Head of the lab
Sarah did a master in Bioscience Engineering: cell and gene technology (major) and food & health (minor) at KU Leuven and graduated in 2004. She then did her PhD research at the Centre of Microbial and Plant Genetics of the KU Leuven under the supervision of Prof. Jos Vanderleyden and Dr. Sigrid De Keersmaecker. Since her master thesis, she has been studying probiotic bacteria, with Lactobacillus rhamnosus GG (LGG) as model probiotic strain. In her PhD research from 2004-2008, she has mainly explored molecular adaptation and probiotic factors for the application against inflammatory bowel diseases. In her postdoc research, she has first worked on protein glycosylation in lactobacilli and then switched to vaginal lactobacilli and mucosal immunology. Thanks to a joint research project (Centre of Excellence) with Prof. J. Balzarini and Prof. D. Schols from REGA at KU Leuven, she became interested in how vaginal lactobacilli could inhibit viral pathogens such as HIV and HSV. In 2011, she started as a research professor at the University of Antwerp, within the Department of Bioscience Engineering and Faculty of Science. She is responsible for the educational line on cell- and gene biotechnology within bioscience engineering. In 2012, she started the Laboratory of Applied Microbiology and Biotechnology in the research group ENdEMIC (Environmental Ecology and Applied Microbiology) of Prof. R. Samson. Her main research interests are still probiotic bacteria and their molecular modes of action, but now especially probiotic applications outside the human gut, including animals and the plant phyllosphere. Since 2016, she is an academic board member of the International Scientific Association on Probiotics and Prebiotics (ISAPP).
Ines is trained as a biomedical laboratory technologist (Artesis Plantijn University College Antwerp, Belgium). After a first position at the Dendritic Cell Bank of the Laboratory of Molecular and Cellular Therapy at the Vrije Universiteit Brussel (Belgium), Ines found her spot at the LebeerLab since 2015. Currently, Ines leads the wet lab experiments in different service research projects in collaboration with several industrial partners, and supports the experimental research of the Ph.D. students and postdocs of the LebeerLab. She coordinates the Illumina MiSeq external services, starting from the wet lab preparations to the sample loading. Together with her fellow lab technician Leen, she runs the lab’s administration, logistics, and stock management.
Leen joined the LebeerLab from the very start in 2012. As a Bachelor in Agro- and Biotechnology she takes care of the administrative, logistic, and technical tasks in and around the lab and the field for the complete ENdEMIC research group. Leen supports the experimental research of the Ph.D. students and postdocs of the LebeerLab. She has a special focus on the safety and well-being of her coworkers.
Ilke has completed her studies of Bioscience Engineering in Cell- and Gene Biotechnology with a minor in Applications for Human Health Engineering at the KU Leuven in 2014. After she graduated, she started her PhD at the University of Antwerp in the LebeerLab, entitled ‘Study of the upper respiratory tract microbiota and the potential of probiotics in the management of chronic rhinosinusitis’. Her PhD was performed in close collaboration with the ear, nose and throat department of the Antwerp University Hospital, led by prof. Olivier Vanderveken (co-promotor of her PhD). In November 2019, she successfully obtained her PhD. Currently, she works as a postdoctoral researcher in the LebeerLab with a main focus on the research line on the potential of probiotics for the upper respiratory tract.
Sandra performed her MSc thesis at the Belgian Universities of Brussels, Leuven, and Antwerp, studying the role of putative lectines from Lactobacillus rhamnosus GG and their potential role in pathogen exclusion. Afterwards, she started a Ph.D. within the framework of the MELiSSA project (Micro-Ecological Life Support System – European Space Agency) in collaboration with the University of Mons (Belgium) and the Belgian Nuclear Research Center (SCK-CEN). She investigated the quorum sensing system of Rhodospirillum rubrum S1H, a bacterium colonizing the second compartment of the MELiSSA loop. After her promotion in 2016, Sandra joined the LebeerLab in 2018 as a postdoctoral researcher. Her main expertise relies on genetic engineering and probiotics research. Currently, Sandra is developing projects for capacity building on probiotics and microbiome research in Peru.
Eline graduated as a Master in Bioscience Engineering with specialization in Cell and Gene Biotechnology and minor in Catalysis at the University of Leuven (Belgium) in 2014. She soon after started her PhD at the LebeerLab at the University of Antwerp (Belgium). Her PhD about topical Lactobacillus applications for modulation of the vaginal and skin microbiota was successfully completed in 2019. She is currently working as a postdoc in the Lebeerlab and continues to work on the vaginal microbiome and the application of lactobacilli in the vagina.
