Despite significant focus on the composition, function and ecology within the human gastrointestinal system the majority of studies remain focused on the microbiome of the faecal samples. While analysis of these samples has advanced from high throughput sequencing to include bacterial culturing and experimental validation, understanding microbial compositions across distinct regions of the 9-meter adult gastrointestinal tract remains to be undertaken in detail. Here we combine shotgun metagenomic sequencing, bacterial culturing and host transcriptomic analysis with detailed experimental validation to understand the relationship between bacterial community and disease state in Inflammatory Bowel Disease patients. To achieve this, we established a paediatric IBD (PIBD) specific bacterial culture collection, comprising 6,416 isolates (207 distinct species, 79 putative novel), cultured from 286 mucosal biopsies (58 PIBD and 42 control patients). This resource, coupled with novel, high-resolution, culture-based shotgun metagenomic sequencing (231 samples) and matched host transcriptomics (231 samples) across three biopsy sites (terminal ileum, caecum, rectum) identified key, functionally distinct bacterial subclades associated with IBD. In vitro validation of these clades demonstrates specific differences in cell cytotoxicity and inflammatory signalling, in intestinal epithelial cells, that matches the colonic mucosa response measured within the patient cohort. The combination of site-specific bacterial culturing, metagenomics and host transcriptomics from patient biopsies allows identification of key microbial communities, classification and functional validation of key community states and highlights the benefits for functional clade-based analysis for the future of microbiome-based therapeutics.