Characterization of Anaerobic Rumen Fungal Community Composition in Yak, Tibetan Sheep and Small Tail Han Sheep Grazing on the Qinghai-Tibetan Plateau

Comparative study on slaughter performance, meat quality, and rumen microbiota of Hainan Dong goat and its hybrid with Nubian goat

Introduction

The Hainan Dong goat (DG) is a local meat breed widely raised in Hainan, China because of its good adaptability to local hot and humid weather. However, the growth rate of these DG is much slower than that of commercialised breeds improved in European countries, resulting in poor carcase characteristics, including smaller slaughter weight and carcase weight, which have become increasingly prominent. In recent decades, Nubian goats have been continuously imported into China to improve the production performance of local breeds.

Methods

In this study, the effects of breed on growth performance, carcase and meat quality, and ruminal microbiota were analysed in 40 goats, including 20 DGs and 20 hybrid F3 offspring generated by crossing the DG and Nubian hybrids (NH). All the goats were averagely aged 90 days and weighed at 11  ±  1.34  kg. They were assigned to two treatments, with three replicates per treatment. The two groups were fed the same diet for 90 days before slaughter.

Results

The results showed that the average daily gain, F/G ratio, slaughter weight, and carcase weight of the NH group were higher than those of the DG group (p < 0.05). However, tube circumference, meat-to-bone ratio, and eye muscle pH were lower in the NH group than in the DG group (p < 0.05). The NH group showed a smaller fibre crosssectional area and fibre diameter, but a larger fibre density than the DG group (p < 0.05). Bacteroidetes and Firmicutes were the most dominant phyla in the two groups; however, the two breeds had different ruminal microbial communities.

Discussion

In the present study, the differences in growth performance between two groups of goats under the same feeding environment and feed conditions were compared. The correlation between feed sources and rumen flora has been demonstrated, and the results of this study show that the same diet has similar effects on rumen microorganisms, which in turn have related effects on growth and production performance.

Conclusion

In summary, hybrids can improve the growth and slaughter performance of local breeds, which may be related to changes in the rumen microorganisms. This study revealed that crossbreeding of Nubian goats with Dong goats has the potential to be used in a wide range of applications owing to its effectiveness in increasing production efficiency.

Profiling the dynamic adaptations of CAZyme-Producing microorganisms in the gastrointestinal tract of South African goats

The gastrointestinal tract of goats serves as a habitat for anaerobic microbial populations that work together to break down complex plant material, including lignocellulose. This study explored the microbial diversity and metabolic profiles across different gastrointestinal tract compartments. Significant diversity differences among the compartments were observed (ANOSIM p < 0.006), with the abomasum showing a distinct species composition and a decreased alpha diversity (Mann-Whitney/Kruskal-Wallis test p = 0.00096), possibly due to its acidic environment. Dominant microbial phyla included Proteobacteria, Bacteroidetes, and Firmicutes, with Proteobacteria being the most prevalent in the abomasum (50.06 %). Genera like Proteus and Bacteroides were particularly prominent in the rumen and reticulum, highlighting their significant role in feed degradation and fermentation processes. Over 65 % of genes at Kyoto Encyclopedia of Genes and Genomes level 1 were involved in metabolism with significant xenobiotic biodegradation in the abomasum. The dbCAN2 search identified Glycoside Hydrolases as the most prevalent CAZyme class (79 %), followed by Glycosyltransferases, Polysaccharide Lyases, and Carbohydrate Esterases, with Carbohydrate-Binding Modules and Auxiliary Activities accounting for 1 % of the hits. Higher CAZyme abundance was observed in the reticulum and omasum compartments, possibly due to MAGs diversity. In conclusion, the gastrointestinal tract of South African goats harbors diverse CAZyme classes, with Glycoside Hydrolases predominating. Interestingly, higher CAZyme abundance in specific compartments suggested compartmentalized microbial activity, reflecting adaptation to dietary substrates.

