Aquaculture is the fastest growing food-producing sector world-wide, but is simultaneously challenged by suboptimal conversion of fish feed limiting revenue and burdening the environment. This project used state-of-the-art metagenome sequencing to obtain new functional insights about the health effects of the microorganisms inhabiting the rainbow trout (Oncorhynchus mykiss) gut. The results will facilitate development of more effective feed protocols in fish farming. The ability to reduce the use of expensive fish feed, antibiotics and vaccines in aquaculture, offers a huge potential to boost economic gains and reduce environmental impacts. Currently, more than 50% of consumed fish are farmed and the increasing human demand for high quality protein indicates that this global trend will continue. A key challenge for securing the continued growth and development of the aquaculture industry is to develop sustainable solutions to improve feed efficiency as feed accounts for >50% of the total cost of producing a fish.
Animal protein is often used in fish feed, but it is increasingly being substituted by plant based ingredients, such as rapeseed and sunflower, due to the increasing prices and the insufficient availability of animal derived ingredients. Hence, originally piscivorous (meat eating) fish are being turned into vegetarians, but the effects of such a radical diet change on the composition of gut-microorganisms, gut health and ultimately on the growth of farmed fish remains poorly understood.
It is well established that microorganisms in the gut play a crucial role in the overall health of the host organism, including us humans, by conveying nutritional advantages and increased immunity against pathogens. Research detailing the complete assembly of all enteric microorganisms (gut-microbiota), and their combined genome (i.e. metagenome), is currently revolutionizing the way that we understand how microbes shape human and animal health by interacting with metabolic and immunological pathways of the host. While these methods are quickly advancing into livestock production, their use in fish farming lacks behind even though the FAO prioritizes the increased integration of genomic tools into aquaculture research.
So, if we are to gain a more complete understanding of the overall health and growth in farmed fish, we have to use of a hologenomic ‘metaorganism’ perspective including knowledge about host-microbe interactions. In this project I have taken advantage of a new potential offered by metagenome sequencing to characterize hitherto unknown functions of individual genes in the metagenome for the aquaculturally important rainbow trout. This is in contrast to any previous study in fish that have all relied on a single gene marker for characterising broad changes in species composition, but have not been able to directly study the functions provided by the gut microbiota.
The overall objectives have been to introduce metagenomic techniques into the aquaculture research field by using an interdisciplinary approach to current challenges by investigating the effects on the rainbow trout microbiota when reared on different types of feed with and without addition of supposedly beneficial bacteria as we already know from our everyday dairy products.
