A microbial basis for Atlantic Salmon energetics

Lead Research Organisation: University of Glasgow
Department Name: College of Medical, Veterinary &Life Sci


Production of the global salmonid aquaculture industry now exceeds 2.4 megatons per annum. Major European producers expect to expand their outputs between 30-50% over the next five years. Ambitions for expansion on this scale create major concerns around fish welfare, ecological impact and the sustainability of salmon feed components.
Nutrition lies at the heart of the issue. In the wild, Atlantic salmon are specialized carnivores. In aquaculture, in a move away from the unsustainable use of wild fish protein and oil, proteins of plant origin now constitute the majority (>60%) of their diet. Associated digestive abnormalities are common. In addition, plant-based diets may affect the rate at which nutrients are absorbed and the associated growth rate of salmon, which determines how quickly they grow in marine cages. Rapid marine growth is desirable since it permits more extensive fallowing of coastal aquaculture sites, which reduces the impact of farmed fish on the marine environment (pathogen transfer, nutrient pollution). Finally, while wild fish protein can be replaced by plant protein in salmon diets, oils cannot. Key omega-3 fatty acids must be sourced from the marine environment; a significant burden on wild fisheries. Ensuring the efficient assimilation of fatty acid components from salmonid diets is of paramount importance to safeguard the sustainable exploitation of marine resources.
Salmon energetic phenotypes are composites of several interlinked traits: metabolic rate, body fat content, growth, energy harvest from food, energy economy in times of starvation. These traits underpin concerns around salmon nutrition. Significant energetic variation exists in both wild and farmed salmon with multiple possible drivers - both genetic and environmental. Importantly a wealth of new data indicates a role for intestinal microbiota - the bacteria that live in the guts of all vertebrates - in determining host energy metabolism.
Understanding how gut bacteria influence Atlantic salmon energetics is thus fundamental to understanding their role in nutrition. This is the principal aim of this project. To achieve this we will establish the influence of gut bacteria on the energetics of salmon living in salt and freshwater, in both wild and aquaculture settings. First, in a unique experimental river system established in Burrishoole, Mayo (Marine Institute/University College Cork, ROI) we will track introduced juvenile salmon through their freshwater lifecycle, measuring both metabolic and gut microbiome variation. This 'wild' cohort will include wild and released farmed fish to establish whether differences between gut microbiota contribute to the poor performance of farmed juveniles in the wild. Secondly, we will undertake parallel freshwater experiments in simulated aquaculture conditions in the laboratory at the University of Glasgow (UoG),UK. Finally, in association with Marine Harvest, we will carry out corresponding experiments on saltwater phase pre-adult salmon in Norway.
Alongside experiments with live fish, we propose to harness bioengineering expertise at the School of Engineering, UoG and biotechnological expertise via industry partner Alltech to build an artificial salmon gut system. Via the transfer and maintenance of gut bacteria from metabolically different fish from farmed and wild settings into our gut model we aim to establish how bacterial fermentation underpins differences in energy harvest from feed. Once these 'artificial' bacterial communities are established, a final exploratory phase of the project will involve their transplantation into laboratory reared juvenile salmon to evaluate their potential impact on host metabolism.
Understanding how salmon gut bacteria change energetic phenotypes will open new avenues to improve fish health, nutrition and productivity. A model Atlantic salmon gut in a world class UK bio-engineering laboratory puts in place an invaluable tool for salmon aquaculture in the UK

Technical Summary

Atlantic salmon are anadromous salmonids of major commercial, cultural and recreational importance, in the UK, Ireland and worldwide. Metabolism, feed conversion efficiency and growth lie at the core of salmonid aquaculture productivity and its ecological impact and sustainability. The role of gut microbiota in driving energy metabolism in vertebrates is increasingly clear, opening up new avenues to fine-tune salmon metabolism and growth.

The aim of this project is to establish the microbial basis for different energetic phenotypes in Atlantic salmon. In doing so, we will establish the role of microbiota in influencing host performance and energy economy. The broad project objectives are as follows:

1)Determine the links between energetic phenotype and microbiota in the natural environment, in order to explore the full variation in both sets of traits.
2)Examine the same links in fish of different life stages but in laboratory/farm settings where food is continually available and where nutritional intake can be standardised and measured.
3)Establish the role of microbiota in driving maladaptive energetic phenotypes in farm escapes and hatchery reared fish deliberately released into the wild.
4)Establish a synthetic salmon intestinal microbiome system through which to validate the energetic profiles we find in farmed and wild fish.
5)Undertake pilot microbiome transplantation to establish the causal role of microbiota in determining the phenotype of the host.