Yeoman C, Grace S, Borgogna JLC, Foote AP, Nagy YI, Kashef MT, Yassin AS, Elshahed MS, Youssef NH. Diversity and community structure of anaerobic gut fungi in the rumen of wild and domesticated herbivores

The rumen houses a diverse community that plays a major role in the digestion process in ruminants. Anaerobic gut fungi (AGF) are key contributors to plant digestion in the rumen. Here, we present a global amplicon-based survey of the rumen AGF mycobiome by examining 206 samples from 15 animal species, 15 countries, and 6 continents. The rumen AGF mycobiome was highly diverse, with 81 out of 88 currently recognized AGF genera or candidate genera identified. However, only six genera (Neocallimastix, Orpinomyces, Caecomyces, Cyllamyces, NY9, and Piromyces) were present at >4% relative abundance. AGF diversity was higher in members of the families Antilocapridae and Cervidae compared to Bovidae. Community structure analysis identified a pattern of phylosymbiosis, where host family (10% of total variance) and species (13.5%) partially explained the rumen mycobiome composition. As well, diet composition (9%-19%), domestication (11.14%), and biogeography (14.1%) also partially explained AGF community structure; although sampling limitation, geographic range restrictions, and direct association between different factors hindered accurate elucidation of the relative contribution of each factor. Pairwise comparison of rumen and fecal samples obtained from the same subject (n = 13) demonstrated greater diversity and inter-sample variability in rumen versus fecal samples. The genera Neocallimastix and Orpinomyces were present in higher abundance in rumen samples, while Cyllamyces and Caecomyces were enriched in fecal samples. Comparative analysis of global rumen and feces data sets revealed a similar pattern. Our results provide a global view of AGF community in the rumen and identify patterns of AGF variability between rumen and feces in herbivores Gastrointestinal (GI) tract.IMPORTANCERuminants are highly successful and economically important mammalian suborder. Ruminants are herbivores that digest plant material with the aid of microorganisms residing in their GI tract. In ruminants, the rumen compartment represents the most important location where microbially mediated plant digestion occurs, and is known to house a bewildering array of microbial diversity. An important component of the rumen microbiome is the anaerobic gut fungi (AGF), members of the phylum Neocallimastigomycota. So far, studies examining AGF diversity have mostly employed fecal samples, and little is currently known regarding the identity of AGF residing in the rumen compartment, factors that impact the observed patterns of diversity and community structure of AGF in the rumen, and how AGF communities in the rumen compare to AGF communities in feces. Here, we examined the rumen AGF diversity using an amplicon-based survey targeting a wide range of wild and domesticated ruminants (n = 206, 15 different animal species) obtained from 15 different countries. Our results demonstrate that while highly diverse, no new AGF genera were identified in the rumen mycobiome samples examined. Our analysis also indicate that animal host phylogeny, diet, biogeography, and domestication status could play a role in shaping AGF community structure. Finally, we demonstrate that a greater level of diversity and higher inter-sample variability was observed in rumen compared to fecal samples, with two genera (Neocallimastix and Orpinomyces) present in higher abundance in rumen samples, and two others (Cyllamyces and Caecomyces) enriched in fecal samples. Our results provide a global view of the identity, diversity, and community structure of AGF in ruminants, elucidate factors impacting diversity and community structure of the rumen mycobiome, and identify patterns of AGF community variability between the rumen and feces in the herbivorous GI tract.

