The gastrointestinal microbiome plays key roles in the development and modulation of innate immune responses. Despite these known associations, mechanistic understanding of the host-microbiota interactions in the gut that recapitulates the nature and complexity of host state driven by these diverse bacteria remains to be established. Applying our novel site-specific bacterial culturing from patient intestinal mucosal biopsies, we have found key bacterial subclades that associated with host state in matched bacterial metagenomic and host gene transcriptional analysis. To experimentally validate these findings in vitro, mucosal bacterial isolates were co-cultured with intestinal epithelial cells which resulted in a clade-specific cell cytotoxic phenotype and transcription of host genes belonging to the unfolded protein response (UPR) and endoplasmic reticulum (ER) stress pathways. This host cell phenotype was subsequently observed following bacterial co-culture in Transwell assays and similarly in response to conditioned media from epithelial cells that were treated with candidate bacterial isolates. However, epithelial cell cytotoxicity and transcription of ER stress and UPR genes were abrogated upon treatment with heat-treated bacterial lysates. This indicates that there may be specific microbiota effector proteins or metabolites that function as mediators of epithelial cell signalling pathways important in regulating cellular stress and intestinal inflammation. A comprehensive understanding of bacterial-host cell interactions will provide key insights toward harnessing gut bacterial candidates for novel microbiome-based therapeutics that target disorders with a complex pathophysiology such as inflammatory bowel disease.