Irina obtained a joined Ph.D. degree in Bioscience Engineering in 2018 at the Catholic University of Leuven (Belgium) and the University of Antwerp (Belgium). Her thesis focused on the oral and intranasal application of genetically modified probiotics in mouse models of allergic asthma to modulate airway function and inflammation, and the gut microbiome. Currently, she works as a postdoctoral researcher at the LebeerLab, interested in the immunomodulatory and anti-pathogenic effects of topically applied probiotic lactobacilli in the respiratory, vaginal and skin niches. She implements in vitro models of skin and vaginal infection (e.g. Staphylococcus aureus, GBS) alongside mouse models of viral respiratory diseases (e.g. RSV). In addition, she is interested in genetic manipulation of probiotic lactobacilli for heterologous (e.g. fluorescent) protein expression, and in microbiome modulation by probiotics in health and disease.
Dieter obtained a Master in Bioscience Engineering with a specialization in Cell and Gene Biotechnology at the University of Leuven (Belgium) in 2010. That year he started a Ph.D. at the Laboratory of Gene Technology (KU Leuven) under the guidance of Prof. Rob Lavigne, and the Laboratory for Drug Delivery and Disposition (KU Leuven) led by Prof. Guy Van den Mooter. In this Ph.D. research he studied the processability of bacteriophages into a dry inhalable powder formulation using spray drying as an option to tackle bacterial lung infections in cystic fibrosis patients. After his promotion in 2015, he joined the LebeerLab as a postdoctoral researcher with a focus on environmental probiotics, genetic improvement of novel probiotic strains, and the pharmaceutical processing of probiotics. In 2018, Dieter received a scholarship for the Japanese Society for the Promotion of Science (日本学術振興会) to perform genetic research at the Institute for Biomedical Sciences of the Shinshu University (信州大学) in Japan, under the guidance of Prof. Takeshi Shimosato. Anno 2019, he returned to the LebeerLab, supporting the genetic, environmental, and pharmaceutical processing research lines.
Marianne has completed her studies of Bioscience Engineering with specialization in Cell and Gene Biotechnology and minor Industrial Microbiology at the University of Leuven (Belgium) in 2012. In 2013, she started a Ph.D. at the University of Antwerp (Belgium) at the LebeerLab about the in vitro and in vivo probiotic potential of Lactobacillus spp. for otitis media which she successfully finalized in 2018. At this moment, she is working as a postdoc in the LebeerLab with a focus on the potential of several probiotics for upper respiratory tract diseases and the impact on the local microbiome.
Sarah finished a Master in Forensic Biomedical Sciences at the KU Leuven (Belgium), after which she started her Ph.D. at the LebeerLab in October, 2018. Her research mainly focuses on women’s health and safety. She studies the stability and dynamics of the female microbiome (vagina, skin, and saliva) in Flanders. In addition, she focuses on isolation and characterisation of beneficial vaginal lactobacilli for probiotic purposes. Finally, Sarah is interested in the application of the microbiome in forensic cases through microbial fingerprinting and classification models. She hopes her research contributes to improving women’s health through microbial management and cutting-edge microbiome analyses.
Eline graduated as a Master in Bioscience Engineering with a specialization in Cell and Genebiotechnology at the KU Leuven (Belgium). She started her Ph.D. at the LebeerLab in 2019 after doing her master’s thesis here. She studies the potential and molecular mechanisms of beneficial lactic acid bacteria in mucosal disorders. The improper use of antibiotic treatments is a leading cause for the selection of multidrug resistant bacteria, which in turn can have an effect on the outcome of many diseases. Within her Ph.D. research, Eline will develop topical probiotic formulations for the treatment of cystic fibrosis patients as an alternative for antibiotics.
Max completed his Master of Biomedical Sciences with a specialization in Environmental and Health Sciences at the University of Antwerp in 2019. He performed his master’s thesis at the LebeerLab investigating the capacity of leaf-associated bacteria to biodegrade volatile organic compounds in the air. Due to his interest in environmental health in relation to air pollution, he now continues this research path in a Ph.D. on the biodegradation of air pollutants, mainly focusing on polyaromatic hydrocarbons. This research includes the isolation, molecular and genetic characterization, and appliance of biodegrading bacteria as an innovative solution to mitigate air pollution.
Lize has completed her Marster in Bioscience Engineering with specialization in Cell and Gene Technology at the KU Leuven (Belgium) in 2018. She started her Ph.D. at the LebeerLab in 2019 and studies the skin microbiome and the potential of topically applied lactobacilli for the treatment of chronic inflammatory skin disorders. The main focus of her research is to find and test a topical probiotic for atopic dermatitis. Among all medical specialties, dermatologists prescribe long-term antibiotic treatments the most. Alternatives for antibiotic treatments in dermatology are therefore highly needed and will contribute to the fight against multidrug-resistant bacteria.
