Research Sarah Lebeer

Abstract

Research into health and well-being has historically been neglected in critical populations, particularly in women, children, and socioeconomically disadvantaged groups. This global issue, characterized by systemic neglect and underfunding, underscores an urgent need for research centres to spearhead transformative initiatives. A multidisciplinary approach is pivotal in addressing these disparities effectively. Our proposal introduces the establishment of the "U-MaMi" Research Centre of Excellence, designed as an integrated ecosystem to drive impactful research, innovation, education, policy, and community engagement, with a keen focus on health equity and microbiome-centric research. This ecosystem involves principal investigators and their team members from key disciplines to achieve these goals: microbiology and microbiome research (Sarah Lebeer), bioethics (Kristien Hens), general medicine (Veronique Verhoeven), paediatrics (Stijn Verhulst), ear-nose-throat specialication (Olivier Vanderveken), sociology (Karel Neels) and marketing (Annouk Lievens). With the chosen name for our centre, "U-MaMi," we do not only recognize the pivotal role of mothers and 'maternal microbes' in shaping the microbiome and health of their children, but also emphasize the importance of a united and inclusive perspective on health and health equity to drive transformative actions.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Hens Kristien
• Co-promoter: Lievens Annouk
• Co-promoter: Neels Karel
• Co-promoter: Vanderveken Olivier
• Co-promoter: Verhoeven Veronique
• Co-promoter: Verhulst Stijn

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Respiratory tract infections and infections of the vaginal mucosa, though affecting different anatomical regions, both represent significant global health challenges due to their viral origins, potential complications, and the burden they place on healthcare systems. Respiratory tract infections, such as influenza, respiratory syncytial virus (RSV), and coronaviruses, are among the leading global causes of morbidity and mortality. While most respiratory infections are of viral origin, secondary bacterial infections significantly increase disease severity, antibiotic use, and the development of multidrug resistance. Similarly, viral infections of the vaginal mucosa, such as human papillomavirus (HPV) and human immunodeficiency virus (HIV), pose major global health risks. HPV, for example, is the most common sexually transmitted infection and is responsible for nearly all cases of cervical cancer, while HIV continues to result in substantial morbidity and mortality through its progressive immune system degradation. Both respiratory and vaginal viral infections not only cause high disease burdens but also increase susceptibility to secondary bacterial infections or co-infections, thereby exacerbating health outcomes. These similarities highlight the need for innovative therapeutic strategies to address these complex infections, potentially including live biotherapeutic products, to mitigate their global impact. 3 It is nowadays well established that the microbiome at the respiratory and vaginal mucosa have an important gatekeeper function for our health. The microbiome can protect against viral infections, but also significantly be disturbed, so that symptoms are increased. Nevertheless, few studies have attempted to target the mucosal microbiota as a strategy to reduce the risk of respiratory infections9. The laboratory of applicant prof. Sarah Lebeer has gained pioneering insights into the role of the mucosal microbiome in health in projects such as ProCure (wwww.procureproject.be) and Isala (https://isala.be/en/) and collected a unique dataset of the vaginal and nasal microbiome in health versus various diseases. In addition, the lab has a unique culture collection or microbiome bank of supposedly beneficial bacteria, mainly lactobacilli, which have therapeutic potential based on preclinical data, mainly from in vitro and cell models. To explore the clinical potential of these strains, clinical trials are required, but they are not straightforward for live biotherapeutic products (LBPs), because they will have to form a new regulatory route compared to standard single-molecule drugs. This SEP project is aimed taking the next steps into the valorization of the microbiome bank. The SEP funding will be applied to optimize the datapackage of the existing culture collection, by performing additional experiments on valorization-readiness of the different strains.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Preterm birth (PTB) remains a significant global health challenge, affecting millions of pregnancies annually. Despite extensive research, preterm birth rates continue to rise worldwide. The vaginal microbiome composition, a.k.a. microorganisms inhabiting the vaginal ecosystem, influences preterm birth risk and neonatal health outcomes. Variation in the vaginal microbiome composition, particularly decreased lactobacilli abundance and colonization by Group B Streptococcus, correlates with a higher risk of preterm labour. Worryingly, current antibiotic therapies have limitations, including emerging resistance and disturbance of host microbiota balance. Thus, there is a need to investigate predictive and novel preventive strategies to decrease preterm birth rates. As predictive strategies, the present project proposes (a) to explore the already available clinical data using novel bioinformatic tools for the identification of predictive factors (b) to map the vaginal microbiome composition and elucidate its interacting networks (not explored before). In addition, as a preventive strategy, we aim to screen the host lab lactobacilli isolates collection against Group B Streptococcus isolates. Finally, utilizing advanced techniques such as the vagina-on-a-chip model, we will select ten lactobacilli and uncover their interaction with GBS within a physiologically relevant environment, guiding the selection of probiotic candidates.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Condori Sandra
• Co-promoter: Donders Gilbert
• Fellow: Marin Andreea-Monica

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Lactobacillaceae are the best documented family of beneficial bacteria with crucial roles in human reproduction, fermented foods, pollinator health, and other "one health"-related functions. However, we know surprisingly little about the beneficial activities of lactobacilli, beyond lactic acid production. Recently, we discovered that, despite the relatively small genomes of most Lactobacillaceae (about 3 Mbp), many species do contain large gene clusters, such as non-ribosomal peptide synthetases (NRPS). Preliminary results indicate unusual chemistry and valuable genetic elements and metabolites, which could contribute to insights into microbial ecology and synthetic re-engineering of non-ribosomal peptides (NRPs). This diverse class of molecules is known to elicit different effects, ranging from antimicrobial activity to immunomodulation and anti-cancer effects. We believe these molecules play a key role in explaining the lactobacilli dominance in specific niches, such as the human vagina and vegetable fermentations. Using in silico analysis, the diversity of NRPS systems in Lactobacillaceae will be classified. The most interesting NRPs will be chemically and functionally characterized in view of their mode of action. Using genetic engineering, we will gain more insight into the important features of these NRPs and explore possibilities for enhancing activity.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Vandenheuvel Dieter
• Fellow: Van Hee Matisse

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The crucial role of the vaginal microbiome in women's health cannot be overstated. Disruptions to this ecosystem by pathobionts can result in the development of prevalent vaginal conditions, including bacterial vaginosis, aerobic vaginitis, and vulvovaginal candidiasis. These infections not only affect physical health but have also broader implications for women's well-being, society, and the economy. Current treatment methods involve the use of antibiotics or probiotics, but concerns about emerging antimicrobial drug resistance and a lack of solid evidence for the efficacy of current probiotics are frequently raised. This PhD project explores an innovative approach using synthetic communities (SynComs) to develop vaginal therapeutics. First, a top-down approach will be used to screen and select consortia of vaginal microbiota, emphasizing synergistic interactions and eliminating antagonistic effects. A bottom-up approach will validate the top-down findings, providing defined communities suitable for automation and scaling up. Simultaneously, these defined SynComs will undergo testing for their probiotic potential, comparing them with single strains through in vitro anti-pathobiont assays, community fitness analyses, and implementation into cutting-edge vaginal cell models. This research project will offer ground-breaking insights into a novel approach to establishing robust, safe, and effective microbiome-targeted therapies.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Allonsius Camille
• Co-promoter: Donders Gilbert
• Co-promoter: Verhoeven Veronique
• Fellow: Victor Maline

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Urbanization is a key global trend. Despite its many advantages, urban life presents significant challenges to human health, potentially disrupting the delicate balance of the human microbiome. Given its pivotal role in preventing local infections and inflammatory diseases, it is crucial to understand the effects of urbanization on the skin microbiome. Therefore, this innovative project aims to investigate urban factors or combinations thereof that impact the skin microbiome composition, and identify potentially beneficial skin bacteria resistant to these urban factors. To address this challenge, we will use comprehensive skin microbiome and metadata from several microbiome projects, which we will combine with public environmental data to obtain groundbreaking insights. Furthermore, we will establish innovative in vitro microbial-based testing platforms suitable to represent children or adults. This will enable us to experimentally validate the impacts of urban-associated factors on the skin microbiome to substantiate the observed microbiome study associations, which has seldom been done in the past. As a final innovative aim, we will identify and characterize beneficial skin microorganisms that mitigate the negative effects of harmful urban factors on the skin. These novel insights will be critical for the advancement of skin disease prevention strategies and promoting overall human health in urban environments.

