| Summary: | Environmental adaptation of ruminants was highly related to microbiota in the rumen. To investigate the diversity and composition of bacteria, fungi, and protozoa in the rumen of high-altitude animals, amplicon gene sequencing was performed using rumen fluid samples derived from both Tibetan goats and sheep at the same pasture in a highland (altitude > 4800 m). Between these two species, the ruminal bacteria and fungi were significantly different at multiple taxonomic levels. The alpha diversity of bacteria was significantly high in goats (<i>p</i> < 0.05). One hundred and sixty-four and 29 Operational Taxonomy Units (OTUs) with significant differences were detected in bacteria and fungi, respectively. The abundance of bacteria, fungi, and protozoa in the rumen was characterized at multiple taxonomic levels, and we determined that Firmicutes, Bacteroidetes, Neocallimastigomycota, and Ciliophora were the most abundant bacteria, fungi, and protozoa. The family Neocallimastigaceae and the genus Metadinium had cellulose degradation capacity in the rumen with high abundance, thereby, suggesting that fungi and protozoa played an essential role in rumen fermentation. In addition, by comparing microbiota in the rumen of goats and sheep it was found, that the fiber-degrading fungi genus (Cyllamyces) was increased in the rumen of sheep (<i>p</i> < 0.05) whereas VFA-producing bacteria (Saccharofermentans and Lachnospiraceae_XPB1014) were increased in the rumen of goats (<i>p</i> < 0.05). Interestingly, in the rumen, no differences in protozoa were observed between goats and sheep (<i>p</i> > 0.05). Furthermore, when compared to sheep, level of acetic acid, propionic acid, and total volatile fatty acid (TVFA) were significantly increased in the rumen of goats (<i>p</i> < 0.05). Taken together, these results suggested microbiota in the rumen drive goats to better adapt to high-altitude grazing conditions.
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