5 Fecal microbial profile of mares and foals from parturition to weaning

Abstract

Colonization of a foal's intestinal microbiome is thought to begin at birth through exposure to maternal and environmental microbes. Therefore, it is hypothesized that microbiome of the foal may be influenced by pre and/or probiotics during the postpartum period. Further, the time for intervention may be short as the foal's microbiome shifts to resemble the dam. Eight gestating Quarter Horse broodmares were maintained on an average of 3.63 kg/d of Purina® Ultium® Growth and 5.44 kg/d Standlee Timothy hay, split over morning (0700) and afternoon (1500) feedings. Foals were offered the same concentrate at 0.23 kg/d starting at 28 d of age; the feeding rate was increased by 0.14 kg every other day until reaching 0.45 kg/month of age. Horses were turned out in dry lot pens with access to hay (1.36 kg/head/day) following morning feeding and then returned to individual stalls before afternoon feeding; mare and foal pairs were housed together but fed separately. Rectal swabs were obtained from all horses on the following days before morning turnout: foaling (d 0), 2, 4, 6, 8, 22, 36, 50, 64, 78, 92, 106, and weaning (d 112) post foaling. Samples were immediately flash frozen and stored at −80°C. 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). Bioinformatics were performed using QIIME2 (ver. 2020.11). Statistical analysis was conducted using Kruskal-Wallis test and PERMANOVA for α (Shannon's Index) and β (UniFrac) diversity, respectively. Relative abundances were compared using ANOVA for repeated measures in R (ver. 3.6.0). A P-value of P ≤ 0.05 was considered significant. Alpha diversity was lower in foals from d 0 to d 4 (P = 0.01) and became more similar to the mares by d 36 through 112 (P > 0.05). Unweighted UniFrac (community composition) was different between mares and foals across all time points (P = 0.001); weighted UniFrac (abundance) was different (P = 0.001) between mares and foals across all time points except d 6, 78, and 106. Mares had higher proportions of Kiritimatiellaeota phylum on d 0 (7.33% vs. 2.91%, P = 0.018) and d 8 (8.88% vs. 0.27%, P = 0.006). Additionally, bacteria belonging to the genus WCHB1–41 were found to be higher in the mares (7.76% vs. 1.11%, P = 0.042) on d 8. Results indicate that the microbiome of the foal is less diverse during the early postpartum period before becoming similar to the mare over time. This short period of plasticity may represent an opportune window of time for intervention. However, the type and dosage of pre and/or probiotics needs to be evaluated.