Browsing Theses - AGRIP by Publication date
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The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality DefectsHigh throughput next generation sequencing, together with advanced molecular methods, has considerably enhanced the field of food microbiology. By overcoming biases associated with culture dependant approaches, it has become possible to achieve novel insights into the nature of food-borne microbial communities. In this thesis, several different sequencingbased approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbeassociated cheese quality defects as well as molecular methods for profiling complex microbial communities. Following this, 16S rRNA sequencing revealed temporal and spatial differences in microbial composition due to the time during the production day that specific commercial cheeses were manufactured. A novel Ion PGM sequencing approach, focusing on decarboxylase genes rather than 16S rRNA genes, was then successfully employed to profile the biogenic amine producing cohort of a series of artisanal cheeses. Investigations into the phenomenon of cheese pinking formed the basis of a joint 16S rRNA and whole genome shotgun sequencing approach, leading to the identification of Thermus species and, more specifically, the pathway involved in production of lycopene, a red coloured carotenoid. Finally, using a more traditional approach, the effect of addition of a facultatively heterofermentative Lactobacillus (Lactobacillus casei) to a Swiss-type cheese, in which starter activity was compromised, was investigated from the perspective of its ability to promote gas defects and irregular eye formation. X-ray computed tomography was used to visualise, using a non-destructive method, the consequences of the undesirable gas formation that resulted. Ultimately this thesis has demonstrated that the application of molecular techniques, such as next generation sequencing, can provide a detailed insight into defect-causing microbial populations present and thereby may underpin approaches to optimise the quality and consistency of a wide variety of cheeses.
The effects of stocking rate and ewe prolificacy potential on the efficiency of lamb production and grass utilisation in pasture based systemsEwe prolificacy potential (PP; predicted number of lambs born per ewe per year) and stocking 314 rate (SR; ewe per ha) are two primary drivers of output in temperate grass-based lamb 315 production systems. The aim of this thesis was to investigate and quantify the effect of ewe 316 PP, SR, and their interaction on animal performance, pasture production and utilisation and 317 the efficiency of lamb production in a grass-based production system. A 2 x 3 factorial design 318 study, consisting of two ewe PP ((medium prolificacy potential (Suffolk X ewes; 1.5 lambs 319 reared per ewe) and high prolificacy potential (Belclare X ewes; 1.7 lambs reared per ewe)) 320 and three SR: low (10 ewes per ha), medium (12 ewes per ha), and high (14 ewes per ha) was 321 conducted. Each treatment was managed in a rotational grazing system. Measurements taken 322 included; ewe body weight, ewe body condition score (BCS), number of lambs born and 323 weaned per ewe and per hectare, lamb growth rate, days to slaughter, lamb carcass traits and 324 output, ewe production efficiency (kg lamb live weight weaned: kg ewe live weight mated), 325 herbage dry matter (DM; kg) production and utilisation, sward quality and morphology, and 326 DM and energy (Unite fourrage laite per kg DM; UFL) consumption. High PP ewes produced 327 more lambs both per ewe and per hectare, with HP lambs achieving a higher average daily 328 gain (ADG) on a per hectare basis and yielded a higher lamb carcass output per hectare 329 compared to MP ewes. The total quantity of DM and UFL consumed per ewe and lamb unit 330 for the full production year did not differ by ewe PP. The HP system required a lower quantity 331 of DM and UFL to produce a kilogram of lamb carcass. The use of higher stocking rates 332 demonstrated the potential to increase lamb carcass output per hectare in a grass-based lamb 333 production, with the LSR and MSR systems achieving similar levels of performance for pre-334 weaning lamb ADG and days to slaughter. Increasing stocking rate increased herbage 335 production, utilisation and sward quality and leaf content. Limitations to increasing stocking 336 rate above 12 ewes per hectare in a grass-based lamb production system due to reductions in 337 individual animal performance and increases in DM and UFL consumption per ewe and lamb 338 unit and per kilogram of lamb carcass produced at the HSR were recorded. The findings from 339 this thesis demonstrate the potential to increase lamb output and the efficiency of lamb 340 production from a temperate grass-based lamb production system through targeted increases 341 in ewe PP and SR levels.