The ELDERMET biobank: Isolation and characterization of the intestinal microbiota from elderly Irish subjects

The human gastrointestinal (GI) tract is colonized by a dense and diverse bacterial community, the commensal microbiota, which plays an important role in the overall health of individuals. This microbiota is relatively stable throughout adult life, but may fluctuate over time with aging and disease. The adaptation of the gut microbiota to our changing life-style is probably the reason for the large inter-individual variation observed among different people. Since the gut microbiota plays an essential role in interactions with host metabolism, it is of utmost importance to explore this relationship. The elderly intestinal microbiota has been the subject of a number of studies in recent years. The results presented in this thesis have further contributed to the expansion of knowledge related to gut microbiota research highlighting the combined effect of culture based and molecular methods as powerful tools for understanding the true impact of microbes. The degree of correlation between measurements from both methods suggested that a single method is capable of profiling intestinal Bifidobacterium spp., Lactobacillus spp. and Enterobacteriaceae populations. Bacteriocins have shown great promise as alternatives to traditional antibiotics. In this respect, the isolation and characterisation of bacteriocinogenic strains are important due to growing evidence indicating bacteriocin production as a potential probiotic trait by virtue of strain dominance and/or pathogen inhibition in the mammalian intestine. The selection pressure applied on the bacterial population during antibiotic usage is the driving force for the emergence of antibiotic resistant bacteria. Identification of antibiotic resistant isolates opens up the possibility of using such probiotics to offset the problems caused by antibiotics to the gut microbiota and to improve the intestinal microbial environment. Future work is required to explore the culture collection housing thousands of bacterial isolates as a valuable source of potential probiotics for use for the elderly Irish community.

Established cardiovascular disease and CVD risk factors in a primary care population of middle-aged Irish men and women

Contemporary Irish data on the prevalence of major cardiovascular disease (CVD) risk factors are sparse. The primary aims of this study were (1) to estimate the prevalence of major cardiovascular disease risk factors, including Type 2 Diabetes Mellitus, in the general population of men and women between the ages of 50 and 69 years; and (2) to estimate the proportion of individuals in this age group at high absolute risk of cardiovascular disease events on the basis of pre-existing cardiovascular disease or as defined by the Framingham equation. Participants were drawn from the practice lists of 17 general practices in Cork and Kerry using stratified random sampling. A total of 1018 people attended for screening (490 men, 48%) from 1473 who were invited, a response rate of 69.1%. Cardiovascular disease risk factors and glucose intolerance are common in the population of men and women aged between 50 and 69 years. Almost half the participants were overweight and a further quarter met current international criteria for obesity, one of the highest recorded prevalence rates for obesity in a European population sample. Forty per cent of the population reported minimal levels of physical activity and 19% were current cigarette smokers. Approximately half the sample had blood pressure readings consistent with international criteria for the diagnosis of hypertension, but only 38% of these individuals were known to be hypertensive. Eighty per cent of the population sample had a cholesterol concentration in excess of 5 mmol/l. Almost 4% of the population had Type 2 Diabetes Mellitus, of whom 30% were previously undiagnosed. A total of 137 participants (13.5%) had a history or ECG findings consistent with established cardiovascular disease. Of the remaining 881 individuals in the primary prevention population, a total of 20 high-risk individuals (19 male) had a risk of a coronary heart disease event 30% over ten years according to the Framingham risk equation, giving an overall population prevalence of 2.0% (95% CI 1.3 - 3.0). At a risk level 20% over ten years, an additional 91 individuals (8.9%) were identified. Thus a total of 24.4% of the population were at risk either through pre-existing CVD (13.5%) or an estimated 10-year risk exceeding 20% according to the Framingham risk equation (10.9%). Thus a substantial proportion of middle-aged men are at high risk of CVD. The findings emphasise the scale of the CVD epidemic in Ireland and the need for ongoing monitoring of risk factors at the population level and the need to develop preventive strategies at both the clinical and societal level.

