New tools for authentication and traceability to assure the integrity of pig chain

Several voluntary label claims are declared on the label of meat and meat-based products assuring high-quality food with peculiar properties - Raised without antibiotics, No antibiotics ever, Antibiotic-Free - as a consequence of the green transition that meat production systems have undergone. This trend may hide novel threats to the integrity of food systems since new kinds of fraudulent practices may emerge. In this regard, approaching the issue with the classic tools may be not successful in the modern meat market since new assurances may require innovative approaches. The omics sciences represent an emerging field spread on distinct levels - Genomic, Transcriptomic, Proteomic, Metabolomic, and Lipidomic - widely explored in different scientific fields such as food authenticity, and precision medicine. Among the omics hierarchy, the metabolome represents the most sensitive to internal factors like the health status of the organism, and the genetic background and to external factors like environmental inputs, nutrition, and pollutants. All these factors can affect the phenotypic outcome of an organism which can be investigated on metabolite levels through metabolomics. In this Ph.D. thesis, the definition of animal welfare was considered as a starting point to gain a comprehensive overview of the internal and external factors affecting animals’ phenotypic outcomes. Finally, the theoretical framework allowed to set up the experimental framework by employing the untargeted metabolomic approach to compare two different phenotypes of pigs, antibiotic-free and antibiotic-treated, respectively. Therefore, the current Ph.D. thesis was divided into five parts, as follows. In the first chapter, Introduction, a brief contextualization of the case of the antibiotic-free claim as a vulnerable factor for the integrity of the meat chain was outlined considering the scientific and legislative background and the future projections. In the second chapter, Aims of the Ph.D. thesis, both the overall scope of the present thesis and the aim of each study were described. The third chapter is organized into two main sections dealing with the feasibility of metabolomics as a new tool to explore animal welfare and the case of antibiotic-free label claims. In the first section, Metabolomic Insights into Animal Welfare, both the Animal Welfare definition and the application of omics approaches in the field of animal sciences were reviewed. All domains - nutrition (I), environment (II), health (III), behaviour (IV), and mental state (V)- were discussed considering the omics application within each domain. Additionally, the workflow of metabolomics was described to discuss the feasibility of this approach as new a tool for investigating new objects in the field of animal welfare. In the second section, Metabolomic insights into Antibiotic-Free label claims, three case studies exploring both an NMR- and HRMS-based untargeted metabolomics for the comparison between antibiotic-free versus antibiotic-treated pigs were illustrated. In the fourth chapter, Discussion, a general discussion about all the critical aspects was performed to highlight critical points both on experimental and theoretical levels. The fifth chapter, Conclusion, overall conclusion, and outlooks were outlined.