Researcher(s)

• Promoter: Spacova Irina
• Co-promoter: Gehrmann Thies
• Co-promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The composition of the vaginal microbiome is crucial for women's health. Its composition changes significantly with age, environment, lifestyle, physiological condition, biogeography and ethnicity. Yet we lack a in-depth comprehension of the factors fostering a healthy vaginal ecosystem, slowing down the development of much needed effective diagnostic and therapeutic approaches. Notably, there exists a substantial knowledge deficit regarding the vaginal microbiome in regions like Sub-Saharan and Central Africa. This PhD project aims to bridge this gap by delving into the vaginal microbiome dynamics in Central Africa (Cameroon) using state-of-the-art microbiome analyses. The study encompasses four distinct cohorts: healthy women residing in rural and urban areas, HIV-positive pregnant women, and HIV-negative pregnant women in Cameroon. Each participant contributes four vaginal swabs for comprehensive analysis: eNat swabs for DNA extraction and microbiome sequencing, Eswab for culturomics and metabolomics, a sterile swab for vaginal pH measurement, and another sterile swab for bacterial vaginosis assessment using the Nugent score. Furthermore, participants provide valuable insights into their dietary patterns, socio-economic status, personal hygiene practices, as well as reproductive and sexual health via a comprehensive survey. By integrating these metadata with microbiome data analysis, this research aims to unravel novel insights into the vaginal microbiome in Cameroon, identifying new avenues for diagnostic and therapeutic interventions.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Kenfack Zanguim Marie Josiane

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

In an era marked by escalating concerns over antibiotic and antimycotic resistance, the need to explore unconventional sources of antimicrobial agents has become increasingly urgent. The emergence of antibiotic-resistant pathogens challenges the efficacy of traditional antibiotics, thereby causing serious global public health risks and a worldwide pandemic. In this context, lactobacilli, traditionally renowned for their probiotic properties, have recently emerged as a promising source of novel antibiotics. These lactic acid bacteria, abundant in various natural habitats including the human vagina and fermented foods, present a unique opportunity for the discovery of antimicrobial compounds that could potentially address the growing antibiotic resistance crisis. This research project aims to elevate recent discoveries regarding potential antibiotic production, including a novel type of bacteriocins, by lactobacilli from the host laboratory to a higher Technology Readiness Level (TRL). Our objectives include purifying and characterizing these compounds by assessing their antimicrobial efficacy against key pathogens, including yeasts like Candida albicans and ESKAPE pathogens and elucidate their mode of action. Hereto, we will assess their safety and efficacy in in vivo models and initiate the development of a (multispecies) bacterial formulation that can be used in future studies. The ultimate goal is to amass a robust dataset that can attract industrial partners for future endeavors aimed at clinical applications. Through innovative approaches, we aspire to unveil and harness the untapped antimicrobial potential of lactobacilli, providing a ray of hope in our ongoing battle against antibiotic resistance.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project website

Project type(s)

• Research Project

Abstract

Space agencies are developing regenerative life support systems that provide air, water, and staple foods through hydroponic cultivation of a limited number of plants using crew waste as fertilizer, but these, mostly vegan, diets lack a number of essential nutrients found in a balanced diet. The aim of this project is to develop sustainable microbial-based food supplements for space travelers on long-duration space missions to the Moon and Mars. We will research and select suitable microbial-based food supplements, providing essential nutrients and vitamins to maintain human health and wellbeing, and still be active under stressful space conditions, including chronic exposure to reduced gravity and cosmic radiation. The growth and nutritional content of the microbial products and their safety and efficacy for human consumption in space will be evaluated, also by using reduced gravity simulators and space radiation analogs. In addition, it will be explored how on-site substrates (e.g. CO2 gas, regolith, etc.) could be used. The final outcome of the project will be a set of microbial strains or products that can be used as a reliable supplement to complete a space diet, improving the viability of human colonies on celestial bodies, and a first step towards a concept on how such a DIY production payload could look like.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Spacova Irina
• Fellow: Ellena Gabriele

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Our economy is undergoing a complete transition from the current fossil-based to a sustainable biobased economy as a solution to the large societal and economic challenges. This transition creates a strong need for new technologies to convert renewable resources into a broad range of bioproducts, biomaterials and bioenergy. Industrial biotechnology, driven by metabolic engineering and synthetic biology, has been identified as a key enabling technology in the building process of libraries of potential microbial cell factories (MCFs) for producing such bioproducts. However, the transformation of wild type microorganisms into efficient, productive and robust MCFs remains an ennobled trial and error process. To this end, evolutionary biotechnology has attracted attention in recent years: adaptive laboratory evolution (ALE) is combined with high throughput screening methods, to generate and screen a massively diverse set of phenotypes and variants. In this project, we want to accelerate the industrial timeframe of traditional ALE approaches and apply an innovative and accelerated ALE to the non-model organism Lactobacillus casei for defined production of chitinpentaose. These molecules have a vast repertoire of application possibilities in sectors such as pharma, food, feed and cosmetics. Industry would greatly benefit from a probiotic chitooligosaccharides production system, starting from renewable resources, taking into account downstream processing and regulation costs.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Primary crop production is facing serious challenges with respect to climate change, sustainability, food security and socio-economic profitability. With an average yield loss of 23%, plant diseases and pests are an important threat to global food security. Chemical plant protection products (PPPs) are widely used to control diseases and pests. Due to their environmental impact and the resistance development of pathogens and pests against several PPPs, their application becomes more and more restricted. The European Farm to Fork strategy envisages to reduce the overall use and risk of chemical PPPs with 50% by 2030. To achieve this ambitious goal, alternative and highly effective management strategies, based on innovative technologies are needed. The SynBioS consortium aims to develop an innovative concept of synergy, where biocontrol technologies with different modes of action are being combined. To target insects, we will develop a root-associated microbe based approach to enhance plant resistance, and an indirect approach based on phages, targeting bacterial symbionts of the insects. To target fungi and bacteria, SynBioS will explore the composition and functionalities of the phyllosphere microbiome and use this data to develop a synthetic microbial community specifically tailored to tackle diseases. The different approaches will be combined and evaluated for potential synergies. Finally, to strongly increase the valorization potential of the SynBioS results, we will analyze the social acceptability and economic feasibility of the innovative biocontrol strategies. The SynBioS project will focus on strawberry as a first proof-of-concept and against its most important airborne diseases and pests. However, we expect that the groundbreaking technology-driven toolbox, developed by the SynBioS consortium, can be extrapolated to other crop production systems and will lead to a breakthrough in the efficacy and adoption rates of biological control.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Female specific health conditions are underrepresented in research. The taboo felt by women to talk about intimate wellbeing is fed by this gender gap in scientific knowledge. This project aims to meet these needs by studying one of the most prevalent female-specific infections, vulvovaginal candidiasis (VVC), and paving the way towards its efficient diagnosis and treatment. About 70% of women worldwide suffer from vaginal candidiasis at least once in their life. An episode of this fungal infection is accompanied by a burning sensation, pain, and a reduced mental wellbeing. Some women (about 5%) encounter such infectionsat least four times a year, referring to recurrent(R) VVC. The design of efficient diagnostic and therapeutic strategies for (R)VVC is hindered by a knowledge gap surrounding vaginal health. To meet the absolute need for more information, this project will characterize the role of the microbiome, metabolome, immune system, and pathogen characteristics in (R)VVC. To this end, a large sampling platform of women with/without VVC will be established in this project. We will identify the most important and clinically relevant micro-organisms, metabolites, and immune factors in VVC pathogenesis. VVC models will be developed and optimized, which will be used to validate the causality of the correlations identified in the cohort. Identified correlations will be proposed as biomarkers, and microbes, metabolites, and combinations, which effectively lower pathogenicity of Candida species, will be further investigated for therapeutic potential. State-of-the-art tools and know how in the consortium will allow us to unravel the involved molecular pathways and elucidate how these can be exploited to optimize therapeutic efficacy. Finally, the knowledge gathered in this project will be used to improve literacy of women on VVC using platforms established by the consortium as well as novel tools to be developed in this project.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Mobile genetic elements (MGEs) are genetic elements that can move around within genomes or between cells. It is known that MGEs play a crucial role in prokaryotic ecology and evolution. However, due to limitations of current MGE detection tools in prokaryotic genomes, the full size and diversity of the prokaryotic mobilome is unknown, as well as the extent to which MGEs interact. In addition, current knowledge on the host range of various types of MGEs is limited. This project aims to explore the full mobilome of the important orders Lactobacillales and Enterobacterales, two taxa that are densely sampled in terms of the number of strains with sequenced genomes in public databases. First, a novel tool will be developed that can predict the full mobilome of a set of genomes in a database-independent manner, based on comparative genomics. Second, this tool, as well as existing MGE prediction tools, will be applied to both taxa. The predicted MGEs will be clustered, and presence/absence correlations between the resulting clusters will be determined to assess interactions between the elements. Third, the co-evolutionary history of MGE clusters and their host genomes will be explored and ancestral MGE transfer events inferred. Finally, the host clades of the MGEs will be predicted and validated through CRISPR spacer matching. Together, these analyses will yield new insights into the "dark matter" of the prokaryotic mobilome.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Wittouck Stijn

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

In this project, we will study the vaginal microbiome and the microbiome of endometrium biopts via amplicon sequencing 16S via standard pipelines of the host lab for wetlab and in silico analyses. The partner is the main coordinator if this project. We provide a service.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Women's health is receiving increased attention, but science is still not filling society's needs when it comes to vaginal health. For instance, in the last 40 years, no major breakthroughs have been made to manage bladder and vaginal infections. One way in setting a societally relevant research agenda is actively involving citizens in scientific dialogues. We have founded the Isala project as a citizen-science project to significantly advance research, diagnostics and therapeutics for the vaginal microbiome. In the first pioneering phase of the project, more than 5500 women have provided intimate samples and data; proposed research objectives and survey questions; and helped disseminate and interpret results. Thanks to the enthusiasm of the Belgian citizens participating and cocreating the research questions, we have built the largest citizen-science project in the world on the vaginal microbiome. And we are still expanding! Now, we want to expand this cohort in Belgium and across the world, to jointly taboos on women's health, increase scientific literacy and provide new insights in associations of lifestyle with the vaginal microbiome and work on and tangible solutions such as microbiome-modulating strategies.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