Studies relating to the population dynamics of the European badger (Meles meles) in Ireland

European badgers (Meles meles) are an important part of the Irish ecosystem; they are a component of Ireland’s native fauna and are afforded protection by national and international laws. The species is also a reservoir host for bovine tuberculosis (bTB) and implicated in the epidemiology of bTB in cattle. Due to this latter point, badgers have been culled in the Republic of Ireland (ROI) in areas where persistent cattle bTB outbreaks exist. The population dynamics of badgers are therefore of great pure and applied interest. The studies within this thesis used large datasets and a number of analytical approaches to uncover essential elements of badger populations in the ROI. Furthermore, a review and meta-analysis of all available data on Irish badgers was completed to give a framework from which key knowledge gaps and future directions could be identified (Chapter 1). One main finding suggested that badger densities are significantly reduced in areas of repeated culling, as revealed through declining trends in signs of activity (Chapter 2) and capture numbers (Chapter 2 and Chapter 3). Despite this, the trappability of badgers was shown to be lower than previously thought. This indicates that management programmes would require repeated long-term efforts to be effective (Chapter 4). Mark-recapture modelling of a population (sample area: 755km2) suggested that mean badger density was typical of continental European populations, but substantially lower than British populations (Chapter 4). Badger movement patterns indicated that most of the population exhibited site fidelity. Long-distance movements were also recorded, the longest of which (20.1km) was the greatest displacement of an Irish badger currently known (Chapter 5). The studies presented in this thesis allows for the development of more robust models of the badger population at national scales (see Future Directions). Through the use of large-scale datasets future models will facilitate informed sustainable planning for disease control.

Investigation of the genetic susceptibility to osteoporosis in the Irish population

Osteoporosis is a complex skeletal disorder characterized by compromised bone strength. Variation in bone mineral density (BMD) is a contributing factor. The aim of this research as to select informative single nucleotide polymorphisms (SNPs) in potential candidate genes from loci suggestively linked to BMD variation for fine mapping. The gene regulated by oestrogen in breast cancer 1 (GREB1), located at 2p25.1, was selected. GREB1 transcription is initiated early in the oestrogen receptor alpha regulated pathway. There was significant association between GREB1_03 and BMD variation at the lumbar spine and femoral neck (FN) in the discovery cohort. Significant association was observed between GREB1_04 and FN BMD in the replication cohort. The development and differentiation enhancing factor 2, the integrin cytoplasmic domain associated protein 1 and A-disintegrin and metalloprotease 17 were selected due to their respective roles in cell mobility and adhesion. There was no linkage or association observed between the Chr2 cluster SNPs and BMD. Two factors in bone remodelling are the attraction of bone cell precursors and endocrine regulation of the process, primarily through the action of parathyroid hormone (PTH). The C-C chemokine receptor type 3 (CCR3) encodes a CC chemokine receptor expressed in osteoclast precursors. The PTH receptor type 1 (PTHR1) encodes a G-protein coupled receptor for PTH. Association was observed between CCR3 haplotypes and BMD variation at the FN. There was no linkage or association observed between PTHR1 SNPs and BMD variation. Population genetic studies with complex phenotypes endeavour to elucidate the traits genetic architecture. This study presents evidence of association between GREB1 and BMD variation and as such, introduces GREB1 as a novel gene target for osteoporosis genetics studies. It affirms that common genomic variants in PTHR1 are not associated with BMD variation in Caucasians and supports the evidence that CCR3 may be contributing to BMD variation

Assessment of dietary background exposure of the Irish adult population to dioxins and PCBs particularly taking into account additional exposure due to the 2008 Irish dioxin food contamination incident

