Chronic kidney disease (CKD) affects millions of people and represents a major health problem with diagnostic and therapeutic challenges. Conventional biomarkers such as serum creatinine and estimated glomerular filtration rate have limitations. The gut-kidney axis is a key factor in the pathogenesis of CKD, influenced by microbial dysbiosis and altered metabolite production. Harmful metabolites such as indoxyl sulfate, p-cresyl sulfate and trimethylamine-N-oxide promote inflammation, endothelial dysfunction and fibrosis. Loss of protective short-chain fatty acids impairs barrier integrity and immune regulation. The review includes the oral-intestinal-kidney axis, multicomics, and computational approaches to biomarkers. Microbial-targeted interventions include dietary strategies, prebiotics, probiotics, synbiotics, oral adsorbers, and fecal microbiota transplantation. These are being evaluated for efficacy, safety and readiness for use.