Comparative genome analysis of human bifidobacteria with commercial potential

This thesis describes two newly sequenced B. longum subsp. longum genomes and subsequent comparative analysis with publicly available B. longum subsp. longum, B. longum subsp. infantis and B. longum subsp. suis genomes (Chapter 2). The acquired data revealed a closed pan-genome for this bifidobacterial species and furthermore facilitated the definition of the B. longum core genome. The comparative analysis also highlights differences in the potential metabolic abilities of all three sub-species. Interestingly, phylogenetic analysis of the B. longum core genome indicated the existence of a novel B. longum subspecies. Characterisation of restriction-modification systems from two B. longum subsp. longum strains is described in Chapter 3. These defence mechanisms limit the uptake of genetic material, which was successfully demonstrated for some of the identified systems. When these systems were by-passed by methylation of DNA prior to the transformation procedure, the resulting transformation efficiency of both B. longum subsp. longum strains was increased to a level that allowed for the generation of mutants via homologous recombination. Arabinoxylan metabolism by B. longum subsp. longum NCIMB 8809 was investigated in Chapter 4 of this thesis. Transcriptome analysis allowed the identification of a number of genes involved in the degradation, uptake and utilisation of arabinoxylan. Biochemical analysis revealed that three of the identified genes encode arabinofuranosidase activity. Phenotypic assessment of a number of insertion mutants in genes identified by the transcriptome analysis revealed the essential role of two of these enzymes in arabinoxylan metabolism, and a third enzyme in the metabolism of debranched arabinan. Furthermore, this investigation revealed that B. longum subsp. longum NCIMB 8809 does not completely degrade arabinoxylan, but utilises the arabinose substitutions only, while leaving the xylan backbone untouched.Finally, Chapter 5 outlines that B. longum subsp. longum NCIMB 8809 is capable of removing ferulic and p-coumaric acid substitutions that originate from arabinoxylan. Analysis of the genome sequence led to the identification of a candidate gene for this activity, which was subsequently cloned and expressed in E. coli. Biochemical analysis revealed that the enzyme, designated here as FaeA, is indeed capable of releasing both ferulic and p-coumaric acid from arabinoxylan. Furthermore, it is shown that a derivative of B. longum subsp. longum NCIMB 8809 carrying an insertion mutation in faeA had lost the ability to release ferulic and p-coumaric acid from arabinoxylan, and that growth of this mutant strain is negatively affected when cultivated on growth-limiting levels of arabinoxylan.

The spiritual and professional impact of stillbirth

Stillbirth is without question one of the most devastating experiences of grief for parents and families. The death of a baby is also a distressing experience for healthcare professionals who share hopes of a live healthy baby at the end of pregnancy. It is a sad reality however, that in Ireland one in 238 babies will die before birth. The creation and nurture of new life in pregnancy is a spiritual experience as a new baby is at the same time experienced and anticipated. There is little in the published literature concerning the spiritual impact of stillbirth on healthcare chaplains who are the main providers of spiritual care for parents and staff colleagues in Irish maternity units. In addition there are few qualitative studies that explore the impact of stillbirth on consultant obstetricians and no published studies on the spiritual impact of stillbirth on bereaved parents. This study explored the spiritual and professional impact of stillbirth on Irish maternity healthcare chaplains, consultant obstetricians and bereaved parents. Following an overall review of spiritual care provision following stillbirth in the Irish maternity services, thematic analysis was used in the first phase of the study following in-depth interviews with maternity healthcare chaplains. Interpretative Phenomenological Analysis was used in the second and third phases with consultant obstetricians and bereaved parents respectively. The data from both maternity healthcare chaplains and consultant obstetricians revealed that stillbirth posed immense personal, spiritual and professional challenges. Chaplains expressed the spiritual and professional impact of stillbirth in terms of perception of their role, suffering, doubt and presence as they provided care for bereaved parents. A review of spiritual care provision in the Irish maternity services revealed a diversity of practice. The data from consultant obstetricians identified considerable personal, professional and spiritual impact following stillbirth that was identified in superordinate themes of human response to stillbirth, weight of professional responsibility, conflict of personal faith and incongruence between personal faith and professional practice. Data from bereaved parents revealed that stillbirth was spiritually challenging and all parents expressed that stillbirth posed considerable challenge to their faith/ belief structure. The parents of only three babies felt that their spiritual needs were adequately addressed while in hospital. The data had six superordinate themes of searching for meaning, maintaining hope, importance of personhood, protective care, questioning core beliefs and relationships. Other findings from the data from bereaved parents outlined the importance of environment of care and communication. This study has revealed the immense impact of stillbirth on healthcare chaplains, consultant obstetricians and most especially the spiritual impact for bereaved parents. Recommendations are made for improvements in clinical and spiritual care for bereaved parents following stillbirth and for staff wellbeing and support initiatives. Further research areas are recommended in the areas of spiritual care, theological reflection, bereavement care, post-mortem consent procedures and staff wellbeing.