CRISPR immune defence systems and their effects on phage-bacterium co-evolution in the fish pathogen Flavobacterium columnare (Kone Foundation)

Main funder

Funds granted by main funder (€)

  • 57 600,00

Project timetable

Project start date: 01/03/2018

Project end date: 29/02/2020


I am applying for a grant to fund the remaining two years of my PhD thesis. My research centers around the molecular-level interactions between bacteria and their parasites, bacteriophages. In addition to gaining basic knowledge on ecological and evolutionary aspects of phage-bacterium interactions, my results will also be useful in the applied fields of phage therapy and genome-editing.

Bacterium-borne fish diseases are a huge global problem, resulting in millions of dollars worth of damage annually. One pathogen responsible is Flavobacterium columnare, a fresh-water fish bacterium, which causes deadly lesions in fish skin and gills. As the power of antibiotics dwindles due to development of resistance, alternative measures are constantly being sought. Phage therapy, the use of phages in combating bacterial diseases, is one promising solution. However, our knowledge of phage-bacterium interactions is still limited. In my research, I focus on a specific bacterial immune system known as CRISPR. This system grants bacteria adaptive immunity against phages, allowing them to adapt to pre-existing phages, which hampers the power phage therapy. The details of this system in F. columnare and its phages is unknown, although understanding them is crucial for the development of effective treatments.

CRISPR is also known for its use in genome-editing. A recently discovered CRISPR type is found in F. columnare and elucidating its functions may yield important information for the genome-editing industry.

I have been working on the thesis since March 2016. The first publication of the project regarding phages and bacteria in their natural environment has been published in Nature Communications in July 2017. I am currently performing laboratory experiments for the second publication (,olecular details of the CRISPR systems of F. columnare in controlled laboratory settings). These experiments are set to finish by the end of 2017 and the manuscript written in Spring of 2018. In the beginning of 2018 I will start the experiments for my third publication, which will study and compare the roles and relationships of different immune systems in F. columnare - this paper is due to be out by the end of 2018. After this I will concentrate on possible bacterial gene expression regulation by the CRISPR system - this study will take most of 2019. I aim to graduate in Spring 2020.

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Last updated on 2021-17-03 at 12:06