Background The association of microbiota with clinical outcomes and the taxa associated with colitis in horses remains generally unknown. Objectives Describe the fecal microbiota of horses with colitis and investigate the association of the fecal microbiota with the development of laminitis and survival. Animals Thirty‐six healthy and 55 colitis horses subdivided into laminitis (n = 15) and non‐laminitis (n = 39, 1 horse with chronic laminitis was removed from this comparison) and survivors (n = 27) and nonsurvivors (n = 28). Methods Unmatched case‐control study. The Illumina MiSeq platform targeting the V4 region of the 16S ribosomal RNA gene was used to assess the microbiota. Results The community membership (Jaccard index) and structure (Yue and Clayton index) were different (analysis of molecular variance [AMOVA]; P < .001) between healthy and colitis horses. The linear discriminant analysis effect size (LEfSe; linear discriminant analysis [LDA] >3; P < .05) and random forest analyses found Enterobacteriaceae, Lactobacillus, Streptococcus, and Enterococcus enriched in colitis horses, whereas Treponema, Faecalibacterium, Ruminococcaceae, and Lachnospiraceae were enriched in healthy horses. The community membership and structure of colitis horses with or without laminitis was (AMOVA; P > .05). Enterobacteriaceae, Streptococcus, and Lactobacillus were enriched in horses with laminitis (LDA > 3; P < .05). The community membership (AMOVA; P = .008) of surviving and nonsurviving horses was different. Nonsurviving horses had an enrichment of Enterobacteriaceae, Pseudomonas, Streptococcus, and Enterococcus (LDA >3; P < .05). Conclusion and Clinical Importance Differences in the microbiota of horses with colitis that survive or do not survive are minor and, similarly, the microbiota differences in horses with colitis that do or do not develop laminitis are minor.

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