Comparative metagenomic analysis of the gastrointestinal tract of the rainbow trout
Lead Research Organisation:
University of Nottingham
Department Name: School of Veterinary Medicine and Sci
Abstract
Fish, are one of the most efficient converters of feed into high quality food and increasingly recognised for nutritional and health-promoting qualities. Over the past 40 years, the aquaculture industry has developed, expanded and intensified in line with increasing global population and now produces almost 50% of the world's food fish. In order to maintain high levels of productivity, food security and allow expansion of key areas of the industry, improved fish management and effective disease control is essential. The UK aquaculture industry is diverse, with trout the second largest fish market after salmon and the cost of disease and mortalities estimated at £6 million/annum. The application of improved health management strategies is one of the contributing reasons for the success of the intensification of the UK salmon industry. If the trout industry is to continue to intensify and match this success, a greater insight into the health of the trout and subsequent response to disease is vital.
In commercial rainbow trout farming, growth of female fish is preferred as they have faster growth rates and are generally less aggressive than male fish, minimising stress related complications during rearing. Triploid fish are increasingly being farmed for food as they are sterile and therefore minimise reproductive-related production loss. The host and bacterial gastrointestinal (GI) balance is known to play important role in the nutrient acquisition, immune development and tolerance and also disease resistance in fish. This balance forms an integral part of the innate immune defence system of the GI tract and allows differentiation of food particles and pathogenic bacteria from normal bacterial flora. The role that the individual microbe plays in the health and nutrition of fish is still poorly understood, making investigations of the composition of the intestinal microbiota crucial for future health management strategies for the aquaculture industry. Further to this, very little is known about the differences in immune gene expression and GI function in diploid and triploid fish and the role this has in overall fish nutrition and health.
The aim of this project is to compare the expression of key immune genes related to GI health in diploid and triploid rainbow trout and to characterise the intestinal microbiota using a combination of culture based and bioinformatic assessments. This will include analysis of the expression of selected host genes and the construction of primary microbial gene catalogue, to determine if there is a difference in the gastrointestinal composition and function between the diploid and triploid species.
Objective 1: To identify and characterise the microbiome of the gut in diploid and triploid rainbow trout.
Bacterial cell counts and characterisation will be performed on gastrointestinal tissue and DNA isolated for genome sequencing to determine the resident bacterial population within the GI tract. These will be compared to bacteria isolated from water and food samples using typical microbiological tests including antibiotic susceptibility testing.
Objective 2: To characterise and identify key immunological markers of the rainbow trout GI tract other key immune tissues.
The GI tract, head kidney and spleen will be analysed to determine any differences in expression of immune gene receptors and cytokines which play a crucial role in the early innate response to infection.
An understanding of differences in immune function and microbiome composition of the diploid and triploid trout will assist in the development of strategies for better health management of trout, particularly through manipulation of 'healthy' gut bacteria. This will have important implications for the overall health and welfare of farmed fish and is likely to enhance the productivity and sustainability within this industry.
In commercial rainbow trout farming, growth of female fish is preferred as they have faster growth rates and are generally less aggressive than male fish, minimising stress related complications during rearing. Triploid fish are increasingly being farmed for food as they are sterile and therefore minimise reproductive-related production loss. The host and bacterial gastrointestinal (GI) balance is known to play important role in the nutrient acquisition, immune development and tolerance and also disease resistance in fish. This balance forms an integral part of the innate immune defence system of the GI tract and allows differentiation of food particles and pathogenic bacteria from normal bacterial flora. The role that the individual microbe plays in the health and nutrition of fish is still poorly understood, making investigations of the composition of the intestinal microbiota crucial for future health management strategies for the aquaculture industry. Further to this, very little is known about the differences in immune gene expression and GI function in diploid and triploid fish and the role this has in overall fish nutrition and health.
The aim of this project is to compare the expression of key immune genes related to GI health in diploid and triploid rainbow trout and to characterise the intestinal microbiota using a combination of culture based and bioinformatic assessments. This will include analysis of the expression of selected host genes and the construction of primary microbial gene catalogue, to determine if there is a difference in the gastrointestinal composition and function between the diploid and triploid species.
Objective 1: To identify and characterise the microbiome of the gut in diploid and triploid rainbow trout.
Bacterial cell counts and characterisation will be performed on gastrointestinal tissue and DNA isolated for genome sequencing to determine the resident bacterial population within the GI tract. These will be compared to bacteria isolated from water and food samples using typical microbiological tests including antibiotic susceptibility testing.
Objective 2: To characterise and identify key immunological markers of the rainbow trout GI tract other key immune tissues.
The GI tract, head kidney and spleen will be analysed to determine any differences in expression of immune gene receptors and cytokines which play a crucial role in the early innate response to infection.
An understanding of differences in immune function and microbiome composition of the diploid and triploid trout will assist in the development of strategies for better health management of trout, particularly through manipulation of 'healthy' gut bacteria. This will have important implications for the overall health and welfare of farmed fish and is likely to enhance the productivity and sustainability within this industry.
