The training programme


The MANNA consortium provides 11 three-year doctoral programmes, co-supervised in co-tutelle by two beneficiary participants in two different universities located in different countries and a non-academic/industrial supervisor for specialized training purposes.

The three Training areas of MANNA of will provide each ESR with the following skills:

Core research skills will be acquired via the original research projects and are integrated in the research Work Packages of MANNA.

Advanced Research Skills provided by Local Training specific for each project will be delivered by the individual doctorate programmes and by research and industrial training during the secondment to the partners.

Transferable Skills will also be acquired by the network wide training supplemented by local training. Network-wide training events includes one Common course of two weeks and three Summer Schools

A common course of two weeks has been held at the University of Glasgow at the beginning of the first year, aiming to bridge the gaps between individual ESR, and providing each of them with the basic knowledge in animal science related disciplines and an introduction to OMICS, with all participants contributing. The programme of the core course could be found here.

The three Summer Schools provide a mix of specific hard-skill focused instructions and soft skills that are of direct relevance to the research programs. Each Summer School is held in conjunction with a MANNA conference where each ESR will present a report on the progress of their dissertation. International experts will be invited to give plenary lectures. Members of the external evaluation board will also be present to provide valuable feedback on the development of the ESRs and the progress of their projects. The programme of the summers schools are:

Summer School in OMICS, -Milano (I)- Advanced Biotechnology applied to Animal Health and Nutrition Transcriptomics, proteomics, metabolomics, bioinformatics and their applications in Animal Health and Nutrition.

Summer School in Essential Management Skills and Media Communication -Zagreb (HR), focused on

  • Scientific Dissemination among the Scientific Community, including how to write papers, meeting presentations,
  • Scientific dissemination and communication among public consumers and stakeholders
  • Innovation management

Summer School in Translation of research into Commercial Product and Applications -Bonn (DE)- focused on

  • Field trials and assessment of functional feed/probiotics in animal nutrition
  • Technology transfer of bioscience outputs to commercial product: biomarkers, immunoassay and diagnostic kits
  • Transfer of technology: launching of new products to the market – SPRIM


The first Summer School held from the 22nd to the 26th of July at the Milan school of Veterinary Medicine in Lodi and it was organized by the University of Milan under the coordination of Fabrizio Ceciliani and Filippa Addis with the invaluable assistance of the Project Officer Chiara Mariani and by the ESRs based in Milan: Thi Xuan Nguyen (ESR 1), Gabriela Avila Morales (ESR 2) and Tamil Selvi Sundaram (ESR 9).

1. First day focused on transcriptomics.

By the end of the day, participants were able to understand the basic principles and applications for both short and long read RNA sequencing, including the opportunity to learn from case studies taken from the past experiences of the speakers.

This information will greatly assist in key decision-making steps with regards to the methodology adopted for various projects.

Lectures by Bianca Castiglioni and Paola Cremonesi, from the Institute of Agricultural Biology and Biotechnology – National Research Council (IBBA-CNR) and followed by Fabrizio Ceciliani (Professor at the University of Milan and MANNA Supervisor).

2. The second day was focused on proteomics and metabolomics techniques.

A complete overview on the importance of these techniques and their applications in Animal Sciences giving both theoretical and practical examples.

Lectures by Filippa Addis (Professor at the University of Milan and MANNA Supervisor), Muriel Bonnet (INRA and MANNA Supervisor), Donatella Caruso (Professor at the University of Milan) and Laurence Bernard (INRA)

3. The third and last day of the school was focused on microbiomics and bioinformatics.

It covered all the aspects related to bacterial metagenomics, metaproteomics and how to develop a bioinformatic pipeline in a precise and efficient way.

Lectures by Armand Sanchez Bonastre (Professor at the University of Barcelona and MANNA Supervisor), Filippa Addis, Mike Salter (AbAgri) and Carlotta Catozzi (PhD student of the University of Milan).

Master’s students, PhD students and other researchers from all over the world (Italy, Croatia, Germany, Lithuania and Iran were some of the countries represented) attending the lectures.





