The application of next generation sequencing to profile microbe related cheese quality defects

High 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 sequencing-based approaches were applied with a view to better understanding microbe associated quality defects in cheese. Initially, a literature review provides an overview of microbe-associated 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.

An assessment of the influence of the industry distribution chain on the oxygen levels in commercial modified atmosphere packaged cheddar cheese using non-destructive oxygen sensor technology

The establishment and control of oxygen levels in packs of oxygen-sensitive food products such as cheese is imperative in order to maintain product quality over a determined shelf life. Oxygen sensors quantify oxygen concentrations within packaging using a reversible optical measurement process, and this non-destructive nature ensures the entire supply chain can be monitored and can assist in pinpointing negative issues pertaining to product packaging. This study was carried out in a commercial cheese packaging plant and involved the insertion of 768 sensors into 384 flow-wrapped cheese packs (two sensors per pack) that were flushed with 100% carbon dioxide prior to sealing. The cheese blocks were randomly assigned to two different storage groups to assess the effects of package quality, packaging process efficiency, and handling and distribution on package containment. Results demonstrated that oxygen levels increased in both experimental groups examined over the 30-day assessment period. The group subjected to a simulated industrial distribution route and handling procedures of commercial retailed cheese exhibited the highest level of oxygen detected on every day examined and experienced the highest rate of package failure. The study concluded that fluctuating storage conditions, product movement associated with distribution activities, and the possible presence of cheese-derived contaminants such as calcium lactate crystals were chief contributors to package failure.

Effect of galactose metabolising and non-metabolising strains of Streptococcus thermophilus as a starter culture adjunct on the properties of Cheddar cheese made with low or high pH at whey drainage

Cheddar cheese was made using control culture (Lactococcus lactis subsp. lactis), or with control culture plus a galactose-metabolising (Gal+) or galactose-non-metabolising (Gal-) Streptococcus thermophilus adjunct; for each culture type, the pH at whey drainage was either low (pH 6.15) or high (pH 6.45). Sc. thermophilus affected the levels of residual lactose and galactose, and the volatile compound profile and sensory properties of the mature cheese (270 d) to an extent dependent on the drain pH and phenotype (Gal+ or Gal-). For all culture systems, reducing drain pH resulted in lower levels of moisture and lactic acid, a higher concentration of free amino acids, and higher firmness. The results indicate that Sc. thermophilus may be used to diversify the sensory properties of Cheddar cheese, for example from a fruity buttery odour and creamy flavour to a more acid taste, rancid odour, and a sweaty cheese flavour at high drain pH.

Work, class and conflict: a comparative study of three Cork factories, incorporating oral testimony

This dissertation presents a comparative study of three factories in Cork Harbour area, Sunbeam Wolsey (1927-90), Irish Steel (1939-2001) and the Ford Marina Plant (1917-84). All three factories were significant industrial employers in both a domestic (Irish) and a local (Cork) context and are broadly representative of the Irish manufacturing industry that was developed under the policies of tariff protection introduced in the 1930s and gradually phased out between the late 1950s and the mid-1980s. Sunbeam Wolsey was a textile and clothing concern located on the north side of Cork City that possessed a borderline monopoly within its economic sector and was among the largest private employers of female labour in twentieth century Ireland. Irish Steel was the country’s only steel mill, located on Haulbowline island, a brief ferry-ride from the seaside town of Cobh, and was unusual in being one of the few manufacturing concerns operated as a nationalised industry under the auspices of the state. The Ford Marina plant predated the introduction of protectionism by more than a decade and began as the centre of the Ford empire’s tractor manufacturing business, before switching to the production of private motor vehicles for the Irish market in 1932. All three industries were closed or sold off when the state withdrew support, either in the form of tariff protection (Ford, Sunbeam) or direct funding (Irish Steel). While devoting much attention to the three firms, the central concern of this dissertation is not the companies themselves (though the economic history portion of the dissertation is substantial), but the workers they employed, examining the lives of these individuals both as members of the Irish working class, and, more specifically, as employees of the three factories under consideration. The project can be best described as a comparative factory study, comparing and contrasting the three workforces, focusing primarily on industrial relation and the experience of work. This dissertation utilises both documentary evidence and a significant quantity of oral testimony, breaking new ground by making the workplace the central focus of its investigation. The principal aims of the study are: 1. To document the lives of those who worked in these factories, capturing through oral testimony their subjective experiences of social class and factory life, as well as differences among narrators in terms of gender and status. In achieving this aim, the study will provide a broader social context for its detailed analysis of work and industrial relations in each firm. 2. To analyse the three workplaces and determine how and why each developed such distinct systems of industrial relations at the factory level, as well as to compare and contrast these systems. 3. To examine the nature of work in each factory and to determine how work and industrial relations in each firm developed over time, relating these changes both to internal and external factors. Additionally, the project will provide a comparative analysis of these changes.