Linkages between rumen microbiome, host, and environment in yaks, and their implications for understanding animal production and management

Livestock on the Qinghai-Tibetan Plateau is of great importance for the livelihood of the local inhabitants and the ecosystem of the plateau. The natural, harsh environment has shaped the adaptations of local livestock while providing them with requisite eco-services. Over time, unique genes and metabolic mechanisms (nitrogen and energy) have evolved which enabled the yaks to adapt morphologically and physiologically to the Qinghai-Tibetan Plateau. The rumen microbiota has also co-evolved with the host and contributed to the host's adaptation to the environment. Understanding the complex linkages between the rumen microbiota, the host, and the environment is essential to optimizing the rumen function to meet the growing demands for animal products while minimizing the environmental impact of ruminant production. However, little is known about the mechanisms of host-rumen microbiome-environment linkages and how they ultimately benefit the animal in adapting to the environment. In this review, we pieced together the yak's adaptation to the Qinghai-Tibetan Plateau ecosystem by summarizing the natural selection and nutritional features of yaks and integrating the key aspects of its rumen microbiome with the host metabolic efficiency and homeostasis. We found that this homeostasis results in higher feed digestibility, higher rumen microbial protein production, higher short-chain fatty acid (SCFA) concentrations, and lower methane emissions in yaks when compared with other low-altitude ruminants. The rumen microbiome forms a multi-synergistic relationship among the rumen microbiota services, their communities, genes, and enzymes. The rumen microbial proteins and SCFAs act as precursors that directly impact the milk composition or adipose accumulation, improving the milk or meat quality, resulting in a higher protein and fat content in yak milk and a higher percentage of protein and abundant fatty acids in yak meat when compared to dairy cow or cattle. The hierarchical interactions between the climate, forage, rumen microorganisms, and host genes have reshaped the animal's survival and performance. In this review, an integrating and interactive understanding of the host-rumen microbiome environment was established. The understanding of these concepts is valuable for agriculture and our environment. It also contributes to a better understanding of microbial ecology and evolution in anaerobic ecosystems and the host-environment linkages to improve animal production.

Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes

Background

The ruminant gastrointestinal contains numerous microbiomes that serve a crucial role in sustaining the host's productivity and health. In recent times, numerous studies have revealed that variations in influencing factors, including the environment, diet, and host, contribute to the shaping of gastrointestinal microbial adaptation to specific states. Therefore, understanding how host and environmental factors affect gastrointestinal microbes will help to improve the sustainability of ruminant production systems.

Results

Based on a graphical analysis perspective, this study elucidates the microbial topology and robustness of the gastrointestinal of different ruminant species, showing that the microbial network is more resistant to random attacks. The risk of transmission of high-risk metagenome-assembled genome (MAG) was also demonstrated based on a large-scale survey of the distribution of antibiotic resistance genes (ARG) in the microbiota of most types of ecosystems. In addition, an interpretable machine learning framework was developed to study the complex, high-dimensional data of the gastrointestinal microbial genome. The evolution of gastrointestinal microbial adaptations to the environment in ruminants were analyzed and the adaptability changes of microorganisms to different altitudes were identified, including microbial transcriptional repair.

Conclusion

Our findings indicate that the environment has an impact on the functional features of microbiomes in ruminant. The findings provide a new insight for the future development of microbial resources for the sustainable development in agriculture.

Research on bacterial community characteristics of traditional fermented yak milk in the Tibetan Plateau based on high-throughput sequencing

Background

The Tibetan Plateau has an abundance of yak milk resources. The complex microbiota found in traditional fermented yak milk produced and sold by local Tibetans endows the yak milk with unique quality characteristics such as tissue morphology, flavor, and function. However, the diversity of bacterial flora in traditional fermented yak milk have not been elucidated.

Methods

In this study, 15 samples of fermented yak milk were collected for 16S rRNA high-throughput sequencing to analyze the bacterial community composition and function.

Results

After filtering for quality, 792,642 high-quality sequences were obtained, and 13 kinds of different phyla and 82 kinds of different genera were identified, of which the phylum Firmicutes (98.94%) was the dominant phylum, Lactobacillus (64.73%) and Streptococcus (28.48%) were identified as the dominant genus, in addition, the bacterial community richness and diversity were higher in Manang Village, followed by Bola Village. Bacterial community richness and diversity in Huage Village were relatively low. Based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) functional classification, the microorganisms in traditional fermented yak milk have rich metabolic functions (77.60%). These findings suggest that a large number of bacteria in traditional fermented yak milk contain abundant metabolic genes and can carry out a variety of growth and metabolic activities. This study established a theoretical foundation for further exploring the microbial flora of traditional fermented yak milk in Gannan.

