Multi-omics analysis of changes in the microbiota–gut– spinal cord axis in spinal cord injury

A growing body of research demonstrates the critical involvement of gut microbiota in the initiation and progression of central nervous system disorders. Notably, gut dysbiosis has been shown to impair immune responses, metabolic pathways, and behavioral phenotypes, positioning it as a key focus in contemporary central nervous system disease research. In this study, we aimed to elucidate the pathological and physiological processes by which microbiota-gut-brain communication mediates neural repair, particularly in the context of secondary injury after spinal cord injury. We established a traumatic spinal cord injury model at thoracic level 10 in mice. Neurological restoration in spinal cord injury mice was evaluated using behavioral testing and histopathological analysis in a time-dependent manner. The gut microbiota and short-chain fatty acids were analyzed via 16S rDNA sequencing and gas chromatography-mass spectrometry, respectively. Gene expression profiling of the colon was conducted through transcriptome sequencing. The expression levels of short-chain fatty acid-related receptors and transporters were detected via quantitative polymerase chain reaction. Serum cytokine profiles were analyzed via a cytometric bead array. 16S rDNA sequencing showed dynamic alterations in the gut microbiota at different stages after spinal cord injury, and indicated a lack of gut microbial recovery following injury. Moreover, targeted metabolomic analysis demonstrated that the levels of major short-chain fatty acids (acetic acid, propionic acid, and butyric acid) fluctuated across different phases after spinal cord injury, exhibiting a trend consistent with observed behavioral changes. Transcriptome sequencing showed that the gut exhibited different types of immune responses at different phases following injury and that the humoral immune response, innate immune response, and adaptive immune response dominated during the acute, subacute, and chronic phases, respectively. These responses were accompanied by alterations in short-chain fatty acid receptor and transporter profiles in the colon and cytokine profiles in the serum. Integrated spearman correlation analysis showed that changes in the gut microbiota and metabolite-short-chain fatty acid interactions were significantly correlated with behavioral outcomes, which suggests that gut dysbiosis might have crucial effects on neural repair through short-chain-fatty-acid-mediated secondary injury. The findings of this study provide a comprehensive map of microbiota-gut-spinal cord axis alterations after spinal cord injury, and suggest novel therapeutic strategies for mediating secondary injury, including alterations in the gut microbiota and metabolites.