The project brings together: Irish and UK expertise in fish biology, population genetics, microbial ecology; a world class UK bio-engineering laboratory; and major industrial partners (Marine Harvest, Alltech) to open new avenues to improve fish health, nutrition and productivity. The establishment of a model Atlantic salmon gut puts in place an invaluable tool for salmon aquaculture that will boost the UK's aquaculture research capacity in the lifetime of the grant and into the future.

Planned Impact

Production of the global salmonid aquaculture industry now exceeds 2.4 megatons per annum. Major European producers (e.g. Norway, Scotland, Ireland) expect to expand their outputs between 30-50% over the next five years. Ambitions for expansion on this scale create major concerns around fish welfare, ecological impact and the sustainability of salmon feed components.

Nutrition lies at the core of many of the underlying concerns. Thus, addressing knowledge gaps around salmon nutrition is crucial to ensuring the sustainable expansion of the aquaculture industry. This project addresses knowledge gaps by 1) Establishing the role of gut microbiota in driving nutritional energy harvest, nutrient assimilation, metabolic rate and growth in farmed and wild Atlantic salmon. 2) Establishing and validating an artificial salmon gut system to test novel feed additives aimed at improving sustainable aquaculture production and improving fish welfare. Impacts on fish welfare include not only improved feed formulations, but also a significant potential reduction in the number of in vivo trials necessary for feed development.

The principal beneficiaries of this research are the UK and Irish economies. Combined, their aquaculture industries support >10,000 jobs directly, and many more in service economies indirectly - especially in often rural and remote communities with otherwise limited access to employment. The proposed project promises to improve the efficiency of salmon growth and nutrition. In doing so it will positively benefit the competitiveness of the UK and Irish salmonid aquaculture industries, paving the way for sustainable growth and expansion of a valuable export economy.

The aquaculture industry stands to benefit significantly from this research. Recognition of this fact in the first instance is the cerca £300,000 in-kind and cash contribution committed by industrial project partners. In a recent industry-wide poll of research interest areas at a recent Scottish Auaculture Innovation Centre workshop (http://scottishaquaculture.com/events/sustainable-aquafeed-workshop), themes linked to salmon gut microbiota, novel feeds, and sustainable use of feeds (including DHA and EPA from fish oil) were identified as the top three areas of concern and interest. Our research findings with respect to the microbial drivers of Atlantic Salmon energetics, as well as the artificial gut tool we will develop - with potential for testing novel feeds, feed additives and microbial therapies - is strongly aligned with industry needs.

Ultimately, via the improved understanding of the role of microbiota in salmon energetics nutrition that this project offers, there is potential to improve the efficiency of salmon aquaculture and concomitantly: 1) reduce the impact of intensifying salmonid aquaculture on coastal ecosystems as well as 2) reduce the reliance of salmonid aquaculture on wild capture fisheries.


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Description Please not that it is to early in the project to list 'key findings' for a lay audience. We are making progress against the study objectives a follows:

Objective 1: To establish the link between salmon energetic phenotype and microbiome diversity a) in a population of wild juvenile salmon that will express natural variation in both traits; and in laboratory-reared fish in simulated aquaculture conditions at the b) freshwater and c) marine life stages.

Objective 2: To establish the role for intestinal microbiota in driving maladaptive energetic phenotypes in farmed salmon escaped or released into the wild using: a) domesticated farmed fish and b) captive-bred wild fish.

Objective 3: To establish the basis for microbial energetic differences using ex-vivo and transplantation approaches via a) development of an artificial salmon microbiome system to validate microbial energetic profiles we find in fresh and saltwater settings, and b) transplantation of ex-vivo microbiota into salmon, sequence-based evaluation of transplantation success and energetic phenotype follow-up.

Methodology and research activities (tasks) to address Objectives 1 & 2, 3.

