Analysis of the rumen bacteria and methanogenic archaea of yak (Bos grunniens) steers grazing on the Qinghai-Tibetan Plateau

• Bacteroidetes and Firmicutes dominated the prokaryotic community of yak rumen.
• Methanobrevibacter is the predominant archaea of rumen microbiota in grazing yaks.
• Highly diverse microflora of uncultured or unclassified microorganisms.
• Prevotella was the predominant genus, account for 28.5% of all rumen genera.

Yak is an important domesticated ruminant on the Qinghai-Tibet Plateau in China. The prokaryotic community of yak remains largely uncharacterized when compared to that of other livestock species. In the present study, high-throughput sequencing of 16S rRNA genes (targeting bacterial and archaeal) and clone library of mcrA gene (targeting methanogenic archaea) were applied to investigate the rumen prokaryotic community structure. High-throughput sequencing results indicated that the rumen prokaryotic community consisted of 29 phyla, 40 classes, 63 orders, 77 families, and 79 genera. Bacteroidetes (59.1%) was the most abundant phylum, followed by Firmicutes, Proteobacteria, Fibrobacteres and Euryarchaeota. Prevotella was the predominant genus, averaging 28.5% of all rumen prokaryotic genera. Archaea accounted for 2.26% of the total prokaryotic community, with their community dominated by Methanobacteriaceae (82%), followed by Methanomassiliicoccaceae, and Methanosarcinaceae. Compared with the clone library of mcrA gene, high-throughput sequencing of 16S rRNA genes yielded a greater coverage of methanogenic archaea diversity. However, both molecular techniques showed that Methanobrevibacter is the predominant archaea of rumen microbiota in yaks grazing natural pastures. Our results should facilitate understanding of the complex rumen ecosystem and the main process of ruminal methanogenesis, which may help to further mitigate CH4 emissions from ruminants.