Research team

Environmental Ecology & Applied Microbiology (ENdEMIC)

Expertise

My research expertise involves studying the beneficial role of microbiota members in the respiratory tract and other body niches at the experimental and clinical level. Specifically, I focus on the interactions between beneficial bacteria and the host immune system, and/or invading viral and bacterial pathogens. As a bioscience engineer, I also implement genetic modification of beneficial lactic acid bacteria and microbiome modulation by probiotics in health and disease.

The first cornerstones towards microbiome-friendly underwear 01/11/2021 - 31/10/2023

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.

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Genetic screening, analysis and engineering of vitamin production in non-gut lactobacilli 01/11/2021 - 31/10/2023

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.

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Unraveling direct interactions between the airway microbiota and respiratory syncytial virus. 01/10/2021 - 30/09/2024

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.

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