Using metagenomic sequencing, researchers have identified changes in populations of bacteria and viruses that occur after spinal cord injuries in mice. The novel metagenomic data sets, presented in mSystems, an open-access journal of the American Society for Microbiology, provide new information on the taxonomy and function of diverse microbes, including viruses. This information may help to better predict how spinal cord injury-induced changes in the microbiome influence systemic and neurological outcomes after traumatic spinal cord injury.