In this project, we will explore the process of fruit fermentation via lactic acid bacteria and yeast to have a safe, tasty product with an enhanced shelf-life of use in bakeries. This project is confidential and no details can be disclosed.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The aim of this project is to gain a better overall understanding of the relationship between the respiratory microbiota (upper and lower) and the intestine in pigs, which will provide a deeper insight into both composition and functionality of the microbes present. These insights will reveal genetic characteristics of pathogenic bacteria (such as virulence factors). results, but the presence of useful bacteria will also be visualized, which can be used for the optimization of existing workflows and the development of potential probiotics.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The phytopathogenic fungus, Botrytis cinerea, is the most common reason for fruit rejection in small fruit crops such as the strawberry plant. To get rid of this fungus, chemical fungicides are still the most popular worldwide. Due to increased resistance, growing environmental awareness, continued consumer demand for fewer pesticide residues and more stringent policies in many countries, more and more research is being devoted to sustainable alternatives fitting within the framework of integrated pest management. Within this project, biocontrol using lactic acid bacteria is studied as an alternative. Lactic acid bacteria are well known for their protective properties within food applications, but their role on the plant and their potential as a biocontrol organism on the phyllosphere have only been investigated to a limited extent. To avoid inconsistent field performance, a common problem in biocontrol, candidates will be screened for their potential to survive and grow on the phyllosphere. We will focus on the entomovectoring system as the approach to applying these potential biocontrol agents. In this system, a vector, Bombus terrestris, will disseminate an optimized formulation of lactic acid bacteria directly to the strawberry flowers. In this way, pollination and crop protection are done at the same time and efficient delivery towards the target location is guaranteed.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Kiekens Filip
• Fellow: Temmermans Jari

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The microbiota of the upper respiratory tract (URT) is emerging as a gatekeeper to respiratory health, but it is currently underexplored at the functional level compared to other body sites. URT diseases such as otitis media (OM) form leading causes for antibiotic prescription, while the functional role of bacteria in the disease pathology is still not clear. Consequently, new insights into the functional biology and microbial ecology of OM as a microbial disease are needed to design novel therapeutic strategies. Microbiome sequencing of the URT revealed Streptococcus salivarius as one of the primary colonizers of the oral cavity shortly after birth. It is also significantly more abundant in the nasopharynx of healthy children compared to children with chronic OM. Endogenous beneficial bacteria can indeed play a pivotal role in URT health through inhibition of respiratory pathogens and immunomodulation. As a key beneficial commensal, specific strains of S. salivarius could have high potential as URT probiotics. These strains can produce secreted secondary metabolites with bacteriostatic or bactericidal activity, but their role in probiotic effects is currently underexplored. This project will focus on exploring the metabolic properties and functional potential of S. salivarius isolates, which will be evaluated through dedicated in vitro culturing systems, phenotypic screening assays and comparative genomics, combined with an innovative proof-of-concept study in humans.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Boudewyns An
• Co-promoter: Spacova Irina
• Co-promoter: Vanderveken Olivier
• Fellow: Van Malderen Joke

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Fermented foods are defined as foods made through desired microbial growth and enzymatic conversion of food components. Despite being widely consumed, only a few vegetable fermentations (e.g. kimchi) have been extensively studied, but others remain largely understudied. These vegetable fermentations are mostly spontaneous and could benefit from a dedicated starter culture to improve safety, flavor, texture, and health potential, such as production of vitamins. This project will therefore focus on collecting a wide range of fermented vegetable samples through citizen science projects both in Belgium and USA. Species level community dynamics will be explored to understand the ecology of lactic acid bacteria (LAB) in these man-made environments. LAB will be isolated as potential starter cultures. Traditionally, starter culture selection relies mostly on labor intensive trial and error screening but in our project, we propose the use of genome-scale metabolic models (GEMs) for rapid screening of metabolic potential. Starter cultures will be fully characterized both in silico using GEMs and in vitro phenotypic characterization. Based on these results, starter cultures will be metabolically engineered for the increased expression of target metabolites to improve texture, flavor and health potential. This project will result in 5 optimized functional starter cultures together with a metabolic engineering pipeline for future starter cultures.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Van Beeck Wannes

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The aim of this PhD project is to determine the radioprotective mode of action of biotic food supplements including LGG and Limnospira sp.. First (WP1), we will implement the newly GuMI platform using human gut derived organoids and CRC tumoroids, in a radiotherapy relevant setup which has never been done before, then (WP2) to investigate barrier protective and immunomodulatory mechanisms of action of LGG and Limnospira sp. either individually and in a symbiotic combination, and in parallel (WP3) to continue the search for new radioprotective agents of natural origin taking advantage of the higher screening throughput and human physiological applicability provided by the GuMI platform compared to mouse studies. This could also include the use of FMT, as a more holistic gut microbiome-based therapy.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

ODORETION researches and develops technology paths to remediate and prevent malodors in bedrooms, bathrooms and toilets. A research platform with modular methodologies will form a solid basis for identifying the most effective biological and chemical technologies. On top of that, ODORETION aims to be more sustainable than the typically used toxic and less environmentally friendly strategies.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

In this project, together with partners at KU Leuven, we want to investigate the vaginal microbiome in women with iatrogenic menopause caused by breast cancer treatment and its association with vaginal health and sexuality (www.volupta.be).

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Speaking openly about vaginal health is taboo in Peru, and public attention to intimate female care has been neglected for decades. For instance, during the present pandemic, several primary health care centers shut down gynaecological consultations, affecting women suffering from vaginal infections. With the current Laura 2.0 project, we aim to create a national (in Peru) and international research network investigating on vaginal health by actively engaging several key stakeholders from society and academia. Higher education institutions (HEIs) will play a key role in achieving Laura 2.0 aim. Universidad Nacional de la Amazonia Peruana (UNAP) and Universidad Nacional San Agustín de Arequipa (UNSA) are the prominent universities in the Peruvian Amazon and the Highlands regions, respectively. Both HEIs are strengthening their key roles in developing their regions by consolidating their research capacity. The current project will strengthen the national (UNAP-UNSA-UPCH) and international (local partners and UAntwerp) collaboration by actively developing research capacities in a multidisciplinary approach. More importantly involving (for the first time in Peru), citizens (women) in science, via a citizen science project inspired by the Belgian Isala project (https://isala.be/en).

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Brusselaers Nele
• Co-promoter: Condori Sandra
• Co-promoter: Verhoeven Veronique

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Upon gastrointestinal and reproductive homeostasis, there is an intimate crosstalk between mucins (MUCs) and the microbiome at the mucosal surface to maintain barrier integrity but a disbalance between both actors could dictate disease development, such as inflammatory bowel diseases (IBD) and aerobic vaginitis (AV). Indeed, thinning of the epithelium and aberrant MUC1 and MUC13 expression have been associated with barrier dysfunction in IBD. Also MUC1 seems to be increasingly expressed upon vaginal infection. Such defective mucus layer will thus allow microbiota to come in close contact with these mucins and co-elicit inflammation and mucosal damage. Nevertheless, which microbes interact with MUC1 and MUC13 in response to inflammation and dysbiosis and mediate barrier dysfunction in IBD and AV remains poorly understood. Therefore, we will first characterize microbiome diversity and function in IBD and AV using shotgun metagenomic sequencing. In parallel, we will also unravel the MUC1 and MUC13 mRNA isoform landscape using targeted isoform sequencing. Combining both sequencing data will allow to identify microbial-mucin isoform associations in IBD and AV. Finally, we will investigate the mechanism(s) by which abundant microbial species in IBD and AV interact with the aberrantly expressed MUC1 and MUC13 isoforms resulting in barrier dysfunction. To do so, bacterial mutant approaches and human epithelial organoid cultures established from IBD and AV samples will be used.

Researcher(s)

• Promoter: Smet Annemieke
• Co-promoter: Ceuleers Hannah
• Co-promoter: Lebeer Sarah

Research team(s)

• Laboratory Experimental Medicine and Pediatrics (LEMP)

Project type(s)

• Research Project

Abstract

Lactobacilli are among the best documented beneficial bacteria. Humans are unique animals having a reproductive tract dominated by lactobacilli. In the female reproductive tract, Lactobacillus taxa normally dominate this habitat under healthy conditions, with numbers up to 90-100%. However, there exists a major knowledge gap on why this is the case. The biodiversity, dynamics and evolutionary history of vaginal lactobacilli are largely underexplored. In this project, we aim to follow an innovative sequencing and Citizen Science approach to genetically and functionally characterize vaginal lactobacilli (isala.be). This will include shallow shotgun, whole genome and innovative culturomics and characterization strategies. Specific attention will be given to their adaptation to the vagina and antimicrobial properties.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

The urogenital microbiome is a crucial microbiome for human health and reproduction. Lifestyle and hygiene practices are suggested to have a strong influence on the urogenital microbiome. For instance, humans are the only animals that wear clothes, and certain underwear fabrics have been correlated with higher risk of urogenital disease. However, the causal relationship between urogenital health and underwear fabrics is underexplored, especially regarding how underwear could influence the urogenital microbiome. In this project, we first aim to correlate the use of specific underwear fabrics with vaginal health and microbiome, exploring the dataset generated by the host lab from more than 3300 Isala study participants. In parallel, a microbiological in vitro platform will be designed for the evaluation of microbiome-friendly characteristics of (underwear) fabrics through the use of defined microbial communities. Subsequently, a key part of the project will consist of a large-scale study that will explore in vivo interactions between specific underwear fabrics, the vaginal, vulvar and skin microbiome and urogenital health. The ultimate application aim is to better understand how underwear fabrics can affect female health, and implement microbiome-friendly underwear through future collaborations between the academic, health and textile sectors.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Spacova Irina
• Co-promoter: Verhoeven Veronique
• Fellow: Vander Donck Leonore

