PhD Projects » ESR 11: Development of more quantitative viral metagenomics approaches to investigate the role of bacteriophages in the honey bee gut and their effects on health and development

Nikolas Basler

I studied Life Sciences (BSc) and Biochemistry and Molecular Biology (MSc) at the University of Potsdam, Germany. During these studies, I was overwhelmed by the amount of interesting scientific fields to discover in biology and I made sure to see as many of them as possible.

My bachelor thesis revolved around ancient genomics of mammals and in my master thesis I tried to elucidate the genetic mechanism behind a peculiar flower morphology. Finally, I extended my knowledge on bacteriophages by an Erasmus+ internship in the Molecular Virology Research Unit at the Adam Mickiewicz University in Poznań, Poland.

All these projects combined laboratory methodology with computational analysis of sequencing data. With these experiences, my broad interests converged into the decision to become a phage researcher on the interface between wet lab and computer work. This reflects the spirit of the VIROINF ITN which I am happy to be a part of! I am excited and curious to see which synergies will emerge from the collaboration of bioinformatics and virology inside this network.

Host institution:
Katholieke Universiteit Leuven (KU Leuven), Belgium
Local supervisor:
Prof. Dr. Jelle Matthijnssens (KU Leuven)
Local co-supervisor:
Prof. Dr. Philippe Lemey (KU Leuven)
Project partner:
ESR 13, ESR 12
Work packages:
WP 1.1 Virus identification
WP 1.2 Host prediction

Jelle Matthijnssens
Philippe Lemey

Project description

Very few is known about the role of the gut virus population (the virome) in health and disease of honey bees. Our lab developed the NetoVIR protocol to purify viral particle from biological samples and to deep sequenced them using Illumina NGS technology. Using this approach, our lab recently published a paper describing a diverse set of bacteriophages associated with honey bees, and several more papers on eukaryotic honey bee viruses are in preparation. However, this type of research is hampered by the inherent introduction of biases in the viral composition after viral purification and random amplification before Illumina sequencing. Furthermore, the interpretation of the roles of identified novel bacteriophages in health and diseases, is hampered by many factors including the lack of good sequence databases and knowledge about their bacterial host.

In the current project, we will

  • test and validate different approaches to obtain a more quantitative virome protocol;
  • Link novel bacteriophages to their host using bacterial 16S data, as well as novel tools developed in the framework of VIROINF;
  • use these optimized wetlab and in silico protocols to study the role of bacteriophages in honey bee health, using in vitro and in vivo approaches.

For the first aim we will use: (a) approaches to spike in known amounts of viruses into the samples as internal controls, (b) methods to accurately count virus particles by flow cytometry (in collaboration with NIOZ) and (c) test Minion sequencing technology on unamplified extracted viral nucleic acids.

For the second aim we will collaborate closely with ESR 13, ESR 12 and Baseclear for the improvement of the existing bioinformatics analyses and interpretation of the viral NGS data. Their expertise in bacteriophage and eukaryotic virus identification from metagenomics datasets, respectively, and the tools they will develop will be very important for the success of this project.

The third objective of this project is to provide an in depth in silico and in vivo characterization of the bacteriophage population infecting the most important members of the honeybee gut microbiota, as well as studying their role in honey bee health and development. For the sample we have access to samples collected during the European B-GOOD project, headed by Prof. Dirk de Graaf. Both the bacteriome (16s) and the virome (shotgun) inhabiting the digestive tract of these honey bees will be characterized. Furthermore, bacteria will be isolated and characterized from the crop, midgut and hindgut of the collected honeybees, and finally these bacterial isolates will be used to isolate bacteriophages followed by their genome sequencing and functional gene annotation. Depending on the available time, we may also start with inoculation experiments of life honey bees.