Experimental populations of wild-origin (WO), farm-origin (FO) and ranched-origin (RO) salmon (15 families per population) will be established by hand-fertilising stripped eggs in the spawning season of year 1.
In addition to the experimental population established last year (2016/17 cohort) consisting of the progeny of pure wild origin, farm origin and ranch origin, we have produced a new population (2017/18) made up of the progeny of farm and wild salmon including their hybrid progeny. These fish provide excellent extra study opportunities, particularly the hybrids, both under freshwater hatchery conditions and at the new marine out-growing site at Connemara.

The WO population will be offspring of wild fish collected in the Burrishoole river system, Ireland.

Completed as planned for 2017 with an additional wild origin group established in January 2018.

The FO parental fish, which are of Norwegian provenance, will be provided by Marine Harvest and represent the most commonly grown farm strain in Ireland.

Completed as proposed for 2017 with an additional farm origin group established in January 2018.

The RO fish will be hatchery-reared juveniles from a ranched population (i.e. where fish are reared in the hatchery to the smolt stage then released into the wild, with returning adults forming the next brood stock).

Completed as described for 2017 with an additional ranch origin group which was established in January 2018.

Fertilisations will be conducted over a brief (3 day) period and samples of eggs weighed to facilitate comparison of subsequent growth rates. Fin clips from all adults will be retained for subsequent parentage assignment of offspring.

Tissue samples were collected from the parents to facilitate later parentage assignment of juveniles from the 2016/17 experimental population cohort. Biometric data was collected from the parents and the egg offspring. Similarly, tissue samples and biometric data have been collected for the 2017/18 cohort. A full genetic baseline of the parental fish used in the 2016/17 cohort has been completed to facilitate parentage of fish introduced into the river using 20 microsatellite markers.

Eggs from all three experimental populations (WO, FO, RO) will be maintained as family units within the hatchery facility at Furnace on the Burrishoole river system until needed for particular Activities as follows:

The experimental families are being managed in the Newport hatchery facility as described. The experimental population consists of 1,000 individuals of each of farm, wild and ranch parental group. The experimental population is growing well with the expectation fish will smoltify ready for introduction into sea cages in the spring of 2018. Depending on survival rates we will set up a new hatchery based experimental population in the spring of 2018.

Eyed eggs from individual WO families (n = 2000 eggs from each of 15 families) will be counted, mixed and introduced into the experimental Srahrevagh River using artificial nests in early to mid-February.

This task is on schedule. However we introduced the experimental population into the river as swim up fry rather than eggs. The experimental population consisting of 8,213 individuals from 14 wild families and were introduced into the experimental river on 10 April 2017 and 19 April 2017. These were in addition to 10,026 farm progeny released on 6 April 11,270 ranch progeny released on 7 April 2017. The 2017/18 cohort consists of 12 wild, 24 hybrid and 14 farm families and will be put these into the experimental river in April 2018, again as swim up fry.

PIT-tagged hatchery-reared RO parr will also be introduced in late summer of the same year.

The RO eggs were on-grown in the hatchery until the summer/autumn parr stage of development. A total of 291 RO 0+ pre-tagged, measured, and profiled for microbiota community hatchery reared parr were introduced (geolocations data collected for release points) into the Srahrevagh river experimental section over a two week period commencing the first week of October 2017.

In early autumn, 500 juvenile fish (approx.) will be collected in the experimental river by electrofishing, fin-clipped for retrospective DNA-based parentage and population assignment (following [4]), marked with PIT tags, and measured and weighed to determine growth rate (using family egg size as a covariate).

This task was undertaken in September and October 2017. The sampling was delayed due to high river levels following a series of autumn storm events. 99 0+ salmon were of a sufficient size to PIT tag. Measures of size at age were recorded to facilitate growth rate trajectories. The provenance of all the fish sampled were assigned to their parent population using the genetic baseline. The results of the genetic analysis suggest the groups of experimental fish are in similar proportions to the numbers stocked.

Using an on-site respirometry system, the SMR and AS of each hatchery fish will be non-lethally tested under standard conditions

Seasonal metabolic status measures have still to commence on a routine basis. A new freshwater respirometry system (Loligo System, Denmark) has been established at the Newport facility. We are currently carrying out calibration exercises to optimise the system. Standard metabolic rate (SMR) measures have been undertaken for approximately 20 hatchery fish in order to optimise the system. The system when fully operational will be able to process fish from the size range of 8g to 100g. We are also currently exploring respirometry for smaller fish down to a gram in weight. We plan the establishment of a saltwater respirometry system also in Newport and to be operational in early spring.