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Vitamin producing microorganisms are emerging as a natural, cost-effective and sustainable alternative to chemical vitamin production. To date, they have mainly been explored in the gut and fermented food, however, recently, the host group isolated several vaginal lactobacilli capable of vitamin B2 (over)production. Lactobacilli have a long history of safe use and are highly suitable for application as probiotics or for biofortification of foods, yet they are generally still applied as 'black boxes', without full understanding of the genes and molecules that drive their beneficial action. In this project, we will perform in silico and in vitro functional screening of the host group's large biobank of more than 1000 human bacterial isolates with the innovative goal to identify and characterize vitamin producing lactobacilli from untapped non-gut body niches (vagina, upper respiratory tract), and fermented foods. Next, to better understand and enhance the vitamin producing capacity of lactobacilli, untargeted and targeted genetic modification strategies will be implemented. A specific unique and challenging focus will be on the functionalization of the novel CRISPR-Cas9 based tool 'Prime editing' in lactobacilli for targeted genetic alterations leading to vitamin overproduction. Overproduction phenotypes, naturally isolated or resulting from genetic engineering approaches, can then be used in food/feed, as supplements and in human therapeutic applications.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Spacova Irina
• Fellow: Dricot Caroline

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Up to 75% of females worldwide encounter at least one episode of vulvovaginal candidiasis (VVC) in their lifetime and 5%-10% of them suffers from recurrent infections (RVVC). Globally, RVVC is estimated to target 150 million women a year by 2030, leading to universal healthcare related and economic losses. Current treatment of (R)VVC is insufficient and resistance occurs frequently. Therefore, the development of additional, effective therapy strategies has become urgent. In this project, we will investigate the treatment of (R)VVC with probiotics based on S. cerevisiae alone and in combination with Lactobacillus spp., in in vitro and in vivo setups. Additionally, we will generate an overview of the vaginal mycobiome of the Belgian population. This overview will allow us to compare the healthy and (R)VVC-linked microbiome, generating insight into the relationships between microorganisms present in this niche. This could highlight microorganisms that could have probiotic capacities against Candida species.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

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)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Enviromics is a multidisciplinary consortium of UAntwerpen researchers across the board of environmental sciences and technologies. Through impactful fundamental advances and interdisciplinary approaches across biology, (bio)chemistry and (bio)engineering, the consortium offers bio based solutions to ecosystem challenges by a strong interaction between three pillars (i) Environmental applications and nature based solutions, (ii) Sensing and analysis of chemicals and environments and (iii) Microbial technology and biomaterials, supported by sustainable product development and technology assessment. Through a renewed and tighter focus the ENVIROMICS consortium now signs for a leaner and more dynamic shape. Through intensified collaborations with different stakeholders, both national and international, the leverage for creating enhanced business and societal impact is reinforced. The consortium is strongly managed by a team of two highly profiled researchers partnered by an IOF manager and a project manager with clearly defined tasks and in close contact with the consortium members and the central Valorisation Unit of the university. The consortium has a strong and growing IP position, mainly on environmental/electrochemical sensing and microbial probiotics, two key points of the research and applications program. One spinoff was created in 2017 and two more will be setup in the coming three years. The direct interaction with product developers ensures delivering high TRL products. Next to a growing portfolio of industrial contracts, we create tangible societal impact, when relevant including citizen science approaches. Through the stronger leverage created by the new structure and partnerships we will develop both intertwined branches significantly.

Researcher(s)

• Promoter: Blust Ronny
• Co-promoter: De Wael Karolien
• Co-promoter: Dries Jan
• Co-promoter: Du Bois Els
• Co-promoter: Lebeer Sarah
• Co-promoter: Meire Patrick
• Co-promoter: Meysman Filip
• Co-promoter: Samson Roeland
• Co-promoter: Schoelynck Jonas
• Co-promoter: Vandermoere Frederic
• Co-promoter: Vlaeminck Siegfried
• Fellow: Dardenne Freddy

Research team(s)

• Ecosphere

Project type(s)

• Research Project

Abstract

Atopic dermatitis (AD) is a chronic inflammatory disease of the skin that occurs in about 20% of children and 3% of adults in Western countries. AD is characterized by acute flare-ups of itchy eczematous lesions and dry skin. The etiology of AD is complex, the appearance and course of the disease are influenced by both genetic and immunological mechanisms and environmental factors, such as pathogenic microorganisms. In this project,, we aim to characterize the microbiome of children with AD and investigate the impact of a topical therapeutic strategy with well selected lactobacilli.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Hagendorens Margo
• Fellow: Delanghe Lize

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Synthetic biology is a new discipline that allows designing and creating novel, completely man-made biological systems such as metabolic pathways. The innovative technology is a game-changer for the sustainable production of pharmaceuticals, biofuels, enzymes, aroma compounds and bioplastics. The synthetic systems are often implemented in E. coli or yeast cells because the biotechnological toolbox for these organisms is readily available. However, these microbes are often not optimally suited for industrial or medical applications. This project therefore aims to develop a novel toolbox that allows the ethical exploitation of superior non-standard microbes. The project will not only yield an important breakthrough for the efficiency and possibilities of synthetic biology, but also constitutes a research consortium of a team of young and ambitious scientists that will serve as a strategic hub for the further development of synthetic biology in Flanders, thereby helping to maintain its leading position in biotech.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Hens Kristien

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Often a microbiome modification with a "beneficial" microbe does not yield the desired results. This illustrates the need of better tools to study the ecology and evolution of microbiomes, and the effects of artificial modifications to these microbiomes. This project proposes the innovative approach of combining synthetic microbial communities with shallow shotgun metagenomics to gain unprecedented understanding in microbial communities in general. The proposed approach will be developed for a phyllosphere model and used for experimental microbial evolution of whole communities. Successive passaging experiments will be set up where synthetic phyllosphere communities will be moved from one generation of host plant to the next. The results of these experiments will lead to new insights in the ecology and evolution of phyllosphere communities. This project aims at setting up this approach to be more widely useable for testing existing and developing new evolutionary theories. Finally, the impact of the addition of a "beneficial" microbial strain to the phyllosphere model will be studied at the level of the microbiome ecology and evolution, allowing novel insight in long-term effects of artificial modifications of our microbial environment.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Smets Wenke

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Lactobacillus bacteria have a strong, but underexplored potential as sustainable bio-based solutions for many food and health-related problems. Since Nobel-laureate Eli Metchnikoff hypothesized that lactic acid bacteria can promote human health in the gut, the research on lactobacilli and probiotics has mainly focused on the human gut and fermented dairy foods. However, a major knowledge gap exists on the beneficial potential of Lactobacillus species in other human body sites (vagina, skin, upper respiratory tract), animals (e.g. chickens, honey bees), plants, crops, and even on abiotic surfaces. In addition, lactobacilli play a key role in many plant- and vegetable-based fermentations, where they promote the shelf life and nutritional value of food and feed. Yet, why and how Lactobacillus species can be beneficial in such a wide variety of niches is currently underexplored. Therefore, the core aim of this project is a systematic and integrated analysis of the evolutionary history, ecology, and beneficial functions of Lactobacillus species. I propose an unconventional approach situated at the intersections of molecular microbiology (focusing on a single microbe), molecular ecology (focusing on microbial communities) and comparative genomics with an evolutionary perspective on niche adaptation of lactobacilli. By looking deeper into Lactobacillus biology, a paradigm shift can be made moving from a classical ad hoc base to a unique knowledge-based framework for strain selection and analysis of fitness and performance.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Microorganisms have been exploited from the earliest times for baking, brewing, and food preservation. More recently, the enormous versatility in biochemical and physiological properties of microbes has been exploited to create new chemicals and nanomaterials, and has led to bio-electrical systems employed for clean energy and waste management. Moreover, it has become clear that humans, animals and plants are greatly influenced by their microbiome, leading to new medical treatments and agricultural applications. Recent progress in molecular biology and genetic engineering provide a window of opportunity for developing new microbiology-based technology. Just as advances in physics and engineering transformed life in the 20th century, rapid progress in (micro)biology is poised to change the world in the decades to come. The Excellence Centre "Microbial Systems Technology" (MST) will assemble and consolidate the expertise in microbial ecology and technology at UAntwerpen, embracing state-of-the-art technologies and interdisciplinary systems biology approaches to better understand microbes and their environment and foster the development of transformational technologies and applications. MST connects recently established research lines across UAntwerpen in the fields of microbial ecology, medical microbial ecology, plant physiology, biomaterials and nanotechnology with essential expertise in Next Generation Sequencing and Bioinformatics. By joining forces, new and exciting developments can be more quickly integrated into research activities, thus catalyzing the development of novel microbial products and processes, including functional food, feed and fertilizers, probiotics, and novel biosensors and bio-electronics applications. This way, MST aims for an essential contribution to the sustainable improvement of human health and the environment.

