PhD defence by Jacob Agerbo Rasmussen


How salmon hooked me: Host-microbe interactions in aquaculture” a PhD defence by Jacob Agerbo Rasmussen.

Official title: Host-microbe interactions in aquaculture

When: Monday, August 29th , 2022, at 1pm

Where: Øster Voldgade 5, Geological Museum Auditorium, 1350 Kbh K


Recent advances in molecular and computational technology have enabled researchers to decipher complex biological processes related to host and microbe, which are fundamental for the living of higher organisms. The gut microbiota has been in the researcher’s scope for the last decade. Research has resulted in vast associations with a broad palette of its host’s phenotype, including food digestion, nutrient utilization, homeostasis and immune response regulation. Globally, there are more than 33,000 teleost species, representing nearly half of the vertebrate richness and a vast range of physiology, ecology and life histories of the globe. However, despite the abundance of teleosts worldwide, very little information about the gut microbiota in a teleost, their functioning, ecological dynamics, and interaction with their host are unknown. Thus, how these host-microbe interactions play out in teleost are yet to be described. 

In this thesis, I have used a broad palette of data sets to describe to ecology, functioning, phylogenomics, and evolution of the bacteria within intestinal salmonid environments complementing decades of bio-monitoring, using 16S rRNA gene-based technology by providing genomic information for lineages missing a functional context, and allowing us to search for bacterial eco-type variation within the landscape of microbial populations associated with salmonid hosts. 

My research combined untargeted metabolomics with 16S RNA gene metabarcoding and metagenomics to increase the functional knowledge of host-microbe interactions in aquaculture-relevant salmonids. The results demonstrate a framework for using multiomics to investigate interactions between host-microbiota. Our framework enables us to better assess the potential of ’functional feeds’ compared to studies that only measure overall growth performance or characterize microbial composition in intestinal environments. 

Investigations of the host-microbiota interactions of salmonids could lead to potential discoveries for feed and health optimisation resulting in more sustainable solutions, which is highly important for the aquaculture industry.