Influence of gut microbiota on immune system in infants

Master Thesis


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University of Cape Town

Background and Methods: Microbiota play many significant, direct or indirect, beneficial and detrimental roles in humans. Microbiome development is established at infancy where diet plays a directive role in the proliferation of gut microbes. It has been shown that the presence of a defined set of microbes has been known to increase the overall immunological capacity, which vaccines depend on to be effective. To date, little work has been done on the effect of the microbiota on immune system at infancy, thus an analysis of the microbial ecology present in the infant's gut and its correlation with immune activation is needed. Expression of genes involved in mediating and regulating immunity can be measured as an indicator of immune activity. Vaccines work by stimulating an immune response which can be measured by gene expression levels. This affects the infant's ability to establish a strong immune system, which is also dictated at infancy. 16s rRNA sequence data generated from 134 infant stool samples, at vaccination points 0, 6 and 14 weeks from infants that were either breast or formula fed, was analysed using the Quantitative Insights Into Microbial Ecology (QIIME) pipeline to detect different taxonomic groups that make up a particular microbiome. Statistical analysis in R was used to quantify the diversity of the different microbial groups in the gut. Expression levels of immune-related genes were measured from blood samples that were stimulated by a Bacillus Calmette–Guérin (BCG) antigen and correlated with microbiota compositions. Results and Conclusion: Microbiome data showed initial differentiation between breast and mixed fed infants.15% of 5 of the most abundant bacteria for breast fed infants were Bifidobacteriales, which are known for their probiotic properties. The data did not fully cluster as the oldest samples were taken quite early at 14 weeks. Individual bacteria were correlated with individual gene expression level data. The study shows the relative abundance of particular bacteria, comparing against feeding modality and demonstrated how the microbiota correlates with gene expression levels. At week 14, Bifidobacterium of abundance below 0 (heatmap log₁₀ scale) generally correlated with high CASP3 gene expression levels in breast fed babies while abundances above 1 correlated with low gene expression levels. Gene expression at abnormal levels usually has undesirable effects which result in dysfunctional immune reactions that lead to conditions ranging from autoimmune diseases to cancer.