Whole body adiposity ratios will be determined non-lethally via a pressure system

We are exploring the potential of manufacturing a pressure apparatus approach to collect adiposity measures. In meantime we will commence shortly the more conventional fatty acid profiling approach. We have been fortunate to secure an arrangement with the Teagasc Food Research Centre at Moorepark, Fermoy, to undertake this analysis. In mid-September six individuals from each of the experimental groups were sampled for fatty acid profiling. A further ten fish were also sampled from each group in mid-November. An additional 10 fish from each of the experimental groups were sampled in mid-January.

A non-lethal intestinal wash will then be taken for microbial DNA extraction and sequencing. Water and control samples will also be taken to monitor environmental microbiome fluctuations as well as potential contamination

Rather than non-lethal sampling we have been undertaking comprehensive dissections of individual fish

Profiling of the gut microbiota will be via amplification and sequencing of the 16S v4 region on an Illumina MiSeq platform at the CGR Liverpool

First round of sequencing will be targeted at the University of Glasgow cohort of Burrishoole fish in March 2018. 16S profiling of gut communities from the rough river at Burrishoole will commence in April 2018 based on samples collected during spring / winter sampling 2017/18.

Microbial amplicon sequence will be analysed using standard and custom workflows and correlated with fish growth and metabolic traits

At the UoG, workflows are now in place for amplicon sequencing based on SalmoSim farmed fish gut analyses. Metabolic covariates are those collected during respirometry and other energetic measurements (i.e. energy harvest from feeds, conversion efficiency).

To evaluate how these relationships change with season and how gut microbiota predict long-term performance, measurements of metabolism and microbial sampling will be repeated in late winter, while survival/growth will be assessed by five electrofishing surveys over 18 months (initial sampling Autumn, followed in the Winter, Spring, Summer and Autumn of the following year).

We are currently establishing the respirometry system for making measures of metabolic potential, which has taken slightly longer than expected to set up. In November 2017 we sampled five fish from the river for microbiome sampling. We also sampled 5 stocked ranch fish for microbiome analysis in November. In January 2018 we sampled a further 18 0+ salmon from the experimental population and 5 further ranch origin fish were sampled after respirometry.

All fish recaptured at the final sampling will be euthanized and their alimentary canal (cardiac stomach, the pyloric caeca, mid-intestine, posterior intestine) removed for epithelial histology ('villus' -- salmon have densely folded columnar epithelia rather than villi -- density and folding) and morphometric measurements (relative total gut length, pyloric caecum fold number).

Samples are being routinely collected at the MI Burrishoole and guts collected in the appropriate buffers prior to shipment to Glasgow. At Glasgow, Pei Yang has been recruited to oversee histological analyses including Fluorescence In Situ Hybridization to identify the distribution of different microbes in respect of different gut structures.

Juvenile WO salmon brought as eggs from the experimental families produced at the Burrishoole hatchery will be reared on a commercial pelleted food at the aquarium facility in Glasgow.

Eggs from the experimental population established in Newport were successfully transferred to Glasgow in February 2017. These parr are now 20-40 g in weight. An addition subset of experimental eggs from the 2017/18 cohort will be transferred from the Newport facility to Glasgow in February 2018.

At 6 months of age fish (n=90, with 6 fish from each of 15 families) will be transferred to 90 individual flow-through aquaria, which will share a common water source and be held at constant temperature (13°C). They will be fed a fixed ration (1% body mass); after a month-long period of acclimatization, their growth efficiency will be measured, together with SMR and AS

Two range finding experiments have already been carried out on two cohorts of stock parr to identify optimal conditions for the aquarium study. Fish are being left until 12 months to represent the optimal size for the respirometry chambers. The aquarium study will now commence on the first of March 2018 and will feature 20 individuals per group.

To test digestive efficiency, comparative bomb calorimetry of each controlled food
ration and faeces will be monitored over a two day period. Calorific measurements will be repeated in triplicate for each individual fish.

