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 Lacticaseibacillus 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). In 2019, she was awarded an ERC starting grant to explore the beneficial potential of lactobacilli (Lacto-Be, grant agreement ID: 852600). She is very grateful to ERC that she could extent the eligibility period with 1.5 year per child. This grant is game-changing: it is the first fundamental research grant in the group to explore the ecology, evolutionary history and core mechanisms behind the beneficial potential of lactobacilli.
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.
Nele started at the LebeerLab as an internship student on the Isala project (www.isala.be). During this internship, she studied the vaginal microbiome under the main supervision of Sarah Ahannach and Ines Tuyaerts. In the summer of 2020, she graduated as pharmaceutical and biological laboratory technician at the UCLL (Leuven, Belgium). In that same summer, she helped with the assembly of kits and wetlab for Isala as a job student. In October 2020, she started officially as a fully employed lab technician, still assisting in the Isala project, but now also in many other academic and industrial projects. Together with the other lab technicians, Leen and Ines, she is also responsible for the maintenance of the lab and lab equipment. Her main technical expertise is microbial growth experiments, microbiome sequencing and cell culture.
Camille graduated as a Master in Bioscience Engineering with a major in Cell and Gene Biotechnology and minor in Human Health Engineering at the University of Leuven (Belgium) in 2014. She did her master thesis research in the Lab of Gene Technology (KU Leuven), led by prof. Rob Lavigne, on bacteriophage therapy. Afterwards she started her PhD research at the LebeerLab at the University of Antwerp (Belgium) on glycomolecules of Lactobacillus and their interaction with Candida, together with prof. Peter Delputte from the faculty of pharmaceutical and biomedical sciences as copromotor. Camille completed her PhD in June 2019 and started working as a consultant in the in vitro diagnostics industry. In 2020, she returned to academia as a research manager in the group of prof. Filip Meysman (University of Antwerp, Belgium), leading large-scale citizen science project CurieuzeNeuzen. She rejoined the team of the LebeerLab in April 2022 part-time as a postdoc working on female health and the Isala citizen science project. She is also helping to set out the spin-out trajectories of the lab.
Dr. Peter Bron
Peter earned a Master’s Degree in Molecular Sciences from WUR (Wageningen, the Netherlands) in 1999 and continued his research career as a PhD student within TI Food & Nutrition (Wageningen, the Netherlands) on the molecular response of Lactiplantibacillus plantarum during intestinal passage. He has been working in the scientific area of host-microbe interactions ever since and succeeded his career with a 2.5-year post-doc at UCC (Cork, Ireland) investigating Listeria monocytogenes temporal gene expression profiles during infection. In 2007 he returned to TI Food & Nutrition as a post-doctoral researcher in a project on fermentation-enhanced probiotic function. Subsequently, he obtained a senior scientist position within the fermentation workgroup at NIZO (Ede, the Netherlands). In this role he was responsible for a portfolio of contract research projects investigating genetics, genomics and fermentation aspects of probiotic and starter cultures. From 2010-2013 he was programme director of the LAB programme within the Kluyver Centre for Fermentation and Genomics. in 2014 he was one of the principal investigators that co-founded flagship 10 within the BE-Basic consortium that aimed to develop natural methods for strain improvement for the food industry. Peter has been daily supervisor and co-promotor of 10 PhD students and his work has so far resulted in over 70 peer-reviewed publications and 5 patent fillings. Besides his current part-time position as a guest researcher at the university of Antwerp, Peter is an independent consultant offering his genetic and probiotic expertise to the food and health industry.
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 Lacticaseibacillus 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.
Thies joined the LebeerLab as a PostDoc in February 2021. With a Bachelor in computer science at the Heriot Watt University in Scotland, and a Master’s and PhD in bioinformatics (from the TU Delft in The Netherlands), he has a computational background. Previously, he has worked on far flung themes from machine learning, the genetics, epigenetics and transcriptomics in mushroom formation, to the (inherited) genomic factors influencing longevity and the metabolomic and transcriptomic effects of metabolism in healthy ageing. In the LebeerLab, he is working on the ERC Lacto-BE project, investigating the role of lactobacilli across human, fermentative and artificial niches. Notably on the vaginal microbiome within the Isala study.
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.
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.
Wenke started her research by looking for airborne bacteria degrading pollutants in city air. This soon shifted to the research of the bacterial communities on the leaf surfaces in the city (as they are quite different from those in nature). As a postdoctoral researcher at the University of Berkeley, in the labs of Prof. B. Koskella & Prof. S. Lindow, Wenke focused her research more on the fundamental ecology of the leaf communities, which is essential to understand how to shift microbiomes into a healthier state. Now she’s continuing this work in the LebeerLab hoping to one day harness leaf bacteria to benefit both plants and people in urban environments.
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.