Researcher(s)

• Promoter: Meysman Filip
• Co-promoter: Beemster Gerrit
• Co-promoter: Laukens Kris
• Co-promoter: Lebeer Sarah
• Co-promoter: Verbruggen Erik
• Co-promoter: Vlaeminck Siegfried

Research team(s)

• Geobiology

Project type(s)

• Research Project

Abstract

A steady increase in chronic inflammatory diseases can be observed in regions with a high degree of industrialization and urbanization since World War II. The pro-inflammatory capacity of ambient air particulate matter and other air pollutants seems an important factor in the pathogenesis of these diseases, but the underlying mechanisms are not well understood. This project aims to generate more insights in the (micro)biology of air pollution by application of techniques from the fields of molecular microbiology and immunology to investigate the presence of micro-organisms and their endotoxins in particulate matter (PM) and to characterize the pro-inflammatory capacity of PM in detail.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Development of probiotic lactic acid bacteria for HIV-positive Cameroonian pregnant women Kenfack Zanguim Josiane, Sandra Condori, Sebastien Kenmoe, Esemu Livo, Sarah Ahannach, Sarah Lebeer Probiotics are live microorganisms which, when administered in adequate amounts, confer a health benefit to the host. . Probiotic lactic acid bacteria are mainly studied for the gut, but now also increasingly for vaginal health. In fact, lactobacilli-based probiotics have a stronger rationale than the gut, because a healthy vaginal microbiome is generally dominated by lactobacilli. However, this does not seem to be the case for all geographical regions and ethnic groups. African women seem to have a vaginal microbiome that is less dominated by lactobacillibut contains more anaerobic bacteria such as Gardnerella, giving them a high prevalence of BV of 33% . Therefore, lactobacilli-based probiotics seem to have great potential for African women, especially for HIV-positive pregnant women, because they are more at risk to have a disbalanced vaginal and gut microbiome. In this study, we explore the dietary habits and vaginal microbiome in terms of consumption of yogurt, dairy and probiotic products in HIV-positive pregnant women from Cameroon in their second trimester of pregnancy. 23 HIV-positive pregnant women and 32 HIV-negative pregnant women participated and their microbiome will analyzed at UAntwerpen.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Primary crop production is facing serious challenges with respect to climate change, sustainability, food security and socio-economic profitability. With an average yield loss of 23%, plant diseases and pests are an important threat to global food security. Chemical plant protection products (PPPs) are widely used to control diseases and pests. Due to their environmental impact and the resistance development of pathogens and pests against several PPPs, their application becomes more and more restricted. The European Farm to Fork strategy envisions to reduce the overall use and risk of chemical PPPs with 50% by 2030. Biocontrol applications could be valuable alternatives to overcome the disadvantages of these chemical PPPs. Currently, not many bacterial-based PPP strategies exist and the current bacterial strategies are largely focusing on spore-forming bacilli. Here we propose to explore the potential of lactic acid bacteria. If they show activity in the lab against major pathogens, we will explore their most suitable formulation and activity in more relevant conditions.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Mobile genetic elements (MGEs) are genetic elements that can move within or between DNA molecules or cells. These elements, which include conjugative plasmids and prophages, are one of the main drivers of the genome plasticity that we observe in bacteria and archaea. In addition, they are important for the medical world (e.g. as spreaders of antimicrobial resistance) and biotechnology industry (as a source of genetic engineering tools). Therefore, it is highly useful to be able to computationally detect the presence of MGEs in prokaroytic genomes, as well as predict to which strains an MGE can potentially transfer (its host range). However, current techniques for the former are limited because they are dependent on databases of experimentally characterized MGEs, while current host range prediction strategies are very coarse-grained. In this project, a computational tool will be developed that is capable of predicting MGEs in prokaroytic genomes in a databaseindependent way. The tool will achieve this by taking as input a multigenome, multi-species dataset instead of a single genome, and adopting a comparative genomics approach. In addition, a novel strategy for high-resolution host range prediction will be developed, based on comparative phylogenomics and host strain gene content. Both novel techniques, as well as existing tools, will be used to predict and characterize the comprehensive "mobilome" of the medically and economically important order Lactobacillales.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Wittouck Stijn

Research team(s)

Project type(s)

• Research Project

Abstract

The microbiome field has grown tremendously within the last decades. Our research team is at the forefront of this field, with focus on the microbiome outside the human gut (such as skin, upper respiratory tract, vagina) and screening of potential probiotic candidates. This expertise is (inter)nationally recognized, resulting in an increasing request for collaborations from academics, industry, and other organizations. To be able to cope with this increasing demand, the team wants to professionalize their microbiome sequencing and discovery platform and hire and train staff to launch commercial services in a self-sustaining way.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

This application relates to the purchase of new basic research infrastucture, a device for versatile Single Cell Sorting and Dispensing using Microfluidics. The equipment can be used for a variety of applications, including cell line development, monoclonal antibody development, iPSC cloning, single cell omics, rare cell isolation, microbiology, virology, immunology and microbial technology. The equipment works at low pressure and allows easy setup and easy switching between a variety of applications, both with or without infectious agents.

Researcher(s)

• Promoter: Delputte Peter
• Co-promoter: Cos Paul
• Co-promoter: Lebeer Sarah
• Co-promoter: Ogunjimi Benson
• Co-promoter: Vorsters Alex

Research team(s)

• Laboratory for Microbiology, Parasitology and Hygiene (LMPH)

Project type(s)

• Research Project

Abstract

The upper respiratory tract (URT) is a key habitat of the human microbiome, but it's currently underexplored at the functional level compared to other body sites. URT diseases, e.g. otitis media (OM), form leading causes for antibiotic prescription, while the functional role of bacteria in the disease pathology is still not clear. As such, OM is a microbial disease needing new insights into the functional biology and microbial ecology to design novel therapeutic strategies. Based on microbiome sequencing of the URT, Streptococcus salivarius was found as one of the primary colonizers of the oral cavity shortly after birth. It was found to be significantly more abundant in the nasopharynx of healthy children than in the nasopharynx of children with chronic OM. It is recognized that endogenous beneficial bacteria can play a pivotal role in URT health through inhibition of respiratory pathogens and immunomodulation. As a key beneficial commensal, specific strains of S. salivarius could have high potential as URT probiotic. Some strains can produce secreted secondary metabolites with bacteriostatic or bactericidal activity, but their role in probiotic effects is currently underexplored. This project will focus on exploring the metabolic properties and functional potential of S. salivarius isolates, which will be evaluated through dedicated in vitro culturing systems, phenotypic screening assays and comparative genomics, combined with an innovative proof of concept study in humans.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Van Malderen Joke

Research team(s)

Project type(s)

• Research Project

Abstract

The nasal epithelium forms the first line of defense against environmental insults. Damage to epithelial structure and function, is involved in the pathology of chronic rhinosinusitis with nasal polyps (CRSwNP). Bitter (T2R) and sweet (T1R) taste receptors are upper airway sensors that detect and induce a rapid immune response against secreted bacterial ligands. Activation of T2Rs on nasal epithelium results in rapid calcium release that stimulates the secretion of antimicrobial compounds and production of nitric oxide, consequently killing the bacteria and increasing ciliary beating. Activation of T1R antagonizes the host's T2R mediated immune response. Moreover, T1R agonists increase bacterial survival and propagation. In line with this, we have previously demonstrated that patients with CRSwNP have an increased presence of pathogenic bacteria and a decrease in beneficial lactic acid bacteria, which are able to modulate barrier homeostasis. Unfortunately, limited studies focus on the relationship between the nasal microbiome and taste receptor function in CRSwNP patients. As such, in this project we will investigate the effect of bacterial ligands, produced by the nasal microbiome, on taste receptor function in CRSwNP.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Viruses infecting the respiratory tract encounter a diverse resident airway microbial community (the microbiota). While the majority of research on the host-virus-microbiota nexus focuses on virus and microbiota interplay with host immunity, the impact of airway microbiota on viruses through direct interactions is poorly understood. The goal of this project is to come to a new understanding of how direct microbiota-virus interactions in the airways influence viral pathogenesis using respiratory syncytial virus (RSV) as a model. Innovative targeted isolation of RSV-binding bacterial strains from the airways of infants with RSV disease will be performed, in parallel with an in-depth functional and species-level taxonomic airway microbiome analysis. Focusing on beneficial bacteria, the effects of direct bacterial interactions with RSV will be analyzed using a suite of novel and state-of-the-art in vitro assays tailored to investigating the host-microbiota-virus nexus. Localization and properties of key anti-RSV bacterial compounds will be investigated. The effects observed at microbiome level and in vitro will be aligned with in vivo read-outs in an infant mouse model of RSV infection, to conclude whether they translate into clinically relevant outcomes. Understanding the role of direct interactions between airway microbiota and viruses will add a potentially groundbreaking new dimension to the interplay within the host-virus-microbiota nexus in the respiratory niche.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Delputte Peter
• Fellow: Spacova Irina

Research team(s)

Project type(s)

• Research Project

Abstract

Dit is een confidentieel bedrijfsproject over hoe nuttige micro-organismen en bacteriën ingezet kunnen worden in ventilatiekanalen. Hiervoor moet ook de chemische samenstelling van stof beter gekend zijn.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

The demand and need for products influencing the microbiome of the armpit skin (odour problems) and the mouth (periodontitis, caries, halitosis and oral thrush) is huge.This project wants to seize this opportunity to develop new products for these conditions using probiotherapy. By using beneficial probiotic bacteria, and hereby restoring a possible (microbial) imbalance towards a more balanced and healthy state, we will positively impact the microbiome. However, the development of specific solutions for these problems raises specific scientific challenges on the microbiological, formulation (technological & biopharmaceutical) and health/pathology level. These will be addressed in this project.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

The main objective of this project is to acquire new biological and genetic insights on the application of microorganisms as bioremediation of PAHs in air pollution. Such new insights will lead to a scientific underpinning of a new air purification application based on the spread of benign bacteria in the environment.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Dekeukeleire Max