Faecal samples from range finding experiments have been submitted for bomb calorimetry at the University of Stirling. We are awaiting data.

Faecal sampling, microbial diversity profiling and gut morphological analysis will also be carried out. Microbiota in water and feed will be 16S profiled as controls.

16S amplification and library preparation from range finding experiments is complete and these samples are awaiting sequencing at the University of Glasgow.

Eggs from each of the WO and FO populations will be transferred to the Nofima research facility (rented by Marine Harvest) in Norway, for on-growing to the marine stage of development. 100 fish from each population (WO and FO) will be transferred to salt water test facilities where equivalent experiments to those described in Activity 1b will take place in marine phase post-smolts (300-500g).

The transfer of eggs to the NOFIMA research facility in Norway was scheduled for mid-February 2017. Subsequently it was planned to transfer the eggs to the Marine Harvest experimental facility at Ardnish, Lochailort, Scotland rather than NOFIMA Norway. Both plans have now been superseded by a new arrangement with the marine Institute enabled by the establishment of their new marine research site at Bertreach Bui in Connemara. We have established two experimental populations in the hatchery. The first is an opportunistic study and consists a group of pure farm Mowi strain fish (n=5,083) and a group of captive bred Burrishoole ranch strain fish (n=4,751). These fish were introduced into sea cages as S1/2 in December 2017 having been subject to light manipulation to advance their physiological development. As a control prior to their introduction to the sea cage in 6 December 2017 microbiota were sampled from 22 individuals in addition to 12 individuals for fatty acid profiling. Subsequently we have been undertaking regular sampling of individuals (6 samples per visit) in the sea cages 18, 22 and 27 of December and most recently on the 5 January and 26 January. A full dissection has been undertaken on these fish including gut microbiota from stomach, pyloric caecae, mid gut and hind gut. In addition environmental water samples were also collected.For the scheduled study in the proposal approximately 1,000 swim up fry from each of the three experimental groups, farm origin, wild origin and captive bred ranch origin were transferred to the main hatchery facility at Burrishoole in March 2017. In September n=15 parr were sampled from each of the experimental groups for microbiota profiling in order to establish a baseline of the gut bacterial communities and stored at -80oC. These were on-grown to mid-October 2017 when 100 parr from each of the experiment groups were individually PIT tagged and measured, weight and length, to facilitate, monitoring of growth, transferred into three new tanks to provide triplicate equal mixtures of the experimental groups, each tank now consisting of 300 parr. In mid-January 2018, 27 fish, 9 of each experiment group identified on the basis of their PIT tag were sampled (i.e. 3 x9). The experimental hatchery population are scheduled to be introduced to the sea cages in mid-April 2018.

Gut compartments will be set up across three linked Applikon bioreactors based at the University of Glasgow, School of Engineering (SoE). At the core of each Applikon bioreactor are six adjustable control loops to set basic parameters like temperature, pH, dissolved oxygen, agitation, level and foam.

Gut compartments will be set up across three linked Applikon bioreactors based at the University of Glasgow, School of Engineering (SoE). At the core of each Applikon bioreactor are six adjustable control loops to set basic parameters like temperature, pH, dissolved oxygen, agitation, level and foam. All basic parameters have been established. The bioreactors are now connected and the first run is underway and scheduled for completion on the 21st of Feb. Live stream to monitor foam over on reactors can be found here: https://www.youtube.com/watch?v=hov_eaBUWOA

Homogenised, filtered samples of different salmon gut compartments will be subjected to proteomics analysis via the University of Glasgow PolyOmics centre using tandem liquid chromatography (LC), high-pressure liquid chromatography (HPLC) and mass spectrometry (MS) to identify major digestive enzyme classes present. A similar system will be applied to smaller non-volatile digestive secretions (e.g. bile salts). Once protein and bile salts are identified, in-house HPLC at the SoE can be used to differentially assess abundance. Volatile components of intestinal contents, especially short chain fatty acids (SCFAs), can be identified in house at the SoE using a tandem gas chromatography (GC)-MS system. Commercial availability of the various enzymes will be assessed to identify the 'best match' in terms of function and activity for inclusion in the model.

