Abrupt dietary changes between grass and hay alter faecal microbiota of ponies

Horses may develop metabolic disturbances in response to dietary changes. The aim of this study was to compare the faecal microbiota of ponies abruptly changed from grazing ad libitum to being fed a restricted hay-only diet and vice versa. The experiment consisted of 2, 14-day periods. On day 0 six ponies were abruptly transitioned from grass to a hay-only diet. At the end of period 1, ponies then were abruptly transferred back to grass for a further 14-days. Faecal samples were collected on days 1-3, 7, 14 of each period. Faecal microbial DNA was extracted and 16S libraries encompassing the V3 and V4 regions were generated prior Illumina NGS of 16S rRNA gene. α-diversity of the microbial communities was evaluated in QIIME, β-diversity was evaluated using UniFrac. Biomarker analysis was performed using LEfSe on Galaxy. There were no differences in α-diversity. LEfSe revealed 46 biomarkers, associated with day of the diet (LDA score >2, P 0.05). LEfSe identified differences in phylum Actinobacteria and phylum Spirochaetes on day 14 of each experimental period between grass and hay diets. Class Bacilli, order Lactobacillales, family Lactobacillaceae, and genus Lactobacillus were presented in increased relative abundance on day 2 after an abrupt dietary change from hay to grass compared to all other days (P 0.05). A clustering of equine faecal samples by dietary group on days 1 and 3 following the abrupt change was observed on PCoA plots, while no clustering was observed on day 7 or 14 after an abrupt dietary change. There were 282/2221 (12.69 %) OTUs, which differed among individual ponies (P 0.05). On day 0, day 14 on hay and day 14 on grass Bacteroidetes was the most abundant phyla with Firmicutes being the second. However, on day 1 after an abrupt dietary change from grass to hay and on day 1 after an abrupt dietary change from hay to grass, Firmicutes was identified as the most abundant phylum followed by Bacteroidetes. The microbiota of grass-fed ponies responded differently to the abrupt change to hay compared to the response of hay-fed ponies abruptly transferred to grass in days 1-3. Abrupt changes from grass to hay and vice versa affect the faecal microbial community structure; moreover, the order of dietary change appears to have a profound affect in the first few days following the transition. An abrupt dietary change from hay to grass may represent a higher risk for hindgut pH to drop compared to abrupt change from grass to hay.