The response of the gut microbial community to therapeutic and nutritional interventions in preterm infants

Abstract

The gut bacterial community plays a vital role in human health with a diverse and complex composition, sculpted by complex host – microbe interactions. Neonates born prematurely are vulnerable to various infections due to their weak immune system and the immaturity of the gut. The most significant diseases are necrotising enterocolitis (NEC) and sepsis. With the advent of molecular techniques the development of the microbial community were better characterised. Leading to better understanding of the microbial contribution to preterm diseases and how clinical and dietary interventions can be tailored to reduce their incidence. The aim was to study the impacts of clinical and dietary interventions on the community structure and function of the preterm gut microbiota by using high throughput molecular techniques. The microbial communities derived from clinical samples that are implicated in gastrointestinal disease were explored. By utilising ecological theory, high-throughput sequencing, metabolomic profiling, and statistical modelling to identify how the assembly, phylogenetic diversity, and overall function of these communities impact on disease state. The comparison of archeal and fungal diversity between preterm infants diagnosed with NEC and/or sepsis, compared to healthy controls, showed no significant differences in the community profiles between health and disease. To study if microbial load was associated with NEC, independent of community profiles, total bacterial load was quanitified temporally in NEC infants and matched. The results showed no significant differences in the bacterial load between NEC samples before or at diagnosis, compared to healthy controls, with the only difference occurring following diagnosis, with NEC samples showing significant reduced bacterial load. To better understand clinical intervention in shaping the developing microbial community and the resulting contribution to NEC and sepsis disease mechanisms, the commonly administered antibiotics and probiotic supplementation were investigated. The result of the findings confirm existing publications, showing probiotic species administered to preterm infants significantly reduce the abundance of potentially pathogenic bacteria associated with NEC and LOS. In the first study of its kind, the study followed the same neonates longitudinally through probiotic administration, including post discharge several months after cessation. Crucially, this novel analysis revealed that supplemented bifidobacteria was able to colonise the gut long-term, but supplemented Lactobacilli did not. As well as changes in the bacterial profiles, further metabolomic profiling of functional small molecules confirmed that probiotic supplementation caused functional changes in the preterm gut microbiota. Antibiotic administration represents the most important element of current clinical practise that causes profound shifts in the gut microbiota. To further explore the routinely used antibiotics in neonatal intensive care units and to what extent this intervention alters the preterm gut microbiome, the infants were followed temporally through different antibiotic courses. This revealed that antibiotics differentially affected the preterm gut microbiome, with no single combination found to cause consistent changes between individuals. At a time when antibiotic use is under scrutiny, the outcomes show that much greater understanding of the short and long-term effects on the developing microbiome is necessary. This thesis has combined a range of molecular methods to explore the microbial community in the developing preterm gut microbiota, including bacteria, fungi, and archaea, finding no association in pathogenesis of NEC. Metabolite profiling was also performed, determining how changes in the gut microbiota cause functional changes in the gut. Combining the data from these powerful analyses revealed probiotics help to modulate a healthy gut microbiome, but antibiotics may disturb the developing bacterial community. Ultimately, better understanding of the consequences of clinical intervention will lead to more refined and personalised care