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The overall aim of this thesis was to investigate the effects of pasture versus conventional indoor cow feeding systems on the composition, quality and characteristics of milk, dairy products and rumen microbiota. Initially the effects of perennial ryegrass (GRS), perennial ryegrass and white clover pasture (CLV) and total mixed ration (TMR) feeding of cows on the composition and nutritional quality of raw milk throughout an entire lactation was examined (Chapter 2). Cow diet was shown to have a significant effect (P < 0.05) on both the macrocomposition and fatty acid content of milk throughout lactation. Milk from pasture fed cows had significantly higher (P < 0.05) concentrations of fat, protein, true protein and casein. Pasture derived milk was shown to have significantly higher (P < 0.05) content of conjugated linoleic acid and omega 3 fatty acids while TMR derived milk had significantly higher (P < 0.05) palmitic acid and omega 6 fatty acids. The aim of Chapter 3 was to examine the effects of different feeding systems on the composition, quality and sensory properties of mid lactation sweet cream butter. The nutritional composition of butters was improved by pasture feeding. Alterations in the fatty acid composition of butter between feeding systems contributed to significant differences in textural and thermal properties of the butters. Volatile analysis of butter by GC-MS identified 25 compounds present in each of the butters, five of which differed significantly (P < 0.05) based on feeding system. Chapter 4 examined the effects of diet on the composition, quality and sensory properties of Cheddar cheese throughout nine months of ripening. This study demonstrated the benefits of pasture derived feeding systems for production of Cheddar cheeses with enhanced nutritional and rheological quality compared with TMR feeding system. Pasture derived feeding systems were shown to produce Cheddar cheeses more yellow in colour than that of TMR, which was positively correlated with cheese β-carotene content. Feeding system had a significant effect on the fatty acid composition of the cheeses. Differences in the cheese fatty acid content were correlated with alterations to the Cheddar cheese rheological properties. Feeding system and ripening time had a significant effect on the volatile profile of the Cheddar cheeses. Principal component analysis of average fatty acid profiles in milk, butter and Cheddar cheese showed clear separation of the products from the grazed pasture-based diets to that of a TMR system throughout lactation, offering insight into the ability to verify pasture derived milk and products by fatty acid profiling. In Chapter 5, 16s RNA MiSeq sequencing was applied to both solid and liquid fractions of cow rumen to examine the effect of cows feeding system on the rumen microbiota. There was a clear separation between the liquid and solid fractions. No major differences in the rumen microbiota composition between cows exposed to different diets was found, which is likely as a result of a shortened adaptation period. It is also clear that the majority of the rumen microbiota is still undiscovered. As such, further work is required to fully understand the effects of these diets on the rumen microbiota and its functionality. Untargeted 1 H-NMR was used to examine the effects of cows feeding system on the rumen and milk metabolome (Chapter 6). Our results show that feeding system impacted significantly on both the rumen and milk metabolome. This study has highlighted that 1 H-NMR metabolomics coupled with multivariate analysis is capable of distinguishing both rumen-fluids and milk samples derived from cows on different feeding systems. Finally, Chapter 7 discusses the major findings and general conclusions arising from the studies presented in this thesis.

The presence of chlorate in milk and dairy products can arise from the use of chlorinated water and chlorinated detergents for cleaning and sanitation of process equipment at both farm and food processor level. Chlorate and other oxychlorine species have been associated with inhibition of iodine uptake in humans and the formation of methemoglobin, with infants and young children being a high‐risk demographic. This comprehensive review of chlorate and chlorine derivatives in dairy, highlights areas of concern relative to the origin and/or introduction of chlorate within the dairy supply chain. This review also discusses the associated health concerns, regulations, and chemical behavior of chlorate and chlorine‐derived by‐products, and provides a summary of mechanisms for their detection and removal.