Characterization of Foal Fecal Microbiome from Birth to Weaning and the Relationship to Mare Milk and Mare Feces.

The objectives of this experiment were to characterize the development of the foal fecal microbiome from birth to 4 mo and determine its relationship to mare milk and fecal bacteria. Mare milk, mare fecal, and foal fecal samples were collected from 9 mare and foal pairs at birth, d 0, 2, and 7 postpartum, and then monthly until 4 mo. Mare fecal samples were collected by rectal palpation and foal fecal samples were collected manually using sterile gloves. All samples were placed in sterile conical tubes and immediately frozen until further analysis. Mare udders were cleaned and milk samples were obtained according to aseptic procedures used with dairy cows to collect samples for microbial analysis. Next generation sequencing of the V4 region of the bacterial 16S rRNA gene was performed using the Illumina Miseq according to Earth Microbiome Project protocols. Sequencing data was analyzed using QIIME. Bacteria found in mare milk and mare feces were different in diversity (P < 0.001) and composition (P < 0.05) across all time points. Newborn foal meconium contained low species diversity and a bacterial composition similar to mare milk consisting of the genera Enterococcus, Bacillus, Pseudomonas and Lactococcus. The Firmicutes and Proteobacteria phyla comprised the majority of bacteria in mare milk and foal feces on d 0 and 2. At the genus level, the bacterial communities shifted within the first week in foal feces to be dominated by Bacteroides and Escherichia. By 1 mo the foal fecal microbiome did not differ in composition at the phylum level from mare feces; however, species diversity was still lower in foals and the relative abundance of several genera were different (P < 0.05). Firmicutes, Bacteriodetes, and Verrucomicrobia were the dominant phyla found in both foal feces older than 1 mo and mare feces. To our knowledge, this is the first study to report the bacteria taxa of equine milk using next generation sequencing. These results demonstrate the foal is born with fecal microbial communities similar to milk that rapidly change within the first week of life. Within the first month of life there is a gradual transition of the foal fecal bacterial structure until it resembles that of its dam, remaining constant over the next 3 months. This change is likely due to the introduction of solid feedstuffs, consumption of their dam's feces, and/or environmental exposure.