Research Stijn Wittouck

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)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

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)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

Project type(s)

• Research Project

Abstract

Background The bacterial genus Lactobacillus has historically been the source of many strains with supposed but also proven health benefits. The selection of strains with potential health benefits has always been performed on a rather ad hoc basis based on knowledge on the isolation source of the strain and on expensive and labor-intensive lab screenings. Now that we are able to sequence whole genomes of many bacterial strains relatively cheaply it has become possible, in theory, to identify genomic signatures of strains with potential health benefits to be used for more informed, and more upscalable, screening. For some well-studied probiotic properties, the gene families encoding them have been identified and can therefore be used for probiotic screening. An example are the pili of the well-known probiotic strain Lactobacillus rhamnosus GG that are responsible for adhesion to the human colon epithelium. The gene cluster encoding these pili has been identified and the presence of this cluster can easily be identified in a given bacterial genome. Pili, as well as other potentially probiotic properties, can now already be used as screening criteria for potential probiotic strains. Systematic screening of genomes for these properties has only been performed in a limited way; the most comprehensive study to date included more than 200 species of Lactobacillus, but was limited to only one representative strain per species, while many of these genes are known to be very strain-specific and many more genomes are publicly available. A second way to improve genomic screening for probiotic potential is to systematically identify, on a large scale, genomic signatures associated with Lactobacillus strains engaging in symbiotic relations with Homo sapiens. These genomic signatures can be the presence of certain gene families, such as the gene cluster encoding the pili of LGG, but also gene copy numbers or even the presence of certain pieces of DNA gained from the environment, such as viral genomes or transposons, that betray the habitat of the strain. Goals The goal of this project is to enhance the potential of the genus Lactobacillus as a source of strains with potential health benefits. We aim to do this in two ways. First, we want to characterize already known gene families that encode probiotic properties by assessing their distribution across the more than 2000 Lactobacillus genomes that are publicly available. We will also assess their presence in the more than 100 genomes of strains isolated and sequenced by our own lab. Our second goal is to identify genomic signatures of symbiotic relations with humans as a species. Since we don't know on beforehand which strains are symbiotic for most of the publicly available genomes, we will perform this search in an unsupervised manner. To put it differently: we will look for sets of genomes that are not necessarily closely related, but underwent similar adaptations in their recent evolutionary history. We will look, in other words, for convergent evolution. If we succeed in finding groups of strains that underwent convergent evolution, we can assess whether already known probiotic strains are part of one or more of these groups. This would be a strong indication that other strains within these groups will also show probiotic potential.

Researcher(s)

• Promoter: Wittouck Stijn

Research team(s)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

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)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

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)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

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)

• Environmental Ecology & Applied Microbiology (ENdEMIC)

Project type(s)

• Research Project