Effects of cadmium stress on fruits germination and growth of two herbage species

Cadmium (Cd) pollution is a global environmental problem. It is of great significance to find a kind of pasture that can grow normally in a cadmium environment, especially in the Tibetan Plateau. We studied the fruit germination and fruit growth of Elymus sinsubmuticus S.L. Chen and Elymus tangutorum (Nevski), native plants of the Tibetan Plateau, in different cadmium environments. The results showed that with increased cadmium stress, the fruit germination rate, final germination rate, fruit-vigor, average germination time, and germination-speed index for the two grass species gradually decreased, and the 50% germination time for the seed gradually increased. Root length, biomass, and the number of leaves decreased in both species. We quantified the fruit germination and growth of plants in the cadmium environment and found that E. sinosubmuticus S.L. Chen had better fruit germination and fruit growth, and it had the development potential of cadmium pollution control.

Dynamic changes in the yak rumen eukaryotic community and metabolome characteristics in response to feed type

With diversification of yak breeding, it is important to understand the effects of feed type on the rumen, especially microbiota and metabolites. Due to the unique characteristics of yak, research on rumen microbes and metabolites is limited. In this study, the effects of two diet types on rumen eukaryotic microflora and metabolites were evaluated using the Illumina MiSeq platform and liquid chromatography-mass spectrometry (LC-MS). All identified protozoa belonged to Trichostomatia. At the genus level, the relative abundance of Metadinium and Eudiplodinium were significantly (p < 0.05) higher in the roughage group than that of concentrate group, while the concentrate group harbored more Isotricha. Ascomycota, Basidiomycota, and Neocallimastigomycota were the main fungal phyla, and the Wallemia, Chordomyces, Chrysosporium, Cladosporium, Scopulariopsis, and Acremonium genera were significantly (p < 0.05) more abundant in the roughage group than the concentrate group, while the concentrate group harbored more Aspergillus, Neocallimastix, Thermoascus, and Cystofilobasidium (p < 0.05). Metabolomics analysis showed that feed type significantly affected the metabolites of rumen protein digestion and absorption (L-proline, L-phenylalanine, L-tryosine, L-leucine, L-tryptophan, and β-alanine), purine metabolism (hypoxanthine, xanthine, guanine, guanosine, adenosine, and adenine), and other metabolic pathway. Correlation analysis revealed extensive associations between differential microorganisms and important metabolites. The results provide a basis for comprehensively understanding the effects of feed types on rumen microorganisms and metabolites of yaks. The findings also provide a reference and new directions for future research.

Rumen microbiota of indigenous and introduced ruminants and their adaptation to the Qinghai-Tibetan plateau

The grassland in the Qinghai-Tibetan plateau provide habitat for many indigenous and introduced ruminants which perform important ecological functions that impact the whole Qinghai-Tibetan plateau ecosystem. These indigenous Tibetan ruminants have evolved several adaptive traits to withstand the severe environmental conditions, especially cold, low oxygen partial pressure, high altitude, strong UV radiation, and poor forage availability on the alpine rangelands. Despite the challenges to husbandry associated with the need for enhanced adaptation, several domesticated ruminants have also been successfully introduced to the alpine pasture regions to survive in the harsh environment. For ruminants, these challenging conditions affect not only the host, but also their commensal microbiota, especially the diversity and composition of the rumen microbiota; multiple studies have described tripartite interactions among host-environment-rumen microbiota. Thus, there are significant benefits to understanding the role of rumen microbiota in the indigenous and introduced ruminants of the Qinghai-Tibetan plateau, which has co-evolved with the host to ensure the availability of specific metabolic functions required for host survival, health, growth, and development. In this report, we systemically reviewed the dynamics of rumen microbiota in both indigenous and introduced ruminants (including gut microbiota of wild ruminants) as well as their structure, functions, and interactions with changing environmental conditions, especially low food availability, that enable survival at high altitudes. We summarized that three predominant driving factors including increased VFA production, enhanced fiber degradation, and lower methane production as indicators of higher efficiency energy harvest and nutrient utilization by microbiota that can sustain the host during nutrient deficit. These cumulative studies suggested alteration of rumen microbiota structure and functional taxa with genes that encode cellulolytic enzymes to potentially enhance nutrient and energy harvesting in response to low quality and quantity forage and cold environment. Future progress toward understanding ruminant adaptation to high altitudes will require the integration of phenotypic data with multi-omics analyses to identify host-microbiota co-evolutionary adaptations enabling survival on the Qinghai-Tibetan plateau.

