Quality, shelf-life, and proteomics characterization of organic chicken meat: towards a sustainable poultry supply chain

Our daily food choices have a huge impact on the sustainability dimensions, including the environment. The concerns of consumers including meat eaters about the sustainability of food products they bring to their tables has significantly increased in recent decades (Nguyen et al. 2019; Rocchi et al. 2019; Rocchi et al. 2021). In the production of foods of animal origin, this trend is leading to a rapid and constant growth towards sectors that are more attentive to the extrinsic quality dimensions, i.e., environmental sustainability and animal welfare. Also there is growing concern that non prudent use of antibiotics in animal livestock is linked with the escalating emergence of human infections with antibiotic-resistant pathogens (Moudgil et al. 2018). Chicken meat is the most popular animal protein source in the world. Chicken farming and production methods certainly affects meat sales, in fact not only the price and quality of the product, but also consumer's lifestyle, religious and health concerns, can impact on the choice of food product (Cooreman-Algoed et al. 2022). In this perspective, poultry industries have begun to implement strategies considering the sustainability and animal welfare (Nguyen et al. 2019). Generally speaking, two strategies are being applied to reach these goals. First, the use of biodegradable and compostable packaging materials for the storage of meat and sale has the purpose of communicating to the consumer the company's commitment to environmental protection (Ivonkovic et al. 2017). As researchers, testing the new materials to be used as food packaging for the preservation of quality and appearance of perishable food, such as raw meat, is crucial for consumer’s safety and to provide high quality food products (Chen et al. 2019; Bajer et al. 2020; Gagaoua et al. 2021a; Fernandez et al. 2022; Gagaoua et al. 2022a). Second, the other strategy is to produce high quality-meat by shifting to more extensive farming systems, such as organic production. (Dal Bosco et al. 2021; Prache et al. 2021). Many factors involved in the farming practices can influence the meat quality, including the animal strain and genetic line, the feeding, the lifespan, the access to an outdoor area etc. The impact of organic production systems on chicken meat quality is not yet clearly understood if we refer the scientific literature as only few studies investigated this aspect with controversial results (Cygan-Szczegielniak & Bogucka 2021; Mancinelli et al. 2021; Wurtz et al. 2022). Over the past 50 years, fast-growing chickens were selected and widely used in intensive farming standards. Nowadays, the new farming and production practices are becoming more attentive to sustainability and animal welfare, thus leading to the use of new slow-growing chicken strains (Rayner et al. 2020; Chodová et al. 2021). The use of these new genetic lines and the impact of the farming method on chicken meat quality has not yet been studied in depth by the scientific community. Classic or traditional approaches used to characterize muscle characteristics were based on a small number of proteins and did not consider the complexity of the underlying biochemical mechanisms and their interactions (Picard et al. 2010; Purslow et al. 2021). “Omics” techniques, in particular proteomics, have been proposed as a powerful tool to better understand the phenomenon, thanks to the in-depth characterization of the post- mortem muscle proteome, hence in revealing the unknowns and biological mechanisms associated to meat quality determination (Capozzi et al. 2017; Munekata et al. 2021; Cao et al. 2022; Gagaoua & Picard 2022). Considering the above, the main attempts of my thesis are: • the evaluation of the possibility of using a new biodegradable and compostable packaging for the storage and sale of chicken meat by analysing its impact on meat quality. • the comparison of meat quality and shelf-life parameters of meat produced using organic and antibiotic-free production systems • the application, for the first time, of proteomics approaches to characterize the muscle and meat proteome of two different chicken strains reared within antibiotic- free and organic farming systems. • discovery of putative protein biomarkers of authenticity and the molecular signatures that contribute to the development of specific meat qualities. I structured my thesis manuscript in the following section into four sections: A. An introductive literature review of the state of art about i) the chicken farming systems, ii) chicken meat quality and underlying factors of variation, iii) the impact of packaging on the chicken meat supply chain, and iv) proteomics techniques and applications to research and identify biomarkers of meat quality. B. Main objectives of the thesis and a brief description of the experimental design. C. Presentation of all my results acquired during my three years of thesis, in the form of article chapters starting from i) the study of a new biodegradable and compostable packaging in chicken meat preservation; ii) investigation of meat quality and shelf- life parameters among organic and conventional chicken meat; and iii) proteomics techniques and approaches applied to characterize and better understand the differences in chicken muscle/meat proteome between the two production systems and two chicken strains we selected in my project, including the different the statistical and bioinformatics tools I applied to decipher the unknowns and achieve my goals. D. An overall conclusion and the future perspectives from this thesis work.