In addition, we explore the potential of beneficial lactobacilli in inhibiting skin pathogens, enhancing the skin barrier, and exerting immunomodulatory effects on the skin cells. Our lab has played a founding role in the biotech company YUN. Together, we could already show that topically applied live lactobacilli have promising results for the treatment of acne based on clinical effectiveness and skin microbiome modulation.



The above ground parts of the plant, the phyllosphere, are occupied by diverse microbial communities. We study the effect of environmental factors and urban land use, air pollution in particular, on phyllosphere microbial communities. We also search for beneficial bacteria on the phyllosphere that can protect agricultural crops against diseases, and as such can play a role as a natural and ecological alternative to chemical pesticides and herbicides.

Ferme pekes

Fermented foods

We study the diversity and ecology of the microbial community residing in plant-based fermented foods, with a focus on lactic acid bacteria. Not only are these plant-based fermentations a good source of untapped diversity of lactobacilli, but they are also a good, robust, and simple model ecosystem for ecological and evolutionary studies. In addition, these plant-based fermentations also function as tasty alternative probiotic carriers and matrices. The first novel fermented food succesfully studied in the lab was fermented carrot juice, thanks to an inspiring collaboration with chef Kobe Desramaults. This has stimulated the set-up of a Citizen Science project ‘Ferme Pekes’, in which 40 home fermenting enthusiasts participated (Ferme Pekes).



The molecular mechanisms supporting probiotic effects are not always well understood. We aim to elucidate the mechanisms of action of our most interesting probiotic strains at the genetic and molecular level. Using genetic engineering, probiotics can be selectively ameliorated to create enhanced strains, or to produce industrially interesting and health-beneficial substances such as cellulases, chitinases, and antimicrobial substances. To achieve this goal, in-house designed genetic tools based on phages and natural plasmids are used. In addition, loss of function mutants are created, because their phenotype can learn us a lot of new things about the importance of the inactivated gene.


Lactobacillus taxonomy

Taxonomy is an important tool in biology that allows us to organize organisms in hierarchical groups that reflect shared ancestry and shared characteristics. Using our bio-informatic and ecological knowledge on lactobacilli, we contribute to the revised taxonomy of lactobacilli. Our goal is to achieve species and genera that are monophyletic and biologically meaningful, and have a consistent size. We believe that the revised taxonomy will boost the rational selection of lactobacilli for different human, animal, food, and plant habitats and associated applications.

bacteria (1)-min

Lactobacillus habitat-adaptation

Species of Lactobacillus follow a variety of lifestyles, ranging from free-living to strictly host-adapted. It seems that different Lactobacillus ancestors have independently adapted to the same lifestyle on multiple occasions. We are studying how these ancestors adapted, and what adaptations they have in common within a given lifestyle. Ultimately, the aim is to be able to predict lifestyle from the genome, without relying on functional annotation.