, 2009) Feces provide a noninvasive and more humane means to stu

, 2009). Feces provide a noninvasive and more humane means to study the gut bacterial community. De Fombelle et al. (2003) reported that the number of anaerobic bacterial CFUs differed between the equine hindgut and feces; however, the numbers of cellulolytic bacterial CFUs were similar between the hindgut and feces. Furthermore, Milinovich et al. (2007) used nucleic acid hybridization BMS-354825 to provide evidence that the relative abundance of targeted groups (i.e. Streptococcus spp.) was similar in cecum and fecal samples of healthy horses. However,

owing to the differences described in bacterial community along the equine gut (de Fombelle et al., 2003), future studies should evaluate gut contents to shed light on the etiology and pathogenesis of chronic diseases that plague horses. Pyrosequencing provides a rapid and robust

description of the equine fecal bacterial community; however, the present study has limitations. These limitations include use of a single region (V4) of the 16S rRNA gene for amplicon generation, generation of short sequence read lengths, inability to achieve a rarefaction asymptote at 3% dissimilarity, and presence of a large number of unclassified sequences. The V4 region of the 16S rRNA gene was targeted for the evaluation of equine fecal bacterial communities based on the ability to detect bacterial sequences (Claesson et al., 2009). Kumar et al. (2011) reported that the region of 16S rRNA gene amplification does not appear to impact the numbers of rare or abundant taxa detected; however, the relative

abundance of several genera was ABT-199 solubility dmso influenced by targeted 16S rRNA gene region amplified. The abundance of Eubacterium, Prevotella, Streptococcus, and Treponema, as found in human gingiva, varied depending on the 16S rRNA gene amplified (Kumar et al., 2011). Therefore, the abundance of some groups presented here may be biased owing to second primer selectivity. In this study, we did detect groups, TM7, using the V4 region primers that were not detected with the use of V4–V6 primers by Kumar et al. (2011). Future studies should use two primer sets spanning different regions of the 16S rRNA genes. The sequence read length was limited by the primers utilized; however, the chosen primers have been used previously in bacterial community pyrosequencing studies (Wang et al., 2007; Lopez-Velasco et al., 2011). Furthermore, increasing the specificity by targeting the 16S rRNA gene V4 region helps to overcome the limitations of read length (Nossa et al., 2010). Another source of bias in the present study is DNA extraction technique used; however, Cuiv et al. (2011) reported that beading-based extraction is superior to Gram-positive (i.e. Firmicutes members) lysis. These limitations along with the presence of a large proportion of previously uncultivated microorganisms in the horse feces inhibit complete exposure of the true richness and diversity of the equine fecal bacterial community.

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