UCC Library and UCC researchers have made this item openly available. Please let us know how this has helped you. Thanks! Title Optimisation of protein and lipid extraction from low-value fish sources and investigation of high-value applications Author(s) Egerton, Sian Publication date 2019-07 Original citation Egerton, S. 2019. Optimisation of protein and lipid extraction from low- value fish sources and investigation of high-value applications. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights 2019, Sian Egerton. https://creativecommons.org/licenses/by-nc-nd/4.0/ Item downloaded http://hdl.handle.net/10468/9918 from Downloaded on 2021-10-10T18:05:27Z Optimisation of protein and lipid extraction from low-value fish sources and investigation of high-value applications Thesis presented to the National University of Ireland, Cork for the degree of Doctor of Philosophy by Sian Egerton, BSc. (Hons), MSc. School of Biological, Earth and Environmental Sciences, UCC Department of Microbiology, School of Engineering and Food Science, UCC Teagasc Food Research Centre, Moorepark Academic Supervisors: Prof. Paul Ross, Prof. Catherine Stanton and Prof. Sarah Culloty Enterprise Mentor: Mr Jason Whooley, Biomarine Ingredients Ireland Ltd. July 2019 Table of Contents Declaration ............................................................................................................................................ iv Author Contribution .............................................................................................................................. iv Publications……….................................................................................................................................... v Thesis Abstract ...........................................................................................................................1 Chapter 1 General Introduction ...................................................................................................4 References ............................................................................................................................................ 8 Chapter 2.1 Boarfish (Capros aper): review of a new capture fishery and its valorization potential ............................................................................................................................................ 10 Abstract .......................................................................................................................................... 11 1. Introduction ............................................................................................................................... 12 2. Boarfish, the species .................................................................................................................. 13 3 Boarfish, the fishery .................................................................................................................... 20 4. Valorisation potential ................................................................................................................ 23 5. Concluding remarks ................................................................................................................... 33 Acknowledgements ....................................................................................................................... 34 References ..................................................................................................................................... 35 Chapter 2.2 The gut microbiota of marine fish ........................................................................... 42 Abstract .......................................................................................................................................... 43 1. A historical overview .................................................................................................................. 44 2. The fish alimentary canal ........................................................................................................... 47 3. Development of the gut microbiota in fish ................................................................................ 50 4. Structure of the fish gut microbiota .......................................................................................... 53 5. Diversity of fish gut microbiota .................................................................................................. 60 6. Manipulation of the fish gut microbiota .................................................................................... 66 7. Conclusion .................................................................................................................................. 70 Acknowledgements ....................................................................................................................... 72 References ..................................................................................................................................... 73 Chapter 3 The proximate, protein and lipid composition of three commercially important marine fish; blue whiting (Micromesistius poutassou), boarfish (Capros aper) and Atlantic herring (Clupea harengus) ................................................................................................................ 93 Abstract .......................................................................................................................................... 94 1. Introduction ............................................................................................................................... 95 2. Materials and methods .............................................................................................................. 97 i 3. Results ...................................................................................................................................... 100 4. Discussion ................................................................................................................................ 114 Acknowledgements ..................................................................................................................... 119 References ................................................................................................................................... 120 Supplementary material .............................................................................................................. 127 Chapter 4 Bacteriomes and viromes of three pelagic fish are species specific ............................ 131 Abstract ........................................................................................................................................ 132 1. Introduction ............................................................................................................................. 133 2. Materials and methods ............................................................................................................ 135 3. Results ...................................................................................................................................... 144 4. Discussion ................................................................................................................................ 160 Acknowledgements ..................................................................................................................... 165 References ................................................................................................................................... 166 Supplementary material .............................................................................................................. 172 Chapter 5 Characterization of protein hydrolysates from blue whiting (Micromesistius poutassou) and their application in beverage fortification..................................................................... 174 Abstract ........................................................................................................................................ 175 1. Introduction ............................................................................................................................. 176 2. Materials and methods ............................................................................................................ 178 3 Results and discussion .............................................................................................................. 185 4. Conclusions .............................................................................................................................. 201 Acknowledgements ..................................................................................................................... 202 References ................................................................................................................................... 203 Chapter 6 Replacing fishmeal with plant protein in Atlantic salmon (Salmo salar) diets by supplementation with fish protein hydrolysate ................................................................... 208 Abstract ........................................................................................................................................ 209 1. Introduction ............................................................................................................................. 210 2. Materials and methods