Jelle finished a MSc in Bioscience engineering with specialization in Cell and Gene technology at KU Leuven in 2019. He completed his MSc thesis at the laboratory of gene technology (LoGT) at KU Leuven (under the promotership of Prof. Joleen Masschelein and Prof. Rob Lavigne), where he investigated the biosynthetic potential of plant-associated bacteria. Due to his interest in natural product biosynthesis and human health, he started a Ph.D. in 2020 at the LebeerLab. Certain members of the Lactobacillus Genus Complex are known to produce interesting compounds which have beneficial effects on human health. During his doctorate, Jelle will study these compounds on the genetic and molecular biological level and try to uncover the underlying mechanisms behind these beneficial effects with the aim to characterize novel probiotics.
Tom started his Ph.D. in the LebeerLab in 2019, after completing his Master in Bioscience Engineering at the KU Leuven, with a specialization in Cell and Gene Biotechnology and a minor in Bioinformatics. Using a dual approach of biotechnology and bioinformatics, he will search for novel biotechnology applications of the Lactobacillus Genus Complex, such as a novel cellulase and novel NRPS systems.
Jennifer joined the LebeerLab in 2016 on the ProCure project, after completing her Master studies in Biomedical Science with a focus on infectious disease research. Her Ph.D. research aims to compare the upper respiratory tract microbiome of children with and without chronic otitis media with effusion (i.e. mucus-accumulation in the middle ear cavity for >3 months) and to find novel beneficial bacteria for human upper respiratory tract health.
Marie completed her Master in Bioscience Engineering at the KU Leuven (Belgium) in 2015. After sailing the oceans during one year and starting up a permaculture project in Portugal, she started her Ph.D. at the LebeerLab in 2019. Here she studies the microbial communities on the above ground surfaces of plants, known as the phyllosphere microbiome. Microbes on the phyllosphere interact closely with each other and with the host plant. This might be more clear in the case of diseases, but many mutually beneficial bacteria-plant interactions exist. Her Ph.D. aims to find novel and sustainable solutions to protect crops against diseases by using beneficial microbes extracted from the phyllosphere.
Babette has completed her Master in Biology with a specialization Biodiversity: Conservation and Restoration at the University of Antwerp (Belgium) in 2017. After doing a thesis at the Laboratory of Environmental & Urban Ecology, led by Prof. Roeland Samson, she started her Ph.D. in April 2018, with Prof. Sarah Lebeer as co-promotor. Her research mainly focuses on the phyllosphere and finding the best plant-phyllosphere bacteria combination as an innovative solution to mitigate outdoor air pollution.
Wannes has completed his Master in Biology with a specialization in Cell and Systems Biology at the University of Antwerp (Belgium) in 2016. He then started his Ph.D. in the LebeerLab on the diversity, ecology, dynamics, and niche specialization of different Lactobacillus species in fermented carrot juice as a model ecosystem.
Stijn did a Master in Bioinformatics at the KU Leuven (Belgium) and afterwards started his joined Ph.D. at the LebeerLab and the group of Prof. Vera van Noort (KU Leuven, Belgium) in 2016. His main project is the study of the taxonomy, ecology, and evolution of Lactobacillus bacteria using publicly available genomes, 16S rRNA and metagenomic data. He is interested in what the natural habitats/lifestyles of these bacteria are and how they adapted. In addition, Stijn provides computational analyses for various projects related to the human microbiome research within the lab, mainly for the human upper respiratory tract and female reproductive system. He does exclusively computational analysis, using primarily R and python.
External Ph.D. Students
Eline graduated as a Master in Pharmaceutical Sciences with a specialization in Drug Development. Afterwards, she started her Ph.D. at the lab Pharmaceutical Technology and Biopharmacy at the University of Antwerp. The aim of her project is to formulate a pharmaceutical tablet for the pharyngeal delivery of probiotic bacteria. The development of a successful probiotic tablet formulation is a substantial challenge due to the stress of the compression process. Therefore, the main focus of her research is to optimize the survival rate of the probiotic bacteria during tablet production by investigating the influence of the formulation and process parameters. Her research is in collaboration with the LebeerLab and is supported by the research foundation – Flanders (FWO).
Katarina joined the LeBeerLab and Laboratory of Pharmaceutical Technology and Biopharmacy on the ProCure project in 2017 after completing her Master of Pharmacy studies and an industrial experience. The aim of her PhD is formulation development and process up-scaling for production of pharmaceutical dosage forms containing novel beneficial bacteria in order to prevent or reduce upper respiratory tract infections.
Charlotte obtained her Master degree in Biomedical Sciences with a special focus on basic and translational research at the KU Leuven (Belgium) in 2017. In that same year, she started a joined Ph.D. at the LebeerLab and the interdisciplinary bioscience group of the Belgian nuclear research center, SCK•CEN (Mol, Belgium). Here, she studies microbial therapies including Limnospira indica PCC 8005 and Lactobacillus rhamnosus GG ATCC 53103 to combat gut microbial dysbiosis during pelvic irradiation.