Proteomics and metabolomics are now complete. Biochemical marker identification is underway. Several key markers of microbial metabolism have been identified, including VFAs, lactate and others. We can now assess the abundance of these secondary metabolites directly via HPLC from faecal samples. We now use purified salmon bile to supplement the reactors
In addition to establishing the correct physico- and biochemical conditions, we propose to
introduce artificial mucosal surfaces for bacterial colonisation. Microbial classes in fish intestines are broadly separated into 'adherent' and 'non-adherent'. In common with most vertebrates, salmon mid- and hind-guts possess a thick lining of mucous secreted by goblet cells embedded in the columnar epithelium. After [21] we will therefore introduce beads (AnoxKaldnes K1 carrier, AnoxKaldnes, Sweden) coated with nutrient-free agar incorporating mucins purified from salmon intestine waste (Marine Harvest).

We have adopted the approach described in the project. The K1 beads are coated in mucin-infused agar and are currently floating in the pyloric caecum compartment medium. At the end of the current run, these K1 beads will be sliced, fixed and stained to visualise the distribution and diversity of colonising microbes by comparison to those known to be associated with the gut epithelium. To validate our model system, we will introduce selected fresh and saltwater salmon microbiota into our system and allow these to establish over a 48-hour cycle.

To validate our model system, we will introduce selected fresh and saltwater salmon microbiota into our system and allow these to establish over a 48-hour cycle.

Our primary focus has been on the marine microbiome to date. Gut microbes have been seeded in from marine phase post-smolts. We intend to trial the freshwater gut model in Autumn 2018.

Based on field observations in field experiments, and a small number of metagenomics sequencing runs from early gut simulator runs, we will develop 16S v4 primers targeted at phylum and family level components of the microbiome for qPCR This approach will allow the rapid monitoring of changes in abundance of core taxonomic classes over the course of the experiment. Validation of the system will occur when we can recover matching abundance profiles for core microbiota taxa between the original sample and bioreactor samples (especially the hind-gut compartment) at the end of the cycle.

We have identified 8 taxon-specific primers so far that we will deploy to track our communities at a phylum and species level. In addition we have developed functional qPCR markers to target microbial processes identified from the metabolomic data - methanogensis, acetogenesis etc.

Microbiota cryopreserved from WO field and WO laboratory fish found to have extremes of SMR and AS, in both saltwater and freshwater life stages, will be selected for testing in the model system. Our target is to explant a total 10 microbiomes from salt and freshwater fish, respectively (20 total) into the model.

This activity will occur once artificial system is stabilized - likely to occur early 2019

Digestive characteristics of each microbiome (multiple biochemical markers of bacterial protein, carbohydrate and fat fermentation efficiency, monitored using HPLC and GC at 6-hour intervals, including ammonia, amines, phenols, sulphides, SCFAs, lactate and short chain oligosaccharides) will be measured in each of three independent cycles of each model system

Key markers of microbial metabolism have been identified using metabolomic and metagenomic data acquired from analyses of marine phase salmon guts, as described above. Markers, include VFAs, lactate and others. We can now assess the abundance of these secondary metabolites directly via HPLC based on material that we are systematically sampling from the reactors.

If links between the microbiota and metabolism of fish are found in living and ex-vivo systems, we propose to attempt some exploratory transplantation techniques in normal and broad-spectrum antibiotic treated juvenile salmon with the aim of establishing causation.

The execution of this transplantation task will depend on the success of finding associations between the microbiota and the metabolism of the fish. This task is scheduled for 2019.

We propose to undertake a pilot laboratory transfer experiment whereby energetically-divergent microbiota (originally from high and low energy phenotype fish) from the model system will be reciprocally transplanted via gavage into a cohort of 60 salmon parr (30 'low' energy fish (with low SMR, small AS, low nutritional energy harvest) and 30 'high' energy fish (with the opposite traits). A further 90 parr will act as controls: 30 to receive a sterile gavage, and 60 matching transplants (e.g. low energy microbiome to low energy fish) for comparison with reciprocal transplants. The 150-fish cohort will be followed to detect potential changes in energetic profile.