Basic principles and application for long and small RNA
sequence determination and analysis



for microbiome analysis from raw DNA sequencing data.





What is it and what can we learn from it?



Techniques, approaches and potential applications in veterinary and animal sciences.





and biomarker discovery pipelines.



a list of published studies, with example of experimental designs, focused on Transcriptomic applied to veterinary and animal science.


The second summer school will be organized by the University of Zagreb in Dubrovnik (CROATIA 2020)

The main topic of this Summer School will be:

ProgrammeESR Programme

Scientific Dissemination among the Scientific Community

  • How to write and review a Scientific paper
  • Meeting presentations (Oral and Posters)

Scientific dissemination and communication among public consumers and stakeholders

  • The basis of the scientific and communication, how to translate scientific topic into consumer (and/or non-scientific stakeholders) understandable communication/strategy

How to identify and substantiate valuable scientific benefits

  • Research dissemination to non-academic audience: open access and social media
  • Innovation management: a) trends anticipation and management, b) intellectual propriety, regulatory compliance, marketing, at both local, regional and global level and c) how to launch an innovation on the market

Speakers BIO


PhD in Food Biotechnology. Her research activity performed at Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico of Milan was mainly focused on food technology and allergy field with several international peer-reviewed publications. Since December 2012, in Sprim she participated to several health & marketing corporate and clients’ projects, particularly addressed to stakeholders and healthcare professionals. Currently, she is Head of Brand Activation & Omnichannel Communication for Pharma & Consumer Healthcare companies, mainly focused on multichannel medical detailing, advisoring and trade marketing in the pharmacy channel.


Institute of Medical Biochemistry, Department for Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
PhD in environmental sciences from Wageningen University, The Netherlands. Originally trained in technical chemistry, but early specialization in protein chemistry and protein analytics, mainly on proteins of animal origin and from biological sources. Major focus is on proteomics and two-dimensional electrophoresis (from the beginning of the method on), with a special interest in methodology. Member of the editorial boards of several proteomic and analytical journals; regular reviewer; since more than 10 years Executive Editor (i.e. section editor) for Animal Proteomics in the Journal of Proteomics; during this time among the guest editors for several thematic issues: on farm animal proteomics (together with A. de Almeida and P.D. Eckersall), proteomics in ecotoxicology, gender-related proteomics, and presently one on farm and companion animal proteomics (also together with A. de Almeida and P.D. Eckersall) is in its final state. In case you are interested in further details see here


Principal Scientist and Director of Communication Moredun Research Institute.
Lee has an honours degree in Immunology from the University of Glasgow and a PhD in Tropical Animal Health from the University of Edinburgh. She has conducted research in the area of infectious diseases of livestock at several different research institutes in the UK and Africa and currently leads a group at Moredun Research Institute in Edinburgh working to develop solutions to control diseases caused by protozoan parasites. She has published numerous scientific articles and has developed and delivered several competitively funded national and international research programmes.
Following a sabbatical year spent in Hong Kong, 2002-2003, where she studied journalism and photography, Lee became more interested in science communication and education. Lee took up a new post as Director of Communication at Moredun in 2008, although still retaining her research interests. She was awarded an MBE in the New Years Honours in 2015 for services to scientific research and science communication and also holds Honorary Professorships at Heriot Watt University, University of Edinburgh and University of Glasgow. Lee recently received an award for outstanding contribution to knowledge exchange at the Scottish Knowledge Exchange Awards in 2017, was elected as a Fellow of the Royal Society of Edinburgh in 2017 and an Associate of the Royal Agricultural Societies in 2019.


