Recent Submissions

  • Investigation of the presence and activity of the innate immune component, Complement, in bovine milk

    Maye, Susan (2016-04)
    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.
  • Antibiotic Resistance in the Gut Microbiota

    Fouhy, Fiona (2014)
    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.
  • The Application of Next Generation Sequencing to Profile Microbe Related Cheese Quality Defects

    O'Sullivan, Daniel (2015)
    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.
  • Characterisation and application of fruit by-products as novel ingredients in gluten-free products

    O'Shea, Norah (2014-01)
    Literature has revealed that “waste” left from the processing of fruit can still contain a substantial quantity of macro and minor nutrients. The aim of this thesis was to ascertain the nutritional and structural properties and potential uses of two fruit by-products [apple pomace (Malus domestica Cv. “Karmijn de Sonnaville”) and orange pomace (Citrus sinensis L. Cv. “Valencia”)] in glutenfree bread and extruded snack formulations. The physicochemical and nutritional properties of the fruit by-products were initially studied. Apple pomace contained a high level of fibre and pectin. The isolated pectin was demonstrated to have a high level of methylation which developed viscous pastes. Orange pomace also had high levels of fibre and pectin, and it was an abundant source of minerals such as potassium and magnesium. Orange pomace had a poor gelling ability. The flour obtained after milling dried orange pomace was used in the formulation of gluten-free bread with the aid of a response surface design. Due to the fibrous properties of orange pomace flour, proofing and water addition were also studied. When added at levels greater than 6%, the loaf volume decreased. The number of cells per slice also decreased with increasing orange pomace addition. Inclusion of orange pomace at levels of up to 4% increased crumb softness. An optimised formulation and proofing time was derived using the optimisation tool; these consisted of 5.5% orange pomace, 94.6% water inclusion and with 49 minutes proofing. These optimised parameters doubled the total dietary fibre content of the bread compared to the original control. The pasting properties, rheology, microstructure and sensory characteristics of the optimised formulation (batter and bread) were investigated. Pasting results showed how orange pomace inclusions reduced the final viscosity of the batter, hence reducing the occurrence of starch gelatinisation. Rheological properties such as the storage modulus (G') and complex modulus (G*) increased in the orange pomace batter compared to the control batter. This demonstrates how the orange pomace as an ingredient improved the robustness of the formulation. Sensory panellists scored the orange pomace bread comparably to the control bread. Milled apple pomace was studied as a potential novel ingredient in an extruded snack. As extrusion requires the trialling of a number of extruder parameters, a response surface design was again used to develop an optimised snack. The parameters studied were apple pomace addition, die head temperature and screw speed. Screw speed had the most significant impact on extrudate characteristics. As screw speed increased the favourable extrudate characteristics such as radical expansion ratio, porosity and specific volume decreased. The inclusion of apple pomace had a negative effect on extrudate characteristics at levels greater than 8% addition. Including apple pomace reduced the hardness and increased the crispiness of the snack. Using the optimisation tool, the optimised and validated formulation and extrusion process contained the following parameters: 7.7% apple pomace, 150oC die head temperature and a screw speed of 69 rpm.