Abstract: Background – Horses with colitis have changes in their fecal microbiome composition based upon 16S rRNA gene sequencing. As multiple bacteria can occupy the same ecological niche, changes in taxonomic composition do not always correspond to changes in microbiome function. Shotgun sequencing is a more accurate way to predict functional microbiome changes by directly measuring functional genes. These changes caused by colitis-associated dysbiosis in horses have not been described. Hypothesis/Objectives – We hypothesize that horses with colitis will have altered KEGG ortholog pathways compared to healthy horses and propose to quantify those changes using shotgun sequencing. Animals – Healthy horses (n=40) and horses with colitis caused by antimicrobial use (n=14), Salmonella (n=14) and Clostridia (n=5). Methods – DNA was extracted from feces (PowerSoil Kit, MoBio Labs, Carlsbad, CA) and submitted for shallow shotgun sequencing (Boostershot®, Diversigen, Minneapolis, MN). A Kruskal-Wallis test followed by Tukey’s HSD (Metaboanalyst 5.0) was used to identify metabolic pathways that were significantly different between groups. Significance was set at P< 0.05 for adjusted p-values. Results – Significant differences were observed in 224/379 KEGG pathways at L2, and 404/682 KEGG pathways at L3 between groups. These pathways included bacterial transporters, secretion systems, replication factors, and toxins, among others. Conclusions and clinical importance – Colitis-associated dysbiosis is correlated with a significant number of changes in KEGG pathways, indicating that there is major disruption to the functions of the microbiome. These functional changes may represent novel targets for prognostic or therapeutic purposes.
