Dysbiotic intestinal microbiomes dominated by facultative anaerobes are strongly associated with inflammatory bowel disease (IBD). More recently, data from Baumler and colleagues support a model where mitochondrial dysfunction causes disease-associated dysbiosis by increasing oxygen (O2) availability to the microbiome. We posit that the restoration of epithelial mitochondrial respiration contributes to the restoration of a healthy microbiome dominated by facultative anaerobes such as Firmicutes [that produce short chain fatty acids (SCFA)].