Irish monitoring data on PCDD/Fs, DL-PCBs and Marker PCBs were collated and combined with Irish Adult Food Consumption Data, to estimate dietary background exposure of Irish adults to dioxins and PCBs. Furthermore, all available information on the 2008 Irish pork dioxin food contamination incident was collated and analysed with a view to evaluate any potential impact the incident may have had on general dioxin and PCB background exposure levels estimated for the adult population in Ireland. The average upperbound daily intake of Irish adults to dioxins Total WHO TEQ (2005) (PCDD/Fs & DLPCBs) from environmental background contamination, was estimated at 0.3 pg/kg bw/d and at the 95th percentile at 1 pg/kg bw/d. The average upperbound daily intake of Irish adults to the sum of 6 Marker PCBs from environmental background contamination ubiquitous in the environment was estimated at 1.6 ng/kg bw/d and at the 95th percentile at 6.8 ng/kg bw/d. Dietary background exposure estimates for both dioxins and PCBs indicate that the Irish adult population has exposures below the European average, a finding which is also supported by the levels detected in breast milk of Irish mothers. Exposure levels are below health based guidance values and/or Body Burdens associated with the TWI (for dioxins) or associated with a NOAEL (for PCBs). Given the current toxicological knowledge, based on biomarker data and estimated dietary exposure, general background exposure of the Irish adult population to dioxins and PCBs is of no human health concern. In 2008, a porcine fat sample taken as part of the national residues monitoring programme led to the detection of a major feed contamination incidence in the Republic of Ireland. The source of the contamination was traced back to the use of contaminated oil in a direct-drying feed operation system. Congener profiles in animal fat and feed samples showed a high level of consistency and pinpointed the likely source of fuel contamination to be a highly chlorinated commercial PCB mixture. To estimate additional exposure to dioxins and PCBs due to the contamination of pig and cattle herds, collection and a systematic review of all data associated with the contamination incident was conducted. A model was devised that took into account the proportion of contaminated product reaching the final consumer during the 90 day contamination incident window. For a 90 day period, the total additional exposure to Total TEQ (PCDD/F &DL-PCB) WHO (2005) amounted to 407 pg/kg bw/90d at the 95th percentile and 1911 pg/kg bw/90d at the 99th percentile. Exposure estimates derived for both dioxins and PCBs showed that the Body Burden of the general population remained largely unaffected by the contamination incident and approximately 10 % of the adult population in Ireland was exposed to elevated levels of dioxins and PCBs. Whilst people in this 10 % cohort experienced quite a significant additional load to the existing body burden, the estimated exposure values do not indicate approximation of body burdens associated with adverse health effects, based on current knowledge. The exposure period was also limited in time to approximately 3 months, following the FSAI recall of contaminated meat immediately on detection of the contamination. A follow up breast milk study on Irish first time mothers conducted in 2009/2010 did not show any increase in concentrations compared to the study conducted in 2002. The latter supports the conclusion that the majority of the Irish adult population was not affected by the contamination incident.

A craniometric study of population dynamics and social organisation in the European upper Palaeolithic and Mesolithic

The purpose of this study is to explore aspects of social organisation during the Upper Palaeolithic and Mesolithic periods using craniometric data. Different hypotheses were tested using geometric morphometrics, alongside traditional craniometric data. The clustering of individuals from the same site, as well as a correspondence to an isolation-by-distance model—particular in the Mesolithic samples—points to population structure within these groups. Moreover, discontinuities in cranial traits between the early Upper Palaeolithic and later periods could suggest that the Last Glacial Maximum had a disruptive effect on populations in Europe. Differences in social organisation can often result from cultural norms regarding post-marital residence. Such differences can be tested by comparing cranial data to that of geographic information. Greater variation in male cranial traits relative to females, after controlling for location, suggests that the overall pattern of residence during the Upper Palaeolithic and Mesolithic was one of matrilocality. It has been suggested that coastal occupation was density dependent and these populations show a greater degree of sedentism than their inland counterparts. Moreover, it has been proposed that coastal areas were not continuously occupied until the Late Pleistocene due to spatial restrictions that would adversely affect reproductive opportunities. This study corroborates the pattern seen in cranial traits corresponded with that of a more sedentary population. The results are consistent with the hypothesis that coastal populations are more sedentary than inland populations during these periods. This study adds new information regarding the social dynamics of prehistoric populations in Europe and sheds light on some of the conditions that may have paved the way for the transition to agriculture

Can population-level variation in early childhood development be measured in a manner that supports service planning and intervention?

Background: The Early Development Instrument (EDI) is a population-level measure of five developmental domains at school-entry age. The overall aim of this thesis was to explore the potential of the EDI as an indicator of early development in Ireland. Methods: A cross-sectional study was conducted in 47 primary schools in 2011 using the EDI and a linked parental questionnaire. EDI (teacher completed) scores were calculated for 1,344 children in their first year of full-time education. Those scoring in the lowest 10% of the sample population in one or more domains were deemed to be 'developmentally vulnerable'. Scores were correlated with contextual data from the parental questionnaire and with indicators of area and school-level deprivation. Rasch analysis was used to determine the validity of the EDI. Results: Over one quarter (27.5%) of all children in the study were developmentally vulnerable. Individual characteristics associated with increased risk of vulnerability were being male; under 5 years old; and having English as a second language. Adjusted for these demographics, low birth weight, poor parent/child interaction and mother’s lower level of education showed the most significant odds ratios for developmental vulnerability. Vulnerability did not follow the area-level deprivation gradient as measured by a composite index of material deprivation. Children considered by the teacher to be in need of assessment also had lower scores, which were not significantly different from those of children with a clinical diagnosis of special needs. all domains showed at least reasonable fit to the Rasch model supporting the validity of the instrument. However, there was a need for further refinement of the instrument in the Irish context. Conclusion: This thesis provides a unique snapshot of early development in Ireland. The EDI and linked parental questionnaires are promising indicators of the extent, distribution and determinants of developmental vulnerability.