72 Horses’ fecal microbiome responses to abrupt diet changes

Abrupt diet changes affect horses' gastrointestinal health. This study evaluated the effects of abrupt interchange of exclusive diets of Coastcross hay and complete extruded diet on the fecal microbiome of horses. The project was approved by Animal Care Commite: n° 3083.029756/2017–10. Eight geldings horses were randomly split into 2 groups: A - fed a Coastcross hay diet (CHD); and B - fed a complete extruded diet (CED). After 34 d of diet adaptation, the diets were abruptly interchanged between the groups. Fecal samples were collected directly from the rectum at 0, 24, and 96 h after the diet change. A completely randomized design with repeated measurements was used. The pH and microbiome analyses of the feces were performed. The V4 region of the 16S rRNA gene was sequenced on the MiSeq platform. The sequences were processed using the Mothur software. The results were evaluated using ANOVA and the means were compared by Tukey test (α = 0.05). Beta diversity was obtained using the Bray-Curtis similarity index and community structure was tested by PERMANOVA (α = 0.05). Statistical analysis was performed using statistical package Past3. Horses fed the CHD had higher fecal pH and Shannon index diversity than those fed CED. The bacterial community structure of both groups was distinct. The change from CHD to CED resulted in a reduction in the Shannon index 24 h after the change, followed by a relative abundance decreases of the phyla Firmicutes and Actinobacteria and an increase in the phyla Bacteroidetes and Elusimicrobia. After 96 h of diet change, fecal pH and abundance of the phyla Elusimicrobia and Proteobacteria decreased while the phylum Verrucomicrobia increased. Futhermore, the community structure was different after 96 h. On the other hand, the change from CED to CHD resulted in a fecal pH reduction and in the abundance of Synergistetes 24 h after the change. After 96 h of diet change, an increase in the Shannon index and an abundance of the phylum Lentisphaerae were observed. There was no difference in the group B community structure after changing the diet. In addition, there was an increase of OTUs classified as Bacteroidetes and Treponema in the feces of both groups at 24 h after the diet change, followed by a reduction at 96 h. After changing the diet from CHD to CED bacterial diversity reduction occurs, which is detectable in feces within 24 h. When the diet is changed from CED to CHD, more than 96 h is required for the species diversity recovery of the intestinal microbiome. Therefore, diet composition influenced the response of the equine fecal microbiome to abrupt dietary changes.