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Highlights • Spinal cord injury often results in gut dysbiosis, in both humans and rodent models of disease. • Shifts in gut microbiota results in a marked decrease in butyrate-producing bacteria. • This dysbiosis, along with the “standard of care” use of antibiotics, can negatively affect recovery. • The genito-urinary microbiome is also altered in SCI and may contribute to neurogenic bladder. • Correcting the microbiome can result in improved recovery and neuroprotection., Spinal cord injury (SCI) is a devastating injury to the central nervous system in which 60 to 80% of patients experience chronic pain. Unfortunately, this pain is notoriously difficult to treat, with few effective options currently available. Patients are also commonly faced with various compounding injuries and medical challenges, often requiring frequent hospitalization and antibiotic treatment. Change in the gut microbiome from the “normal” state to one of imbalance, referred to as gut dysbiosis, has been found in both patients and rodent models following SCI. Similarities exist in the bacterial changes observed after SCI and other diseases with chronic pain as an outcome. These changes cause a shift in the regulation of inflammation, causing immune cell activation and secretion of inflammatory mediators that likely contribute to the generation/maintenance of SCI pain. Therefore, correcting gut dysbiosis may be used as a tool towards providing patients with effective pain management and improved quality of life.