Rumen Microbial Community of Saanen Goats Adapted to a High-Fiber Diet in the Northeast of Iran

Swiss Saanen goat is a widespread breed frequently found in commercial herds across the world. The present study aimed to identify the rumen microbial community of exotic Saanen goats adapted to a fibrous diet using barcoded pyrosequencing. Rumen content samples were collected from the four animals via a stomach tube after the morning graze and freeze-dried for DNA extraction. Bacterial and archaeal 16S rRNA and protozoal 18S rRNA genes were sequenced by 454 titanium pyrosequencing and analyzed using the quantitative insights into microbial ecology (QIIME) software package. Obtained results indicated that at the genus level, Prevotella (Bacteroidetes phylum) dominated the assigned sequence, with the relative abundance accounting for 29.41 ± 4.27% of the total bacteria. The second most abundant bacteria in the rumen of Saanen goats was an unclassified Bacteroidales (Bacteroidetes phylum) (11.01±0.94%). In addition, Firmicutes phylum was recorded as the second most frequent phylum and three unclassified genera, which belonged to the order Clostridiales, constituted21.42% of the total bacteria. Entodinium was the most abundant protozoal genus, comprising 46.78 ± 9.13% of the protozoal community, followed by Epidinium and Ophryoscolex (12.37±0.06 and 11.92±7.7, respectively). Almost half the archaeal community (43.71±1.57%) was composed of Methanoplasmatales- related sequences and Methanobrevibacter gottschalkii clade (35.79±4.84%) and Methanobrevibacter ruminantium clade (13.36±6.34%) were the second and third most dominant archaea, respectively. Overall, further efforts should be made to apply culture-based methods for the identification of remarkable number of unclassified bacteria in the rumen of goats.