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

Abstract

Abstract Background Previous studies have identified alterations in the faecal microbiota of horses with colic; however, further work is needed to interpret these findings. Objectives To compare the faecal microbiota of horses presenting for colic at hospital admission, day 1 and day 3/discharge and with different colic duration and lesion locations. Study design Prospective observational clinical study. Methods Faecal 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. Faecal samples were extracted for genomic DNA, PCR‐amplified, sequenced and analysed 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, visualised using principal coordinate analysis (PCoA) and statistically analysed using permutational multivariate analysis of variance (PERMANOVA). The relative abundance of bacterial populations at the different time points and in different types of colic was compared using ANCOM. Results There was a decrease in species richness from admission to day 3/hospital discharge ( P < .05), and a lower species richness ( P = .005) and Shannon diversity ( P = .02) in horses with colic ≥60 h compared to <60 h. Based on PCoA and PERMANOVA, there was a significant difference in bacterial community composition for horses with different colic duration ( P = .001) and lesion location ( P = .006). Several differences in bacterial phyla and genera were observed at different time points and with different types of colic. Main limitations Relatively low numbers and a diverse population of horses. Conclusions The microbiota change from hospital admission to day 3/discharge in horses with colic and horses with colic ≥60 h and large colon lesions have a distinct bacterial population compared to horses with colic <60 h and small intestinal lesions.