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. He is now a postdoc in the lab of prof Maria Marco (UC Davis)
Stijn obtained a master’s degree in bioinformatics from the KULeuven in 2016. He did a joint PhD between the Lebeer Lab and the van Noort group (KULeuven) and is now continuing his research as a postdoctoral researcher at the Lebeer Lab. Stijn studies the ecology and evolution of Lactic Acid Bacteria (LAB) by comparing genome sequences from public databases and in-house isolates of the lab. He develops software to gain new types of insights from these datasets, or to process them on a larger scale. He then applies these novel computational tools as well as existing tools to study how different species of LAB are related to each other, how they adapted to different lifestyles (e.g., free-living vs host-adapted) and how they interact with their viruses and other mobile genetic elements. In addition, he implements pipelines and writes software for the analysis of microbial community data generated within the lab; both for amplicon and metagenomic shotgun sequencing data. Finally, he is involved in the Isala project on the female 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.
Caroline has completed her Master in Bioscience Engineering with a major specialization in Cell and Gene Technology and minor specialization in Molecular Biology at the KU Leuven (Belgium) in 2021. She had already performed a genetic engineering-oriented Bachelor and Master thesis under the guidance of Tom Eilers at the LebeerLab. Soon after graduating, she obtained her own FWO-SB Ph.D. fellowship to study vitamin production in lactobacilli sourced from other environments than the gut. She now focuses on methods to genetically improve their production level the potential and wants to explore the beneficial impact of vitamin producing lactobacilli in the human body. Finally, Caroline is interested in using these promising lactobacilli to lower vitamin deficiencies worldwide and use them as living carriers for vaccines or human biotherapeutics.
Tom started his Ph.D. in the LebeerLab in 2019 on the ERC Lacto-Be project, after completing his Master in Bioscience Engineering, with a specialization in Cell and Gene Biotechnology and a minor in Bioinformatics. In this ERC project, he will study the habitat adaptation and the dominance of Lactiplantibacillus and Leuconostoc in vegetable fermentations with a combination of multi-omics and genetic engineering. Next to this ecological study, he will also characterize potential industrial applications derived from specific Lactiplantibacillus and Leuconostoc isolates.
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.
Jari obtained his Master in Bioscience Engineering with specialization in Environmental technology at the University of Ghent in 2021. He conducted his master thesis at the LebeerLab as a joint thesis between the University of Ghent (Prof. G. Smagghe) and the University of Antwerp under the dedicated supervision of Marie Legein. Jari now investigates the microbiome of the phyllosphere as a potential source for biocontrol organisms in plant protection. In collaboration with the UGent, Jari explores the use of insects for the dissemination of these beneficial micro-organisms onto commercial plants and crops for their protection against harmful plant pathogens. Recently, he took up a project in the lab in which he investigates the use of beneficial micro-organisms for air quality applications. Therefore, he delves into their biodegradation potential and survival under harsh environmental conditions. He aims to use these micro-organisms to reduce the need for chemical cleaning of technical HVAC equipment.
Leonore graduated as a Master in Bioscience engineering with a specialization in Cell and Gene Biotechnology at the University of Ghent in 2021. She conducted her master thesis at the LebeerLab as part of the Isala project, where she focused on the characterization of vaginal lactobacilli and their anti-pathogenic potential. In October 2021 she was granted an FWO-SB Ph.D. fellowship to continue to study the vaginal microbiome, and more specifically explore the interaction and influence of underwear fabrics with and on this microbiome. This will be studied using synthetic vaginal communities at first and finalizes with a large-scale intervention study to explore the interactions in vivo. She is interested in public health, and especially female health. As such, she hopes that her research will contribute to a better understanding of resolving vaginal health issues.
Joke completed her Master in Bioscience Engineering with a major specialization in Cell and Gene Technology and minor specialization in Nutrition and Health at the KU Leuven (Belgium) in 2021. She had already joined the Lebeerlab during her Bachelor and Master dissertation. She started her Ph.D. at the Lebeerlab in 2021. She studies the microbiome of the upper respiratory tract and the potential of lactic acid bacteria as potential probiotics for the URT. Within her Ph.D., she will focus on genetic engineering of beneficial streptococci and their probiotic potential as an alternative treatment for otitis media.
External Ph.D. Students
Cyrelle obtained her Master degree in Veterinary Medicine with a special focus on small animal medicine in 2019 at Ghent University, after which she started her joined PhD at the Lebeerlab and the department of Bacteriology at the faculty of Veterinary Medicine, UGhent. She studies the microbial community present in the external ear canal of dogs. Besides that, she evaluates the effect of a topical probiotic ear formulation on the prevalence of otitis externa in allergic dogs. Dogs with skin allergies are prone to develop ear infections, leading to the frequent use of topical antibiotics and even to treatment failure due to antibiotic resistance. Prevention of the development of ear infections in allergic dogs will lead to a decrease in the application of antibiotic products in canine medicine.
Mathias Aerts (KU Leuven)
Monica Andreea Marin
Reine Audenaert (KU Leuven)
Maryse Cromphout (KU Leuven)
Isabel Erreygers (KU Leuven)
Tippapron Khondee (UAntwerp)
Daan Rooms (UGent)
Philippe van der Heiden (KU Leuven)
Lore Van Santvliet (KU Leuven)