Organisations
People |
ORCID iD |
Sharon Egan (Primary Supervisor) |
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/M008770/1 | 30/09/2015 | 31/03/2024 | |||
1644442 | Studentship | BB/M008770/1 | 30/09/2015 | 20/03/2021 |
Description | We have investigated the bacterial communities in the intestinal tract of two types of trout that are commonly farmed in the UK, diploid and triploid trout. We found that the bacterial communities changed depending on which area of the intestine was examined and that the structure of these communities differed slightly between the two kinds of fish. We found that triploid bacterial communities were more diverse and richer than diploid fish but overall both fish types had similar communities wh |
Exploitation Route | Presentation to wider scientific and aquaculture communities Useful for comparison to future study's results, and prior work. Basis for the development to more advanced experimental methodology eg metagenomics studies |
Sectors | Agriculture Food and Drink |
Description | Further funding from the SVMS in recognition of contributions to the school |
Amount | £6,200 (GBP) |
Organisation | University of Nottingham |
Department | School of Veterinary Medicine and Science Nottingham |
Sector | Academic/University |
Country | United Kingdom |
Start | 06/2017 |
End | 12/2017 |
Description | Students As Change Agents - Histology education project for veterinary and medical undergraduates |
Amount | £300 (GBP) |
Organisation | University of Nottingham |
Sector | Academic/University |
Country | United Kingdom |
Start | 02/2020 |
End | 09/2020 |
Title | Development of a novel Histology learning and revision tool |
Description | Applied for, and was awarded £300 funding for a students as change agents project- developing a novel histology learning and revision tool. Essentially a custom made (3D printed) Guess Who game encouraging veterinary and medical undergraduates through deductive and constructive reasoning to identify gastrointestinal sections, and link this to the gross anatomy and physiology of the tissue. This project is also reported under the further funding section. |
Type Of Technology | Physical Model/Kit |
Year Produced | 2020 |
Impact | Tool will enter use in the University of Nottingham School of Veterinary Medicine undergraduate curriculum in 2020. Pending results a short publication or presentation to the veterinary education community may result. |
Description | Beaver Group visit - What does a Vet Do? |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Visited a local beaver group to discuss animal welfare, what does a vet do, how a vet uses science in their job. Included practical element for cardiac auscultation of live dog, interactive anatomy work sheets, and mini experiment on exercise and heart rate. |
Year(s) Of Engagement Activity | 2019 |
Description | Beaver group visit - What is a vets role in the community? |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Visited a local Beaver group to learn about what is a vets role in the community - discussed the many roles vets can take from the general practitioner through clinical work like speciality or species areas, as well as non clinical routes such as research and communications. Included practical element for cardiac auscultation of live dog, interactive anatomy work sheets, and mini experiment on exercise and heart rate. |
Year(s) Of Engagement Activity | 2020 |
Description | Brownies group visit (Loughborough) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | 40 brownies of various ages attended an evening meeting to learn about my educational path and career - focussing on STEM aspects sparking questions on the transition from vet to researcher, what does a researcher do and why are they important. Afterwards the group leaders reported increased interest in science related activities. |
Year(s) Of Engagement Activity | 2007 |
Description | Primary School visit (Derbyshire) |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Myself and a collaborator at another institution visited a primary school class of 22 6-8 year old students to deliver a STEM workshop, focussing on educational paths to careers in science and technology (topics on materials and anatomy, 3D printing animal skulls and talking about anatomical differences between species eg fish, dogs, people). This sparked alot of excitement and interest. We donated a 3D printed platypus skull to the school afterwards. |
Year(s) Of Engagement Activity | 2019 |
Description | School visit (Leicester), |
Form Of Engagement Activity | Participation in an activity, workshop or similar |
Part Of Official Scheme? | No |
Geographic Reach | Local |
Primary Audience | Schools |
Results and Impact | Attended a "Walking library" event - STEM careers circulated a large all boys school in Leicester to be questioned by Year 9 students about their work, how they got there etc. The school reported an increase interest in careers influenced by post graduate education such as a PhD. |
Year(s) Of Engagement Activity | 2016 |
Description | Secondary School visit to SVMS |
Form Of Engagement Activity | Participation in an open day or visit at my research institution |
Part Of Official Scheme? | No |
Geographic Reach | Regional |
Primary Audience | Schools |
Results and Impact | A group of students of secondary school age visited the SVMS to learn about animal health, welfare and careers in science and medicine. They took part in multiple practical activities and tours, I guided the group during a visit to our small holding cattle and sheep. The students were very reactive to animal contact - initially wary but quickly overcoming fear to interact, lots of questions about agriculture were sparked, which built to a discussion of food security. Teachers reported students were very enthusiastic about the visit and retained alot of what was discussed! Plans for a visit next year have been requested. |
Year(s) Of Engagement Activity | 2018 |