Abstract Background Trigeminal‐mediated headshaking (TMHS) in horses is a form of neuropathic pain of undetermined cause that often results in euthanasia. The role of microbiota in TMHS has not been investigated in diseased horses. Objective To investigate if gastrointestinal microbiota in the cecum is different in horses with TMHS compared to a control population, during a summer season with clinical manifestations of disease. Animals Ten castrated horses: five with TMHS and five neurologically normal controls. Methods All horses were sourced from our institution and kept under the same husbandry and dietary conditions. All horses were fed orchard grass hay for 30 days and then were euthanized due to chronic untreatable conditions including TMHS and orthopedic disease (control group). Caecal samples for microbiota analysis were collected within 20 min after euthanasia. Sequencing was performed using an Illumina MiSeq platform and the microbiome was analyzed. Results The caecal microbiota of horses with TMHS was similar to control horses in terms of diversity but differed significantly with Methanocorpusculum spp. having higher abundance in horses with TMHS. Conclusions and clinical importance Methanocorpusculum spp. was more abundant in the cecum of horses with TMHS. However, its role in disease is unknown. Furthermore, it could also represent an incidental finding due to our small population size.
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