Dr. David McGuinness, a graduate of Dundee University, currently works at Glasgow Polyomics, University of Glasgow, where he provides support for bioinformatic analyses, as well as genomics and transcriptomics services operating in both the ‘wet’ and ‘dry’ labs helping to bridge the gap between. David also conducts research in collaboration with some of the talented researchers based in the University of Glasgow and some further afield. These projects involve creating and adapting novel, cutting edge, methods to investigate the microbiome in a variety of environments, as well as looking at ancient DNA


Phillip Whitfield has longstanding (>25 years) research experience in the application of analytical strategies to investigate health and disease in both human and animal systems. He has extensively employed mass spectrometry in his work with a key focus on the identification and quantification of lipids in inherited metabolic disorders. Phillip completed his PhD at University College London. He subsequently held postdoctoral positions in Adelaide and Cambridge before taking up an academic post at the School of Veterinary Science at the University of Liverpool where he led a research programme in animal metabolomics. He is currently Head of Metabolomics at the University of Glasgow where his research involves the study of metabolism in different areas of biology and medicine.


He obtained a Degree in Animal Science by the University of Évora (1998), an MSc in Tropical Veterinary Medicine by the Fac. Vet. Medicine of the University of Lisbon (2000) and a PhD in Biology by the Instituto de Tecnologia Química e Biológica of the New University of Lisbon (2005). AM Almeida was a Researcher at the Instituto de Investigação Científica Tropical (Lisboa, Portugal) from 2008-2014, after a 3-year post-doc at the same institution. AM Almeida was Professor of Animal Nutrition and Animal Science at Ross University School of Veterinary Medicine (St. Kitts and Nevis, West Indies) from 2015-2016. Since 2017, he is Professor of Animal Science at the Faculty of Agriculture of the University of Lisbon (Portugal).
AM Almeida has made research stays at several institutions outside of Portugal: CSIC/IBMB Molecular Biology Institute Barcelona (Spain), University of the Free State (South Africa), Dryland Research Station (WA, Australia), the USDA (Ames, IA, USA) and Agresearch (Lincoln, New Zealand), among others.
Research interests are vast but are mainly dedicated to studies of nutritional physiology and production of small ruminants and farm animals in general, using Proteomics and Mass Spectrometry. AM Almeida participate(d) in numerous national and international Research projects and was awarded a visiting Scientist Research grant from the government of the State of Western Australia (Perth, WA, Australia) and was Vice-Chair of COST action FA1002 – Proteomics in Farm Animals, financed by the European Science Foundation.
AM Almeida has published 4 books, 24 international book chapters (including one edited by the FAO) and over 100 papers in international peer-reviewed journals, as well as numerous International Congress Proceedings and technical publications. AM Almeida is presently the editor in chief of Tropical Animal Health and Production (Springer) and an invited editor of Journal of Proteomics (Elsevier) and is a regular reviewer for several journals. He currently supervises 5 PhD students in topics related to animal nutrition and using proteomics as a major research tool.


She is an Assistant Professor at the Faculty of Food Technology and Biotechnology, University of Zagreb, Croatia. She was awarded her PhD in Chemistry in 2014 from the Faculty of Science, University of Zagreb. She has 14 years of experience in the fields of protein chemistry, mass spectrometry, proteomics and metabolomics gained through her work in R&D of Pliva Croatia Ltd. R&D, Laboratory for Systems Biomedicine, Ruđer Bošković Institute and VetMedZg proteomic Laboratory, Faculty of Veterinary Medicine, Zagreb. Anita has expertise in analysis of pharmaceutical proteins, as well as samples of clinical and biological origin. Her scientific interest is focused to application of omics technologies in biomedicine and biotechnology to understand the relationships between biomolecules and related biological processes. Except in research activities, she is also involved in teaching and student mentoring. Anita is (co)author of more than 30 papers in peer-reviewed journals, 40 conference proceedings and is listed as inventor on the US patent related to enhanced MS-based protein identification. During her PhD studies, she was honoured for the second place in Alltech Young Scientists competition in Eastern Europe Region in 2012. In 2014, she obtained the L’Oréal award For Women in Science.


The third summer school will be organized by the University of Bonn in Bonn (GERMANY 2021)

The main topics of this Summer School will be:

  • Field trials and assessment of functional feed/probiotics in animal nutrition and
  • Development and testing of novel ingredient and their cost benefit analysis
  • Technology transfer of bioscience outputs to commercial product: biomarkers, immunoassay and diagnostic kits
  • Transfer of technology: launching of new products to the market