10 Characterization of the fecal microbiome of mares from parturition to weaning

Abstract

Recent studies have shown the impact of stressors such as intense exercise, trailering, and restrictive feeding on the fecal microbiome of horses. Therefore, it is hypothesized that the stress of foaling and weaning will alter the fecal microbial profile of the mare. To evaluate these effects, 8 gestating Quarter Horse broodmares were used in a repeated measures design. All horses were maintained on an average of 3.63 kg/d of Purina® Ultium® Growth and 5.44 kg/d Standlee Timothy hay split into 2 daily feedings. All feed refusals were noted, and dietary changes were made to maintain a BCS of 5–6. Horses were turned out into dry lot pens with access to hay (1.36 kg/head/day) following morning feeding (0700) to afternoon feeding (1500) and were then returned to individual stalls. Rectal swabs were obtained on the following days before morning turnout: −7 d from the expected foaling date (340 d from the last day of ovulation), foaling (d 0), 2, 4, 6, 8, 22, 36, 50, 64, 78, 92, 106, and 112 (weaning) d post foaling. Samples were immediately frozen and stored at −80°C until analysis. Bacterial DNA was extracted using Quick -DNA Fecal/Soil Microbe Miniprep kit (Zymo Research, Irvine, CA) and processed using the Illumina 16S Metagenomics Protocol (San Diego, CA). Data were analyzed using QIIME2 (ver. 2020.11). Statistical analysis of α (Shannon's Index) and β (weighted and unweighted UniFrac) diversity metrics were analyzed using Kruskal Wallis test and PERMANOVA, respectively. Relative abundances were compared using one-way ANOVA for repeated measures in R (ver. 3.6.0); normality was assessed using the Shapiro-Wilk test and visual analysis of Q-Q plots. A P-value of ≤0.05 was considered significant. Shannon's Index was different over time ( P < 0.01 ) with a tendency to increase from 7.14 on d −7 to 8.38 on d 0 ( P = 0.07 ), decrease to 7.08 on d 2 ( P = 0.05), and then remain stable through d 112. Weighted UniFrac (abundance) was different over time ( P < 0.05 ) with d 0 driving this effect. However, unweighted UniFrac (community composition) was not significantly different. Relative abundances of phyla and genera at ≥1% were not significantly different over time. Results suggest that foaling, but not weaning, in fact had an effect on fecal microbial diversity, although it appears that this effect is transient. The effect of stressors on the microbiome of the mare, and the relationship of microbial shifts to health, need to be further evaluated to provide insight to better management practices to mitigate gastrointestinal distress that is possible around foaling and weaning.