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Joint Doctorate in Molecular Animal Nutrition

Periodic Reporting for period 2 - MANNA (Joint Doctorate in Molecular Animal Nutrition)

Reporting period: 2020-06-01 to 2022-11-30

The strategic objective of MANNA is to provide a European Double Doctorate level training programme on innovative technologies applied to animal science and nutrition.
The MANNA project has achieved significant outcomes for all of the objectives.

1 The MANNA project effectively gained its goals in delivering a European Double Degree Doctorate level training programme on innovative technologies applied to animal science and nutrition. At current standing 9 of the 11 ESRs have obtained double degrees from two of the University partners in the project and the remaining 2 ESRs are likely to achieve their double degrees in the next 12 months. This has been achieved despite the complications caused by the Covid-19 lockdown requirements and limitations to travel in Europe over the course of the MANNA project.

2. The ESRs on the MANNA project have acquired the capabilities to address current and future needs of industry and academia with a raised awareness and expertise in application of cutting edge omics technology in genomics, transcriptomics, proteomics and metabolomics and also in computer science related to bioinformatics. Of the ESRs who have graduated with double PhD degrees their first career choices have been in academia, industry and science communication.

3. Studies on innovative feeding strategies and bioactive feed additives have been applied in chicken and dairy production. In chickens responses to bacterial endotoxin and effects of potential Neuroceuticals have demonstrated modified metabolomics and proteomic responses (ESR3) while the of use heavy isotopes has allowed protein synthesis rates of individual proteins to be determined for the first time (ESR4). Machine learning has been applied to evaluate the selection process of serum samples from dairy cows pre and post parturition, allowing the contrast between high and low body condition loss to be determined (ESR5).

4. Assessment of the effects of -6: 3 fatty acid ratios in the diet of sows and the supplementation of piglet diet with seaweed, on growth and health parameters has been investigated in linked studies with multiple samples from feeding trials. Proteomic analysis has demonstrated the effect of -6: 3 fatty acid ratio on serum or plasma in sows and piglets and on ileum proteins demonstrating the benefit of reducing the -6 and increasing 3 fatty acids in the diet fatty acid in the diet (ESR1). Faecal samples from the pigs in these trials were studied with development of microbiota and metabolome analysis systems (ESR7). Porcine muscle with extreme values for ω-6: ω-3 fatty acid (FA) ratio has been examined by sequence analysis of RNA with 432 genes shown to be differentially expressed (ESR8). Further study in dairy cows fed with different types of essential fatty acid has demonstrated significant change in the serum proteome (ESR10)

5. The studies on chicken responses to bacterial endotoxin and effects of potential Neutroceuticals demonstrated the potential of natural anti-microbials especially citrus extracts to strengthen innate immunity thus having the potential to reduce the load of antibiotics (ESR3, ESR4). In addition the in vitro studies of on cells from chicken and other species with similar Neutroceuticals have allowed proteomics and genomic studies to further identify the relevant molecular events related to advantages in their use (ESR2).

6. Development of in vitro studies for tissue culture of intestinal cells from pigs, cows and chicken and proteomics and genomic studies has allowed the identification of significant proteome changes in response to modifications of the environment to inclusion of modifiers such as Neutroceuticals (ESR2). Studies using transcriptomics have identified the effects of ω -3 fatty acids on immune cells using cell based in vitro assays thus allowing identification of the genes involved in these host response reactions (ESR9).

7. Using a method developed during the project, exosomes were isolated from both sow milk and colostrum collected during the pig trial. The effects of -6: 3 fatty acid ratios in the diet of sows (Objective 4) on the milk and colostrum was assessed using proteomics, metabolomics and lipidomics to provide a deep assessment of changes in milk and colostrum induced by alteration of the feed (ESR6).

8. A web interface, called OMnalysis, has been developed that can be used by all researchers from within and outside the project for integration of data from their omics studies in order to combine genomic, transcriptomic, proteomic and metabolomic results to allow integrated evaluation of study data (ESR11)
The exploitation of the results have been achieved with one patent application on the OMnalysis software and with the findings of the nutritional studies being available for use by industry partners. The dissemination of the project results has been achieved by the presentation of results at national and international meeting (91 by all ESRs) and the publication of 19 papers in peer reviewed publications with additional manuscripts to be submitted for publication.
The ESRs have all been fulfilling all requirements for training both in research related aspects in the advanced technology involved in the research projects and also in generic aspects for career development. MANNA project training has been delivered in the Core Course (Glasgow 2018), the Summer School (Milan 2019), subsequent Summer Schools in 2020 and 2021 being held by Zoom and organized by Zagreb and Bonn respectively and a final live meeting in 2022 (Milan). These were enhanced by an online course in proteomics with particular emphasis on its use in animal sciences. Each university has also provided training in courses covering topics such as statistics, writing papers, and preparation of thesis. Public engagement has been encouraged with full involvement of ESRs in preparation of Newsletters, Brochures, and Webpages which has been run in collaboration with SPRIM, the scientific communication company who are a non-academic partner.

The MANNA project was affected by the Covid-19 pandemic which has impacted the ESRs in different ways depending on their location at the start of the lockdowns in different countries. Regular virtual meetings were held via Zoom video to ensure that the crisis has as limited effect on the projects as possible. However, the timing of the crisis has had an impact on the projects at a time when many of the ESRs were preparing for transferring location between primary supervisor and secondary supervisor and also planning to visit their non-academic supervisors in industry or research institutes. Supervisors of the ESRs developed modifications to the project plans to mitigate against effects of the covid-19 pandemic to ensure that it will not affect the outcome of their doctoral programmes.

The impact of the project is in the training of a cohort of students who have graduated with double PhD degrees so each has had the valuable opportunity of experiencing diverse research situations and will take this unique experience into their future careers. Wider impact will be through the research outcomes and the benefits of using omic technologies for advancing animal nutrition studies. During the course of the project more studies using omic approached have been appearing in animal science and with the cohort of ESRs now seeking careers in research in academia or industry this will be accelerated in the future.
Milan Summer School
Core Course Consortium Dinner