Research team(s)

• Laboratory of Applied Microbiology and Biotechnology (LAMB)

Project type(s)

• Research Project

Abstract

Beneficial microbes have a plethora of biomedical, environmental and engineering applications. Currently, many fundamental and more applied R&D projects are slowed down by the need for advanced equipment for the upscaling and processing of the microbial cultures. Here, a research consortium of bio-engineers, civil engineers, biologists and pharmaceutical engineers was built to jointly advance the applications and research of beneficial microbes at UAntwerpen. This consortium aims to manage joint equipment and expertise. The core of the equipment is a 100 l pilot bioreactor suited for bacteria, yeasts and algae. It is fully computer controlled and monitored, and equipped with a steam-in-place (SIP) unit. The system is equipped with several sensors and valves allowing automated control of important parameters (e.g. pH, dissolved oxygen, conductivity, turbidity, …). The whole system is GMP- compatible and in pharmaceutical- grade steel. A 10 l bioreactor is foreseen for optimizing culturing conditions. The reactors are complemented with an incubator-shaker for the growth of inocula and postprocessing equipment to professionally process the biomass. The post-processing equipment mainly consists of a large scale, low- to- high speed cooled centrifuge and a pilot spray dryer for final processing for extended shelf life of the biomass and work up of the biomass towards its final application.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Kiekens Filip
• Co-promoter: Meysman Filip
• Co-promoter: Vlaeminck Siegfried

Research team(s)

Project type(s)

• Research Project

Abstract

In this project, a consortium from different Flemish universities jointly owns equipment for high-troughput handling of microbial growth experiments (HITMAN). Promotor is Kevin Verstrepen (KU Leuven). He coordinates the use of this equipment at their campus and faciloties in Leuven.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Isala is a citizen science project at the University of Antwerp. Isala's ambitions are high. And important! For the first time in Belgium, and hopefully in other countries like Peru as well (Laura project), we want to get a better understanding of the female microbiome using state-of-the-art DNA technology. Say what?! Well, your vagina is home to millions of bacteria that play a vital role in your health. They're incredibly important when it comes to protecting you from infections, UTIs and STIs, and we think they probably play a major role in fertility and healthy pregnancies too. But… we don't know for sure. Because until recently, scientific research was very much a man's world and there wasn't much interest in the vaginal microbiome. Isala wants to change that. So in March 2020, we launched a call to find 200 women in Belgium willing to take simple swabs from their vaginas, skin and saliva in the privacy of their own bathrooms. We were looking for 200 women and we found more than 5000. Wow!  Now we're going to make history with all of those women. 

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

In our rapidly urbanizing world, chronic health conditions associated with urban living are on the rise. One of the main current challenges is unravelling the role of reduced access to and reduced quality and quantity of nature and biodiversity in these living environments. Enhanced immune functioning emerges as one promising candidate for a central pathway between nature and health. Despite mounting evidence that people with a diverse microbiome or who interact with green spaces enjoy better health, studies have yet to directly examine how biodiverse urban green spaces might modify the human microbiome and reduce chronic disease. Another challenge is to enhance access to nature for all, which is unevenly distributed among social groups with different socio-economic and cultural backgrounds. In this project, the environmental microbiome, defined as the microbes in soil, on plants, and associated with air dust, will be targeted, as well as its social distribution.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Lactobacilli are an interesting group of bacteria found in a large variety of ecosystems, from the human gut to milk to plant surfaces and other environments. They are used in food fermentations and as health-promoting bacteria. It is not yet clear how lactobacilli are able to survive and thrive in these different environments. Did Lactobacillus strains adapt, each to a specific environment? Or are some strains "nomads", able to survive in many different environments? We will attempt to solve the adaptation question in two ways. First, we will study gene copynumber variation between Lactobacillus strains. The DNA of a bacterial strain can contain multiple copies of a single gene, and this copy-number can differ between strains. It was recently observed that copy-number variation in gut bacteria is often found in genes linked to environmental adaptation. As a second way to investigate environmental adaptation, we will reconstruct the evolutionary history of the Lactobacilli. Bacterial strains can evolve in multiple ways; two important types of evolutionary events are that they can acquire genes from other bacteria or genes can get lost. We will use the full DNA sequences of at least fifty strains per species to find out which genes were acquired and which ones were lost by which ancestors in the course of evolution. We can then see whether there is a connection between these gene gain and loss events and the environment in which these ancestors lived.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Wittouck Stijn

Research team(s)

Project type(s)

• Research Project

Abstract

Respiratory Syncytial Virus (RSV) is the leading cause of severe lower respiratory disease in young children worldwide. Nearly all children are exposed to RSV by the age of 2, approximately 40 % will develop a lower respiratory tract infection such as bronchiolitis and up to 10 % of these children require hospitalization. Severe inflammation is a typical hallmark of the hospitalized children. Despite the discovery of the virus in 1956, prevention and treatment options for RSV are limited. In this project, an innovative approach based on the intranasal application of specific probiotic strains is explored to prevent the severe lung inflammation that follows the acute infection. We will investigate whether delivery of intranasal probiotics prior to RSV infection can prevent the development of severe RSV disease by functioning as immunomodulatory agents that can reduce RSV-associated inflammation. Furthermore, we will test if delivery of an RSV vaccine together with intranasal probiotics enhances both safety and efficacy of this vaccine.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Delputte Peter

Research team(s)

Project type(s)

• Research Project

Abstract

Air pollution is a major environmental and social issue, causing a vast array of negative health effects. Approximately 7 million deaths and an economical cost of 3.28 trillion euros worldwide can be attributed to air pollution. In this research a new, promising method will be tested to fight high urban air pollution levels. More specifically, the potential of leaf-dwelling or phyllosphere bacteria (PB) to degrade urban air pollutants (particulate matter and volatile organic compounds) into less toxic forms, also called bioremediation potential. This will be done with both field and laboratory experiments. The project is divided into four workpackages (WP). In WP1, the different PB present on 70 plant species will be determined and their preferences for leaf characteristics will be tested. WP2 will map which PB typically occur under high levels of urban pollutants and how they change through the growing season. In WP3 the specific bioremediation potential of promising PB will be tested and in WP4 all these results will be brought together. Then the first realistic numbers of what the application of the right plant-PB-combination could mean for the ambient urban pollutant levels will be estimated on the basis of computer models. The ultimate aim of this research is to find the optimal plant-PB-combination to optimize the bioremediation potential of vegetation in the city.

Researcher(s)

• Promoter: Samson Roeland
• Co-promoter: Lebeer Sarah
• Fellow: Muyshondt Babette

Research team(s)

Project type(s)

• Research Project

Abstract

A specific microbial habitat exists where the atmosphere and plant meet. It is called the phyllosphere and is usually dominated by the leaf surfaces. All plant leaves, worldwide, are estimated to cover a surface area that approximates twice the global land surface. The phyllosphere can therefore be considered as a vast microbial habitat, with great potential importance. Recent advances in microbial DNA sequencing approaches have significantly improved our insights in these microbial ecosystems: a few pioneering studies –including from the applying consortium- have now documented that the phyllosphere harbours diverse bacterial communities shaped by both plant physical characteristics and metabolism, and environmental conditions. In turn, decades of physiological research has yet demonstrated that these epiphytic bacteria can affect the host plant by preventing colonization of certain plant pathogens and encouraging plant growth, among other effects. Air pollution and its adverse health effects are still increasing worldwide. Particulate matter (PM), volatile organic compounds (VOCs), soot, diesel exhaust particles and heavy metals are among the most problematic air pollutants. Adverse health effects include heart disease, stroke, respiratory diseases like asthma, Alzheimer's disease and cancer. Various technological solutions to remove air pollutants have yet been developed, of which catalytic filters and motor adaptations have probably made the largest impact on the filtration of polluted exhaust gases. Also for indoor application, various air purification systems exist, but they are mostly chemical, physical or photocatalytic oxidation. There is a clear need for more sustainable, bio- and nature-based solutions to combat air pollution. Bioremediation is the use of microorganisms to degrade or transform environmental contaminants into their less toxic forms. In this project, a novel bioremediation approach is explored, i.e. the potential application of plant-associated bacteria of the phyllosphere to degrade or remove specific air pollutants from the ambient air.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Samson Roeland

Research team(s)

Project type(s)

• Research Project

Abstract

Most of the farmers and industries rely on the microbial inhibition tests as a screening tool for a broad range of antibiotics because it is natural, intuitive, and simple enough to be operated by non-specialists outside laboratories. Unfortunately, it suffers from drawbacks such as long analysis time and sensitivity issues. To improve the on-site screening test, we introduce the pioneering idea to couple cost effective and sensitive amperometric sensors with bacterial inhibition tests. Our method will lower the risks for public health and operational costs for industries.

