Changes in the faecal bacterial microbiota during hospitalization of horses with colic and the effect of different causes of colic

<i>Background</i>: Previous studies have identified alterations in the fecal microbiota of horses with colic; however, further work is needed to interpret these findings. <i>Objectives</i>: To compare the fecal microbiota of horses presenting for colic at hospital admission v. day 1 v. day 3/discharge and with different colic duration and lesion locations. <i>Study design</i>: Prospective observational clinical study <i>Methods</i>: Fecal samples were collected from 17 colic cases at hospital admission, on day 1 and on day 3 post admission or at the time of hospital discharge if prior to 72 hours. Fecal samples were extracted for genomic DNA, PCR-amplified, sequenced, and analyzed using QIIME. Species richness and Shannon diversity (alpha diversity) were estimated. The extent of the relationship between bacterial communities (beta diversity) was quantified using pairwise UniFrac distances, visualized using principal coordinate analysis (PCoA), and statistically analyzed using PERMANOVA. The relative abundance of bacterial populations at the different time points and in different types of colic were compared using ANCOM. <i>Results</i>: There was a decrease in species richness from admission to day 3/hospital discharge (P = 0.049) and a decrease in species richness (P = 0.005) and Shannon diversity (P = 0.016) in horses with chronic compared to acute colic. Based on PCoA and PERMANOVA, there was a significant difference in bacterial community composition for horses with different colic duration (P = 0.001) and lesion location (P = 0.006). Several differences in bacterial phyla and genera were observed at different time points and with different types of colic. <i>Study Limitations</i>: Relative low numbers and a diverse population of horses. <i>Conclusions</i>: The microbiota changes from hospital admission to day 3/discharge in horses with colic and horses with chronic colic and large colon lesions have a distinct bacterial population compared to horses with acute colic and small intestinal lesions.