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Understanding the role of the rainbow trout metagenome on growth and health in aquaculturally farmed fish

Periodic Reporting for period 1 - HappyFish (Understanding the role of the rainbow trout metagenome on growth and health in aquaculturally farmed fish)

Okres sprawozdawczy: 2018-08-01 do 2020-07-31

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.
This project tested the effect of three different feed formulae on the gut metagenome of rainbow trout. This was done by sampling gut content and host tissue from fish reared on three different feed types: 1) control, 2) control + probiotic, 3) control + synbiotic. A probiotic is a life bacterial culture and synbiotics are the combination of a probiotic strain together with a substrate that is intended to further boost the growth of the added probiotic microorganism.

We then build a novel catalogue of the entire metagenome - i.e. the combined genetic material of all microorganisms residing in the gut of the rainbow trout. This metagenome includes 173,000 different genes that can all contribute to the general metabolism of the fish hosts. The metagenome resource also represents the first example generated for any fish species and will help set a new standard for metagenomics research related to the aquaculture field.

We then compared the metagenome profiles among rainbow trout reared on the three feed types. Here, we saw that the two novel feeds including pro- or synbiotic additives caused a significant change in the gut microbiota composition. These differences were caused by a change away from the ‘normal’ microbiome when adding pro- or synbiotics to the feed. However, the results so far suggest that the feed additives may do more harm than good, by interrupting the natural gut microbiota. These results will be followed up in ongoing research, but they have already proven to be of high relevance to the aquaculture industry by adding novel insights to the effect of these feed additives.

Interestingly, we also observed a striking correlation between the presence of a specific bacteria species and important traits related to growth, where rainbow trout having a high abundance of this species also showed better growth performance. These results hold great promise for future work considering gut microbiota to further boost gut health and sustainability in aquaculture fish farming.
The major general impact of the project to go beyond the state-of-the-art is the demonstration of a novel so-called Holo-omics approach to understand the role of microbiomes for their host’s health and fitness. Previously, it was the norm to study either genomes of multicellular organisms or, more recently, their associated microbiomes in isolation as to try and understand the role of either domain in shaping traits such as growth performance in animal productions. The HappyFish project has contributed to advancing holo-omics in relevant research fields, including aquaculture.

It is now expected that the results will continue to move forward the application of full shotgun based whole metagenome sequencing in aquaculture and studies of fish in general. While studies looking at the microbiome in fish, including many of aquaculture relevance, these previous studies have only looked at a single conserved gene which limits the functional insights you get. The full catalogue of 173,000 microbial genes generated here will undoubtly serve to demonstrate the possibility and feasibility of using whole metagenomes to now get more functional information about the role of the gut microbiota in shaping growth and health in fish and similar animal species.

In conclusion, it is now expected that this project will contribute to transition the aquaculture industry into an even more sustainable food production choice, compared to other animal protein sources, for the benefit of all end consumers.