Theses - Food ProgrammeDoctoral and Masters Theseshttp://hdl.handle.net/11019/10662024-03-28T13:28:45Z2024-03-28T13:28:45ZShelf-life extension ingredient and processing technologies applied to Atlantic salmon (Salmo salar)Fogarty, Colinhttp://hdl.handle.net/11019/19692020-06-13T03:33:00Z2020-01-01T00:00:00ZShelf-life extension ingredient and processing technologies applied to Atlantic salmon (Salmo salar)
Fogarty, Colin
These current studies explore the possibility of improving analytical methods to assess freshness in seafood and to investigate the antimicrobial potential of a range of natural ingredients both alone and in combination with packaging and chilled storage temperatures to extend the shelf life of Atlantic salmon.
The aims of this research study were;
• To investigate bacterial growth on Atlantic salmon stored under chilled aerobic conditions thus providing data which may be used to assess which bacterial groups and concentrations are most appropriate for shelf-life determination.
• To characterize the microbiota present in the GI tract of Atlantic salmon, using Miseq Illumina high throughput sequencing
• To develop and validate rapid sensory (QIM and QDA) and ATP derivative based methods for assessing the freshness of Atlantic salmon.
• To investigate the effects of a natural antimicrobial immersion treatment on microbial growth for Atlantic salmon fillets during chilled storage.
• To examine the effects of either a natural antimicrobial immersion or spray treatment on mean bacterial counts in combination with packaging technologies for Atlantic salmon fillets during chilled storage.
• To assess the effects of skin packaging with retail and sub-zero temperatures on the mean bacterial counts for Atlantic salmon fillets.
Doctoral Thesis
2020-01-01T00:00:00ZInvestigation of the presence and activity of the innate immune component, Complement, in bovine milkMaye, Susanhttp://hdl.handle.net/11019/11582019-08-20T17:40:37Z2016-04-01T00:00:00ZInvestigation of the presence and activity of the innate immune component, Complement, in bovine milk
Maye, Susan
The occurrence of Complement in human milk indicates the presence of innate immune components of maternal origin and their putative defensive role in the neonatal gut. In order to ascertain the status of Complement in bovine milk, it was necessary to validate the suitability of the Complement-sensitive bacterial sequestration assay used to monitor human milk. The relative bacteriostatic effects, expressed as a differential between the initial and final assay counts following inhibition of the E. coli O111 marker strain were, 6.20 and 6.06 log CFU/ml for raw bovine and human milks, respectively. Lower levels of Complement activity measured in pasteurised and low-fat milks were observed during the course of heat-inactivation studies, while gravity separation of cream over a 24 h period confirmed a greater degree of attachment by Complement to the rising cream layer. The E. coli O111 sequestration assay strain had restricted growth of 7.5 and 8.2 CFU/ml in the higher and lower gravity-separated fractions, respectively. An animal health effect was observed, with Complement appearing to be more active in milk samples from cows with a higher somatic cell counts (SCC). Inducing sub-clinical mastitis in the healthy quarter of a lactating cow confirmed that increased Complement activity effect was local to the affected quarter and not manifested systemically. Complement activity levels varied in the milks of 7 commercially important prominent dairy breeds and crossbreeds surveyed. Both the Norwegian Red and Kerry breed cows stood out as having higher Complement activity (6.25 and 6.92 CFU/ml, respectively); these two breeds are known to have stronger immunity and a better capacity to resist mastitic infection. The findings of this study have implications for both milk production and processing disciplines. In order to retain the antimicrobial efficacy associated with xi Complement in raw bovine milk, milder process treatments than hitherto practised in industry should be adopted.
Doctoral thesis
2016-04-01T00:00:00ZAntibiotic Resistance in the Gut MicrobiotaFouhy, Fionahttp://hdl.handle.net/11019/11052020-11-04T15:33:55Z2014-01-01T00:00:00ZAntibiotic Resistance in the Gut Microbiota
Fouhy, Fiona
Antibiotic resistance is an increasing threat to our ability to treat infectious diseases. Thus, understanding the effects of antibiotics on the gut microbiota, as well as the potential for such populations to act as a reservoir for resistance genes, is imperative. This thesis set out to investigate the gut microbiota of antibiotic treated infants compared to untreated controls using high-throughput DNA sequencing. The results demonstrated the significant effects of antibiotic treatment, resulting in increased proportions of Proteobacteria and decreased proportions of Bifidobacterium. The species diversity of bifidobacteria was also reduced. This thesis also highlights the ability of the human gut microbiota to act as an antibiotic resistance reservoir. Using metagenomic DNA extracted from faecal samples from adult males, PCR was employed to demonstrate the prevalence and diversity of aminoglycoside and β-lactam resistance genes in the adult gut microbiota and highlighted the merits of the approach adopted. Using infant faecal samples, we constructed and screened a second fosmid metagenomic bank for the same families of resistance genes and demonstrated that the infant gut microbiota is also a reservoir for resistance genes. Using in silico analysis we highlighted the existence of putative aminoglycoside and β-lactam resistance determinants within the genomes of Bifidobacterium species. In the case of the β- lactamases, these appear to be mis-annotated. However, through homologous recombination-mediated insertional inactivation, we have demonstrated that the putative aminoglycoside resistance proteins do contribute to resistance. In additional studies, we investigated the effects of short bowel syndrome on infant gut microbiota, the immune system and bile acid metabolism. We also sequenced the microbiota of the human vermiform appendix, highlighting its complexity. Finally, this thesis demonstrated the strain specific nature of 2 different probiotic CLA-producing Bifidobacterium breve on the murine gut microbiota.
Doctoral thesis, accepted version
2014-01-01T00:00:00ZThe Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality DefectsO'Sullivan, Danielhttp://hdl.handle.net/11019/10742019-08-20T17:40:37Z2015-01-01T00:00:00ZThe Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects
O'Sullivan, Daniel
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 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.
Doctoral thesis
2015-01-01T00:00:00Z