Infant nutrition and the gut microbiota

Establishment of the intestinal microbiota commences at birth and this colonisation is influenced by a number of factors including mode of delivery, gestational age, mode of feeding, environmental factors and host genetics. As this initial establishment may well influence the health of an individual later in life, it is imperative to understand this process. Therefore, this thesis set out to investigate how early infant nutrition influences the development of a healthy gut microbiota. As part of the INFANTMET project, the intestinal microbiota of 199 breastfed infants was investigated using both culture-dependent and culture-independent approaches. This study revealed that delivery mode and gestational age had a significant impact on early microbial communities. In order to understand host genotype-microbiota interactions, the gut microbiota composition of dichorionic triplets was also investigated. The results suggested that initially host genetics play a significant role in the composition of an individual’s gut microbiota, but by month 12 environmental factors are the major determinant. To investigate the origin of hydrogen sulphide in a case of nondrug- induced sulfhemoglobinemia in a preterm infant, the gut microbiota composition was determined. This analysis revealed the presence of Morganella morganii, a producer of hydrogen sulphide and hemolysins, at a relative abundance 38%, which was not detected in control infants. Following on from this, the negative and short term consequences of intrapartum antibiotic prophylaxis exposure on the early infant intestinal microbiota composition were demonstrated, particularly in breast-fed infants, which are recovered by day 30. Finally, the composition of the breast milk microbiota over the first three months of life was characterised. A core of 12 genera were identified amongst women and the remainder comprised some 195 genera which were individual specific and subject to variations over time. The results presented in this thesis have demonstrated that the development of the infant gut microbiota is complex and highly individual. Clear alterations in the intestinal microbiota establishment process in C-section delivered, preterm and antibiotic exposed infants were shown. Taken together, long-term health benefits for infants, particularly those vulnerable groups, may be conferred through the design of probiotic and prebiotic food ingredients and supplements.

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.

Antibiotic resistance in the gut microbiota

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.

Parents' concerns about future pregnancy after stillbirth: a qualitative study

Objectives: As stillbirth has a devastating impact, it is imperative to understand the importance of clinical and emotional care after stillbirth and how it influences subsequent pregnancies. The aim of the study was to gain insight into the consideration and planning of a subsequent pregnancy by parents in the weeks following stillbirth. Design: A qualitative semi-structured interview format was utilized. Interpretative phenomenological analysis was employed as the analytic strategy. Participants and setting: The recruitment strategy focused on couples whereby the parents of ten stillborn babies were contacted; however, five men declined to participate in the study. The final sample of 15 parents were all Irish: ten of whom were female and five of whom were male. Results: Findings revealed two superordinate themes relating to a subsequent pregnancy after stillbirth: aspirations for future pregnancy and expectations of future care. Parents disclosed how the prospect of a subsequent pregnancy was daunting with fears about the potential loss of another child. Despite these fears, parentsâ aspirations differed in the days following stillbirth; mothers wished to plan a future pregnancy while fathers were reluctant to consider any pregnancies. Parents were unsure of what to expect in terms of the level of care that would be provided to them in a subsequent pregnancy. Additional appointments at the maternity hospital were considered crucial to provide reassurance during a subsequent pregnancy. Conclusions: These findings underscore the far-reaching and contrasting effects of stillbirth on parents. These complex needs highlight the importance of the multidisciplinary team approach.Objectives: As stillbirth has a devastating impact, it is imperative to understand the importance of clinical and emotional care after stillbirth and how it influences subsequent pregnancies. The aim of the study was to gain insight into the consideration and planning of a subsequent pregnancy by parents in the weeks following stillbirth. Design: A qualitative semi-structured interview format was utilized. Interpretative phenomenological analysis was employed as the analytic strategy. Participants and setting: The recruitment strategy focused on couples whereby the parents of ten stillborn babies were contacted; however, five men declined to participate in the study. The final sample of 15 parents were all Irish: ten of whom were female and five of whom were male. Results: Findings revealed two superordinate themes relating to a subsequent pregnancy after stillbirth: aspirations for future pregnancy and expectations of future care. Parents disclosed how the prospect of a subsequent pregnancy was daunting with fears about the potential loss of another child. Despite these fears, parentsâ aspirations differed in the days following stillbirth; mothers wished to plan a future pregnancy while fathers were reluctant to consider any pregnancies. Parents were unsure of what to expect in terms of the level of care that would be provided to them in a subsequent pregnancy. Additional appointments at the maternity hospital were considered crucial to provide reassurance during a subsequent pregnancy. Conclusions: These findings underscore the far-reaching and contrasting effects of stillbirth on parents. These complex needs highlight the importance of the multidisciplinary team approach.