Researcher(s)

• Promoter: Vandenheuvel Dieter
• Co-promoter: De Wael Karolien
• Co-promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Plant diseases cause major losses in agriculture and are currently being eradicated with conventional or organic pesticides. Agriculture needs to become more productive as well as more sustainable to face the challenges of a growing population, climate change and other environmental problems. Protecting crops from diseases in an environmentally friendly way is a big challenge. The phyllosphere is the surface of the plant exposed to the atmosphere and it is occupied by microorganisms. The microorganims in the phyllosphere are known to interact with the plant they are inhabiting. It has been shown before that a healthy microbial population on the phyllosphere, a.k.a the phyllosphere microbiome, could help prevent or treat plant diseases and promote plant growth. Furthermore, previous research showed that a greater variety of bacteria in the phyllosphere increases plant productivity. This research aims to better understand the phyllosphere microbiome. This understanding will be used to treat and adjust the phyllosphere microbiome and thereby improve crop production and protection. Mixtures of bacteria that could have a positive effect on the plant, "plant probiotics", will be formulated. These plant probiotics will originate from isolated and cultured phyllosphere bacteria as well as from fermented compost extracts. Finally the effect of these plant probiotics on the phyllosphere microbiome and on plants will be studied.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Samson Roeland
• Fellow: Legein Marie

Research team(s)

Project type(s)

• Research Project

Abstract

In this project, we aim to use a combination of bio-informatic and experimental approaches to explore important aspects of niche flexibility and functions of Lactobacillus strains, using the Lactobacillus casei/rhamnosus group as case study. Here, niche-adaptation of these bacteria will be explored for rather unexplored niches, namely fermented vegetables (carrots), the human vagina and the human respiratory tract, starting from isolates, which are in- house available through previous projects. Experiments will include niche-swap experiments, experimental evolution and functional analyses by constructed knock-out mutants. Special attention in this PhD project will be directed towards the role of adhesion in niche colonization. In previous research, a new type of fimbriae was found in L. casei and this will be further explored and molecularly characterized in this PhD project.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Ahannach Sarah

Research team(s)

Project website

Project type(s)

• Research Project

Abstract

Probiotics are defined as live microorganisms which, when applied inadequate amounts, confer a health benefit to the host (FAO/WHO, 2001). These microbes are generally applied in the gastrointestinal tract via fermented food products or capsules. In previous research, we isolated bacterial strains with potential probiotic properties for the upper respiratory tract based on in vitro laboratory tests and genome sequencing. Here, we want to deliver the POC that – at least one of - these strains has also interesting properties in vivo, i.e. that this strain is able to –temporarily- colonize the upper respiratory tract of healthy volunteers after oral and nasal application.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Kiekens Filip
• Co-promoter: Vanderveken Olivier

Research team(s)

Project type(s)

• Research Project

Abstract

Pelvic irradiation is a common treatment strategy for various cancers such as colon cancer and cervical cancer. High irradiation doses result in many side effects such as diarrhea, inflammation and microbiome dysbiosis. In this project, the effect of Arthrospira on many of these side effects will be explored at a molecular level, in a mouse model developed at SCK. These effects will be compared with the model probiotic Lactobacillus rhamnosus GG. Growth of Arthrospira will also be optimized.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Although not visible by the naked eye, the air is teeming with bacteria. Inevitably, these airborne bacteria are frequent visitors of the respiratory system. Endotoxins are highly inflammatory lipid components of Gram-negative bacteria. In an urban environment, they may act by heightening immune responses in the presence of other pollutants, such as particulate matter (PM). However, our knowledge on the involvement of airborne endotoxins in PM-related inflammation is restricted on the methods used for its collection, quantification and analysis. Until now, collection methods have relied on filter-based samplers which are far from ideal for the recovery of endotoxins. For this reason, our study focusses on developing a new, more efficient, non-filter based strategy for the monitoring of endotoxins in an urban environment. Our first experiments could detect much higher ambient endotoxin concentrations than the available data in the literature for urban studies. This re-sparks the debate of the importance of endotoxins in the health effects of PM. Therefore, detailed studies will be done in cell models to investigate the contribution of endotoxins in PM-associated inflammation in relevant concentrations and in comparison with other pollutants. Finally, responses to natural PM exposure will be analysed in vivo at RNA level in nasal brushing samples and compared with the responses observed in the cell models.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Moretti Serena

Research team(s)

Project type(s)

• Research Project

Abstract

Lactobacilli are an interesting group of bacteria found in a large variety of ecosystems, from the human gut to milk to plant surfaces and other environments. They are used in food fermentations and as health-promoting bacteria. It is not yet clear how lactobacilli are able to survive and thrive in these different environments. Did Lactobacillus strains adapt, each to a specific environment? Or are some strains "nomads", able to survive in many different environments? We will attempt to solve the adaptation question in two ways. First, we will study gene copynumber variation between Lactobacillus strains. The DNA of a bacterial strain can contain multiple copies of a single gene, and this copy-number can differ between strains. It was recently observed that copy-number variation in gut bacteria is often found in genes linked to environmental adaptation. As a second way to investigate environmental adaptation, we will reconstruct the evolutionary history of the Lactobacilli. Bacterial strains can evolve in multiple ways; two important types of evolutionary events are that they can acquire genes from other bacteria or genes can get lost. We will use the full DNA sequences of at least fifty strains per species to find out which genes were acquired and which ones were lost by which ancestors in the course of evolution. We can then see whether there is a connection between these gene gain and loss events and the environment in which these ancestors lived.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Wittouck Stijn

Research team(s)

Project type(s)

• Research Project

Abstract

Aerobic granular sludge (AGS) is an innovative development in biological wastewater treatment. However, AGS systems are very complex, and to be able to further exploit the potential of AGS, more insight is needed into the different factors governing their formation, maintenance, and composition. The goal of this project is to gain more insight into the properties and composition of aerobic granules, and into the mechanism of their formation. To this end, we will explore the feasibility of obtaining aerobic granular biofilms with a pure microbial culture of Pseudomonas sp. CMR12a or with a mixed microbial culture, starting from a pure-culture inoculum.

Researcher(s)

• Promoter: D'aes Jolien
• Co-promoter: Dries Jan
• Co-promoter: Lebeer Sarah

Research team(s)

• Biochemical Wastewater Valorization & Engineering (BioWaVE)

Project type(s)

• Research Project

Abstract

In this project, we will explore microbiological and formulation aspects of micro-encapsulation of live bacteria for probiotherapy of skin applications through collaboration with an Industrial partner.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Respiratory infections know a high morbidity. Nowadays, patients are treated with over-thecounter products such as decongestives and expectorants. There is also an overuse of antibiotics, which leads to antibiotic resistance. Therefore, a new therapy, based on microbiomemanipulation, is imposed. This research will focus on the improvements for this new therapeutic strategy. The human body consists of many microorganisms lives in symbiosis with each other, resulting in beneficial effects for both. Pathogens can disturb this symbiosis. The homeostasis can be restored by probiotic formulations. They will reinforce the innate immunity. It is the aim of this research to develop a solid oral dosage form for the pharyngeal delivery of probiotic bacteria, which can prevent and treat respiratory infections. Mechanical stress during compression can damage the bacteria, which can result in therapy failure. The aim of this research is to protect the bacteria by choosing the correct formulation and process parameters. This research will be combined with detailed microbiological analysis. The stability of the formulation will be investigated by stability tests. Finally, the efficacy and safety of the formulation will be determined by in vitro tests. Successful results can lead to clinical studies on humans and to new businesses. This can result in a medical and economical progress..

Researcher(s)

• Promoter: Kiekens Filip
• Co-promoter: Lebeer Sarah
• Fellow: Byl Eline

Research team(s)

Project type(s)

• Research Project

Abstract

Proposed by the University, the Francqui Foundation each year awards two Francqui Chairs at the UAntwerp. These are intended to enable the invitation of a professor from another Belgian University or from abroad for a series of ten lessons. The Francqui Foundation pays the fee for these ten lessons directly to the holder of a Francqui Chair.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Recent studies indicate that various disorders of the upper respiratory tract (URT) involve an imbalance of the microbiota in this niche, without the clear dominance of a single pathogenic species. These studies highlight that the microbial ecology of these niches needs to properly studied for a better understanding of the pathogenesis of these URT diseases. However, many details on these microbial imbalances need to be unraveled. Therefore, this project aims to characterize the microbiome in the URT by Illumina MiSeq microbial community profiling using the 16S rRNA gene as main target. In addition, we will screen for niche-specific lactic acid bacteria (LAB) as potential beneficial and probiotic microbes and we will compare their occurrence, genetic potential and functional activity with more pathogenic species such as Corynebacterium and Staphylococcus aureus. Chronic rhinosinusitis (CRS), a common URT disease, is chosen as important case-study to unravel the microbiome of the URT. Samples of CRS patients will be functionally and quantitatively compared with healthy individuals.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Wittouck Stijn

Research team(s)

Project type(s)

• Research Project

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

Abstract

This project aims to explore probiotic microbial approaches that can efficiently reduce the incidence and symptoms of diseases of the upper respiratory tract (URT). Hereto, we will set up an enabling platform to (1) select innovative probiotic strains for this original human body niche of probiotic application, (2) develop innovative processes for the formulation, upscaling and application of these probiotic strains and (3) develop innovative services based on cellular, more complex polymicrobial model systems and microbiome analyses of the URT to monitor the impact of probiotics, food and pharmaceutical compounds on the microbiota of the URT.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Kiekens Filip
• Co-promoter: Vanderveken Olivier

Research team(s)

Project type(s)

• Research Project

Abstract

In this project the potential antipathogenic and immunomodulatory activity of exopolysaccharides of model Lactobacillus strains is investigated by in vitro and in vivo models. Methods for extraction, characterization and formulation of the exopolysaccharides are also optimized.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Delputte Peter
• Fellow: Allonsius Camille

Research team(s)

Project type(s)

