Microbial diversity in the rumen, reticulum, omasum, and abomasum of yak on a rapid fattening regime in an agro-pastoral transition zone

Abstract

The ruminant digestive system harbors a complex gut microbiome, which is poorly understood in the case of the four stomach compartments of yak. High-throughput sequencing and quantitative PCR were used to analyse microbial communities in the rumen, reticulum, omasum, and abomasum of six domesticated yak. The diversity of prokaryotes was higher in reticulum and omasum than in rumen and abomasum. Bacteroidetes predominated in the four stomach compartments, with abundance gradually decreasing in the trend rumen > reticulum > omasum > abomasum. Microorganism composition was different among the four compartments, all of which contained high levels of bacteria, methanogens, protozoa and anaerobic fungi. Some prokaryotic genera were associated with volatile fatty acids and pH. This study provides the first insights into the microorganism composition of four stomach compartments in yak, and may provide a foundation for future studies in this area.

Bacterial communities in the solid, liquid, dorsal, and ventral epithelium fractions of yak (Bos grunniens) rumen

“…We also found that Rikenellaceae RC9 and Prevotella were abundant genera in all four fractions, in accordance with previous findings regarding ruminants generally (Henderson et al, ) and yaks (Hu et al, ; Xue et al, ; Zhang et al, ). Rikenellaceae RC9 can reportedly degrade structural carbohydrates and starch in the rumen of cows (Asma et al, ), while Prevotella spp.…”

“…We also found that members of the phyla Bacteroidetes and Firmicutes were the dominant bacteria in the solid, liquid, and ventral epithelium fractions of yak rumen, in accordance with previous findings in ruminants generally (Henderson et al, ) and yaks specifically (Hu et al, ; Xue et al, ; Zhang et al, ; Zhou, Zhong, et al, ; Zhou, Fang, et al, ). These results indicate that the two phyla have adapted to wide ranges of gastrointestinal tract environments and play important roles in rumen ecology.…”

“…These results indicate that the two phyla have adapted to wide ranges of gastrointestinal tract environments and play important roles in rumen ecology. However, Epsilonbacteraeota was the most abundant bacterial phylum in the yak dorsal epithelium fraction, which has not been recorded in previous studies (An, Dong, & Dong, ; Guo et al, ; Hu et al, ; Xue et al, ; Zhang et al, ; Zhou, Zhong, et al, ; Zhou, Fang, et al, ). The comparative genomic analysis revealed that the host‐associated Epsilonbacteraeota lacked genes involved in carbon fixation, but possessed genes involved in osmoprotection, and transport of heme, lipopolysaccharide, and capsular polysaccharides (Waite et al, ), in accordance with presumed requirements for their epithelium‐associated lifestyle.…”

“…These previous findings clearly suggest that fractions of rumen microbiota may generally have distinct compositional and functional signatures. However, although the microbiota in the yak rumen and other stomach components have been examined (Guo et al, ; Huang et al, ; Xue et al, , ; Zhou, Zhong, et al, ; Zhou, Fang, et al, ), we have a little knowledge of the composition of microbiota of the three fractions in the yak rumen and differences between them.…”

Peer Review #2 of "Yak rumen microbial diversity at different forage growth stages of an alpine meadow on the Qinghai-Tibet Plateau (v0.1)"

“…To enhance the fiber digestibility and feed utilization, it is necessary to obtain a deep understanding of the microorganisms in the rumen. Firmicutes and uncultured species were reported to have higher abundance in the yak of the QTP compared to yak at low elevation, and several bacteria (Ruminococcus albus and Prevotella ruminicola) were either not detected or had lower abundance among fibrolytic bacteria (Ruminococcus, Fibrobacter, Clostridium, and Butyrivibrio) in the yaks of the QTP (Yang et al 2010;Dan et al 2016;Huang et al 2017;Xue et al 2017;Xue et al 2018). Previous studies have shown that factors such as diet, age, species, and seasons all impact on ruminal microbes, and diet is a particularly important contributor (Tajima et al 2000).…”