Animals and humans have bacterial populations all over their body. However, the gastrointestinal microbiome is one of the most complex and dense populations studied (Todar, 2012). The mammalian gastrointestinal tract is comprised of about four million bacterial genes with more than 95% located in the large intestine (Galland, 2014). The gastrointestinal microbiota varies along the tract at longitudinal levels and horizontal levels due to particular bacteria attaching to the epithelium in the lumen (Todar, 2012). With DNA sequencing and metagenomic studies becoming increasingly popular, the concept of identifying bacterial colonies throughout the gastrointestinal tract is rising in interest (Marteau et al., 2001). Both the cecal and the fecal
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This is due to the difficulty in sampling, the ethical concerns of cannulating horses, and in vitro studies being conducted with fecal samples (Dougal et al., 2012; Schoster et al., 2013). However, while a majority of the obtained knowledge about the gastrointestinal microbiome comes from studies using fecal samples, researchers are beginning to observe that fecal samples do not accurately reflect the microbiota in the gastrointestinal tract, specifically the cecum (Dougal et al., 2012; Schoster et al., 2013; Stanley et al., 2015). A recent study using euthanized horses, collected samples from the cecum, right dorsal colon, and rectum; in this study it was observed that the bacteria concentrations of the feces minimally reflected the population in the dorsal colon and did not represent the bacteria found in the cecum (Dougal et al., 2012). However, this study had its limitations, in the fact that the horses came from different areas, were on different diets, and the researchers analyzed the bacteria using real time-qPCR, which only provided absolute concentrations of targeted species (Dougal et al., 2012). Therefore, further research needs to be conducted to provide a reliable and accurate guide of the microbiome in monogastric hindgut fermenters, specifically using metagenmoics to identify unknown species (Dougal et al., 2012; Schoster et al.,
This is due to the difficulty in sampling, the ethical concerns of cannulating horses, and in vitro studies being conducted with fecal samples (Dougal et al., 2012; Schoster et al., 2013). However, while a majority of the obtained knowledge about the gastrointestinal microbiome comes from studies using fecal samples, researchers are beginning to observe that fecal samples do not accurately reflect the microbiota in the gastrointestinal tract, specifically the cecum (Dougal et al., 2012; Schoster et al., 2013; Stanley et al., 2015). A recent study using euthanized horses, collected samples from the cecum, right dorsal colon, and rectum; in this study it was observed that the bacteria concentrations of the feces minimally reflected the population in the dorsal colon and did not represent the bacteria found in the cecum (Dougal et al., 2012). However, this study had its limitations, in the fact that the horses came from different areas, were on different diets, and the researchers analyzed the bacteria using real time-qPCR, which only provided absolute concentrations of targeted species (Dougal et al., 2012). Therefore, further research needs to be conducted to provide a reliable and accurate guide of the microbiome in monogastric hindgut fermenters, specifically using metagenmoics to identify unknown species (Dougal et al., 2012; Schoster et al.,