Coeliac disease, an immune-mediated disease triggered by gluten ingestion in genetically predisposed individuals, has a global 1% prevalence despite 30-40% carrying relevant genes suggesting non-genetic factors are involved. Examining the gut microbiome's potential link to coeliac disease development could provide insights into its prevalence, notably in regions like Canterbury with increased rates (1.21%). Recent research underscores the gut microbiome's role in immune disorders like inflammatory bowel disease, obesity, and diabetes, affecting the balance of commensal, probiotic, and pathogenic bacteria, leading to gut dysbiosis. We used 16S rRNA sequencing to characterise microbial populations in eleven (n=11) Canterbury children faeces samples upon diagnosis (active celiac disease) and nine (n=9) after 26 weeks of a gluten-free diet (treated celiac disease). Employing Mothur and Bioconductor, our dual bioinformatics approach facilitated rapid processing and in-depth analysis of diversity measures and classification statistics. Significant reductions in vital commensal and probiotic bacteria were observed, particularly Bifidobacterium (73% reduction in treated celiac disease) and Lactobacillus (67% reduction in active celiac disease). Additional reductions were noted in Enterobacter, Enterococcus, and Streptococcus. Alterations in gut microbiota compositional data were identified in both active and treated celiac disease groups, suggesting gut dysbiosis in the former. Our compositional data also revealed diet-specific alterations, indicative of lower dietary fibre and a shift in energy availability for bacterial utilisation. These findings shed light on host-microbiota interactions, highlighting the impact of immune diseases and diets on gut microflora. This research seeks to uncover coeliac disease-associated microbial shifts, contributing to potential gut microbiome-based therapeutic strategies.