• Research Project

Abstract

Although not visible by the naked eye, the air is teeming with bacteria. Inevitably, these airborne bacteria are frequent visitors of the respiratory system. Endotoxins are highly inflammatory lipid components of Gram-negative bacteria. In an urban environment, they may act by heightening immune responses in the presence of other pollutants, such as particulate matter (PM). However, our knowledge on the involvement of airborne endotoxins in PM-related inflammation is restricted on the methods used for its collection, quantification and analysis. Until now, collection methods have relied on filter-based samplers which are far from ideal for the recovery of endotoxins. For this reason, our study focusses on developing a new, more efficient, non-filter based strategy for the monitoring of endotoxins in an urban environment. Our first experiments could detect much higher ambient endotoxin concentrations than the available data in the literature for urban studies. This re-sparks the debate of the importance of endotoxins in the health effects of PM. Therefore, detailed studies will be done in cell models to investigate the contribution of endotoxins in PM-associated inflammation in relevant concentrations and in comparison with other pollutants. Finally, responses to natural PM exposure will be analysed in vivo at RNA level in nasal brushing samples and compared with the responses observed in the cell models.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Moretti Serena

Research team(s)

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand the client. UA provides the client research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Kiekens Filip

Research team(s)

Project type(s)

• Research Project

Abstract

The goal of this PhD project is to select lactic acid bacteria in order to improve the fermentation process of vegetable juices using an integrated and interdisciplinary microbiological approach. Therefore the microbial diversity of spontaneous fermented vegetable juices will be studied. In a second step lactic acid bacteria isolated from the fermentation process will be studied using phenotypic assays and genome sequencing.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Wuyts Sander

Research team(s)

Project type(s)

• Research Project

Abstract

Ligands of the innate immune system form an important new class of adjuvants, but the desired immunostimulation is often linked with toxicity and serious side-effects. These ligands or 'microbe-associated molecular patterns' (MAMPs) can also be found on the surface of lactobacilli with a 'generally regarded as safe' status. Various studies have demonstrated the specific effects of certain lactobacilli and their surface molecules, but the potential of MAMPs such as exopolysaccharides and glycoproteins of lactobacilli still requires further investigation. Hereto, the project is divided in three parts. First, the molecular interactions between the glycoconjugates and receptors such as Toll-like receptors and C-type lectins will be mapped. Next the in vitro immune response of these molecules in immunological important cells will be investigated. Finally, the potential of selected molecules will be validated in a mouse model.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Delputte Peter
• Fellow: Allonsius Camille

Research team(s)

Project type(s)

• Research Project

Abstract

Lectins, known as carbohydrate-binding proteins, are considered as important signal molecules, which regulate physiological processes and multicellular communities. Lactobacillus species are important beneficial microorganisms that are ubiquitously present on plants, in milk and on mucosal surfaces of animal and human host. Lectins molecules on the cell surface of the Lactobacillus strains that can directly interact with the pathogens or host cells are important for their beneficial functions. In this project we aim to functionally characterise lectin proteins form the gastrointestinal probiotic L. rhamnosus GG, the vaginal probiotic L. rhamnosus GR-1, the vaginal natural isolate L. plantarum CMPG5300 and the L. plantarum strains CMPGlp9 and CMPGlp10, which were isolated from cauliflower soils. The exact sugar/ligand specificity of the lectin molecules, their role in adhesion to variety of host cells and pathogen exclusion will be investigated. Furthermore in this project, we aim to gather more insights in genetic and functional aspects that are involved in the optimal heterologous expression and secretion of lectins by lactobacilli. We will focus on the probiotic L. rhamnosus GG and L. rhamnosus GR-1 strains, and two well-known mannose-specific lectins, i.e actinohivin and griffitsin. Ultimately this project proposal will provide better understanding of the fundamental principles governing the beneficial functions of Lactobacillus species for various niches.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Urbanization has resulted in health-threatening concentrations of air pollutants like particulate matter (PM), a diverse and complex mixture of air-suspended particles. PM affects more people than any other pollutant, and can be associated with e.g. asthma exacerbations and heart and vascular diseases. Studies indicate that many of the observed health effects are related to the capacity of inhaled PM to induce airway inflammation. Although not extensively studied and often neglected in PM sample collection methods, microbial endotoxins are components of PM with naturally high inflammatory potential. This response may be further enhanced with co-exposure to the other pollutants of PM. It has been suggested that transition metals may have a synergistic effect, however, novel approaches are needed to provide information on the biologically reactive state of the metals. This doctoral project therefore aims to develop and validate biologically relevant methods for analysis of airborne endotoxins and transition metals.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Moretti Serena

Research team(s)

Project type(s)

• Research Project

Abstract

Production of poly-3-hydroxyalkanoate (PHA) bioplastic by activated sludge is a promising strategy for valorization of wastewater, which could simultaneously lower the still too high production cost of PHAs. The aim of this project is to develop a fast and reliable quantitative PCR assay for routine analysis of PHA producing microorganisms in activated sludge.

Researcher(s)

• Promoter: D'aes Jolien
• Co-promoter: Lebeer Sarah

Research team(s)

• Biochemical Wastewater Valorization & Engineering (BioWaVE)

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand the Hercules Foundation. UA provides the Hercules Foundation research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Maes Louis
• Co-promoter: Delputte Peter
• Co-promoter: De Meyer Guido
• Co-promoter: Dewilde Sylvia
• Co-promoter: Kumar-Singh Samir
• Co-promoter: Lambeir Anne-Marie
• Co-promoter: Lebeer Sarah
• Co-promoter: Leroy Jo
• Co-promoter: Van Cruchten Steven
• Co-promoter: Wenseleers Wim

Research team(s)

• Laboratory for Microbiology, Parasitology and Hygiene (LMPH)

Project type(s)

• Research Project

Abstract

During the last decades, the modem hygiene hypothesis, which links the increased incidence of immune disorders such as asthma with reduced contact with micro-organisms due to increased hygiene, has gained a lot of attention. This project aims to investigate the molecular basis underlying the hygiene hypothesis, by studying the importance of toll-like receptors (TLRs) in detennining the susceptibility for the development of immune disorders.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

In this project, we aim to perform a molecular analysis of glycoproteins in the beneficial bacterial strain Lactobacillus rhamnosus GG (LGG). Hereto, a thorough genetic, biochemical and functional characterization of the glycoproteins of LGG will be performed in relation to specific aspects of its physiology, cell wall morphology and interactions with the host. The molecular knowledge obtained in this project will provide novel insights in the glycobiology of beneficial microbes.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

Probiotics are primarily known as food additives that can have positive health benefits by improving the microbial balance in the gut. Infections of the throat and nose are also characterized by microbial imbalances. Treatment of these infections with a local spray, tablets or mouthwash of probiotics, in particular with Lactobacillus species, can improve the efficacy of the currently available medication and provide an alternative and novel site of application for probiotics.

Researcher(s)

• Promoter: Lebeer Sarah
• Co-promoter: Kiekens Filip

Research team(s)

Project type(s)

• Research Project

Abstract

The human body is occupied by a vast number of microorganisms, which are collectively called microbiota. They inhabit the skin, oronasopharyngeal cavity, genital tract and gastrointestinal tract. The microbiota present in each of the niches provides to the host a vast number of health effects, including inhibition of bacterial pathogenic colonization, stimulation of immune responses and promotion of immune regulation. Interest in the beneficial functions of the human microbiota has boomed within the last ten years, thanks to major advances in next generation sequencing technologies in so called 'metagenomic studies'. In this rather new 'microbiota field', the potential of nasal and pharyngeal probiotics is currently unexplored, while they hold great promise for multiple reasons. Among these, the facts that (i) upper respiratory tract infections, including acute otitis media, are the leading causes for the prescription of antibiotics in children and that (ii) the oronasopharyngeal cavity is quite accessible and generally populated by a less complex and less dense microbiota than the gut, form a major incentive for the proposed PhD project. In this study, fundamental questions underlying the potential of oronasopharyngeal application of probiotic lactobacilli will be studied. Hereto, a stepwise in vitro experimental design will be followed. The research questions that will be addressed include: (i) are lactobacilli tolerated by upper respiratory tract cells, (ii) can we select lactobacilli with inhibitory activity against typical bacterial respiratory pathogens, (iii) Do these lactobacilli also have potential to counteract aspects of the pro-inflammatory and oxidative activity of air pollution, (iv) which are the molecular mechanisms of probiotic action involved? To study potential modes of action, we will implement the construction and phenotypic analysis of dedicated knock-out mutants of Lactobacilli lacking putative probiotic factors. These in vitro experiments should deliver data for later in vivo animal studies and clinical trials.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: van den Broek Marianne

Research team(s)

Project website

Project type(s)

• Research Project

Abstract

This project represents a formal research agreement between UA and on the other hand Erasmus Mundus. UA provides Erasmus Mundus research results mentioned in the title of the project under the conditions as stipulated in this contract.

Researcher(s)

• Promoter: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project

Abstract

A steady increase in chronic inflammatory diseases can be observed in regions with a high degree of industrialization and urbanization since World War II. The pro-inflammatory capacity of ambient air particulate matter and other air pollutants seems an important factor in the pathogenesis of these diseases, but the underlying mechanisms are not well understood. This project aims to generate more insights in the (micro)biology of air pollution by application of techniques from the fields of molecular microbiology and immunology to investigate the presence of micro-organisms and their endotoxins in particulate matter (PM) and to characterize the pro-inflammatory capacity of PM in detail.

Researcher(s)

• Promoter: Lebeer Sarah
• Fellow: Lebeer Sarah

Research team(s)

Project type(s)

• Research Project