This task will start in early 2019.
Exploitation Route The draft artificial gut system will be of use to multiple stakeholders in the salmonid aquaculture industry
Sectors Agriculture, Food and Drink

Description This project is currently at an early stage ( we are only 10 months in). Therefore we have only very preliminary findings. However, regular interactions with industry partners Marine Harvest and Alltech have occurred in the form of meetings, visits, farm visits, and researcher exchanges. Identification summaries of microbial species from salmon collected from farm sites and from the experimental catchment system have been reported to our industry collaborators. The abundance and diversity of different microbial agents is assisting our partners with microbial management strategy planning. Down the line, we hope to be able to inform our industry collaborators and the wider nonacademic community of the role of different microbes in salmon digestion in metabolism and performance.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Economic

Title A draft model of the Salmosim Gut Microbiome Simulator 
Description A central aim of the project was to develop a gut Microbiome by simulator. An early draft of the simulator is now available. 
Type Of Material Model of mechanisms or symptoms - in vitro 
Year Produced 2018 
Provided To Others? No  
Impact it is currently too early to tell what impact this system will have. 
Title A large panel of tissue and gut content samples from farmed atlantic salmon 
Description We now have a large panel of microbial DNA samples collected from the intestines of farmed Atlantic salmon. 
Type Of Material Biological samples 
Year Produced 2017 
Provided To Others? No  
Impact this collection of samples represents a unique resource for understanding the microbiology of farmed Atlantic salmon. 
Title A panel of live bacterial strains isolated from the gut of farmed Atlantic salmon. 
Description Over 50 different microbial strains have been isolated and characterised the species level. these are currently stored at the University of Glasgow. 
Type Of Material Cell line 
Year Produced 2017 
Provided To Others? No  
Impact We cannot yet foresee the impact of this collection of strains 
Description Collaboration with Industry Partner Alltech 
Organisation Alltech
Country Global 
Sector Private 
PI Contribution We established this partnership at the outset of the project. We are establishing an artificial salmon gut system to understanding the impact of different feed additives on salmon health.
Collaborator Contribution Our partners are providing expertise and training in microbiology, as well paying for a full time PhD student.
Impact None so far with the exception of knowledge exchange
Start Year 2017
Description Collaboration with University College Cork (UCC) and Marine Institute (MI) Ireland 
Organisation Marine Institute
Country Ireland 
Sector Public 
PI Contribution The UCC and MI collaboration are a core component to this project - which represents a joint Science Foundation Ireland / BBSRC endeavor. Full detail of this partnership are included in the award document. The experimental stream system around which a large portion if the award is based is located in a field station in Burrishoole, Co. Mayo Ireland and is operated by MI and UCC. The University of Glasgow (UoG) provides expertise and training in salmonid physiology, microbiology, metagenomics and bioinformatics to >8 PhD students and 4 post doctoral resarchers based at Burrishoole.
Collaborator Contribution UCC/MI provide expertise is salmonid ecology, biology and genetics - providing training to 5 UoG PhD students and 2 post-docs. UCC/MI also contribute substantial research infrastructure in terms of the catchment, trap system, hatchery, marine cages and experimental stream.
Impact Several important publications: e.g. 10.1038/s41598-018-19323-z
Start Year 2013
Description Collaboration with industrial partner Marine harvest 
Organisation Marine Harvest
Country Norway 
Sector Private 
PI Contribution The University of Glasgow research team established a collaboration with Marine harvest. We are contributing knowledge and expertise around the influence of gut microbes on salmon gross and performance. In addition we are developing an artificial guts system that can act as a testbed for novel seeds and seed formulations.
Collaborator Contribution Marine harvest is providing expertise and training to University of Glasgow staff and students. Marine harvest is also providing marine cage facilities for rearing Salmon to undertake experiments as part of this project.
Impact Current outputs are principally focused at knowledge exchange
Start Year 2017
Description Interview for National News (BBC Radio Scotland) 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Media (as a channel to the public)
Results and Impact I was interviewed about the project on BBC Radio Scotland
Year(s) Of Engagement Activity 2017
URL https://www.bbc.co.uk/radioscotland
Description Series of short films about the project posted on youtube 
Form Of Engagement Activity A broadcast e.g. TV/radio/film/podcast (other than news/press)
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Media (as a channel to the public)
Results and Impact With our Irish Project partner we have embarked on a series of videos presenting our work
Year(s) Of Engagement Activity 2018
URL http://www.youtube.com/watch?v=VCoahlcxN9w&feature=share