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Background  Rumen microbiota in ruminants are vital for sustaining good rumen ecology, health, and productivity. Currently, limited information is available regarding the response of yaks ( Bos grunniens ) to fluctuating environments, especially the rumen microbiome. To address this, we investigated the diet, rumen bacterial community, and volatile fatty acids (VFA) of rumen fluid of yaks raised in the great Qinghai-Tibet plateau (QTP) at 2800 (low altitude, L), 3700 (middle altitude, M), and 4700 m (high altitude, H) above sea level.    Results  The results showed that despite a partial diet overlap, H yaks harbored higher fibrous fractious contents than the M and L grazing yaks. Bacteria including  Christensenellaceae_R-7_group ,  Ruminococcus_1 ,  Romboutsia ,  Alloprevotella ,  Eubacterium coprostanoligenes ,  Clostridium ,  Streptococcus , and  Treponema  were found to be enriched in the rumen of yaks grazing at H. They also showed higher rumen microbial diversity and total VFA concentrations than those shown by yaks at M and L. Principal coordinates analysis (PCoA) on weighted UniFrac distances revealed that the bacterial community structure of rumen differed between the three altitudes. Moreover, Tax4fun metagenome estimation revealed that microbial genes associated with energy requirement and carbohydrate metabolic fate were overexpressed in the rumen microbiota of H yaks.    Conclusions  Collectively, our results revealed that H yaks had a stronger herbage fermenting ability via rumen microbial fermentation. Their enhanced ability of utilizing herbage may be partly owing to a microbiota adaptation for more energy requirements in the harsh H environment, such as lower temperature and the risk of hypoxia.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12866-020-02054-5.

Altitude influences microbial diversity and herbage fermentation in the rumen of yaks