The horse’s forage-based diet is rich in fiber, a molecule indigestible by host enzymes. Hindgut bacteria, especially those with fibrolytic metabolism, enable herbivores to thrive on a high-fiber forage-based diet by slowly fermenting these fibers in the hindgut. The horse’s hindgut serves as an ideal anaerobic environment for fiber fermentation. The cecum and colon make up the majority (∼70%) of the equine gastrointestinal tract, and 75% of the mean transit time (23–48 h) is spent in the hindgut (Argenzio, 1975;

Van Weyenberg et al., 2006). Ruminant herbivores obtain up to 80% of total daily calories from microbial fermentation with a mean forage retention time of 57 h (Bergman et al., 1965; Uden et al., 1982). The horse obtains more than 50% of its daily energy requirements from volatile fatty EX527 acids that are the microbial products of fiber PLX4032 nmr fermentation (Argenzio et al., 1974; Glinsky et al., 1976; Vermorel & MartinRosset,

1997). In contrast, humans obtain only 10% of total daily calories through fermentation despite having similar mean retention times (Kelsay et al., 1978; Wrick et al., 1983). Species differences could be due to the fact that larger percentages of the gastrointestinal tract of horses and cattle (69% and 76%, respectively) accommodate microbial fermenters in comparison with humans (17%) (Parra, 1978). Furthermore, the differences in the location of microbial fermentation in the horse (hindgut) vs. the ruminant (pregastric/foregut) may also influence members and old functions of these communities. Differences in diet between horses and other species

likely also influence the members and function of the microbial communities. Compared to the rumen microbiota, the equine hindgut microbiota has received little attention; furthermore, few studies have characterized the equine hindgut bacterial community using culture-independent methods (Daly et al., 2001; Daly & Shirazi-Beechey, 2003; Hastie et al., 2008; Yamano et al., 2008). No studies to date have evaluated the fecal bacterial community in adult horses on a controlled forage diet by the use of pyrosequencing of 16S rRNA gene amplicons. The objective of this study was to characterize the fecal bacterial community of horses fed grass hay using pyrosequencing of 16S rRNA gene amplicons. We propose that the use of high-throughput sequencing will provide an evaluation of the equine fecal microbiome, which may be used to increase the understanding of the relationship between the microorganisms and the host. Fecal samples for this study were taken from two adult Arabian geldings during a companion study (Shepherd et al., 2011). The protocol was approved by the Virginia Tech Institutional Animal Care and Use Committee (#08-217-CVM).