Shifts in xylanases and the microbial community associated with xylan biodegradation during treatment with rumen fluid

Treatment with rumen fluid improves methane production from non‐degradable lignocellulosic biomass during subsequent methane fermentation; however, the kinetics of xylanases during treatment with rumen fluid remain unclear. This study aimed to identify key xylanases contributing to xylan degradation and their individual activities during xylan treatment with bovine rumen microorganisms. Xylan was treated with bovine rumen fluid at 37°C for 48 h under anaerobic conditions. Total solids were degraded into volatile fatty acids and gases during the first 24 h. Zymography showed that xylanases of 24, 34, 85, 180, and 200 kDa were highly active during the first 24 h. Therefore, these xylanases are considered to be crucial for xylan degradation during treatment with rumen fluid. Metagenomic analysis revealed that the rumen microbial community’s structure and metabolic function temporally shifted during xylan biodegradation. Although statistical analyses did not reveal significantly positive correlations between xylanase activities and known xylanolytic bacterial genera, they positively correlated with protozoal (e.g., Entodinium, Diploplastron, and Eudiplodinium) and fungal (e.g., Neocallimastix, Orpinomyces, and Olpidium) genera and unclassified bacteria. Our findings suggest that rumen protozoa, fungi, and unclassified bacteria are associated with key xylanase activities, accelerating xylan biodegradation into volatile fatty acids and gases, during treatment of lignocellulosic biomass with rumen fluid.

The Common Occurrence of Theileria ovis in Tibetan Sheep and the First Report of Theileria sinensis in Yaks from Southern Qinghai, China

PURPOSE

The tick-borne protozoa piroplasms, including Theileria and Babesia, are the cause of substantial economic losses to the livestock industry. However, in southern Qinghai province, China, there are limited information on the molecular characteristics of piroplasms. This study therefore aimed at determining the prevalence and genetic diversity of piroplasms.

METHODS

In order to detect piroplasms, we examined 330 yaks and 236 Tibetan sheep blood samples by nested PCR. The differences in piroplasms prevalence in relation to different risk factors was analyzed using SPSS 26. Phylogenetic analysis based on 18S rRNA sequences was inferred using MEGA 7.

RESULTS

During this study, Theileria spp. were detected in 33.6% (111/330) of yaks and 94.1% (222/236) of Tibetan sheep, but no Babesia was identified. Importantly, a comparison study revealed that T. ovis infection was highly prevalent in sheep (94.1%) but infrequent in yaks (6.1%), while T. sinensis was host-specific to yaks with an infection rate of 27.6%. In addition, male animals were more likely to be infected by T. sinensis and female animals were more likely to be infected by T. ovis. And animals below 4000 m areas reported a higher infection rate with T. sinensis (26.1% vs. 2.9%, p < 0.001). Alongside these differences in prevalence, we found a significantly higher T. sinensis infection rate in separated-grazing livestock (22.2% vs. 3.7%, p < 0.001), while mixed-grazing ruminants had a higher T. ovis infection rate (50.0% vs. 39.0%, p = 0.014). Furthermore, sequence analysis revealed that the 18S rRNA sequences obtained in this study shared 86.9-100.0% identities with each other and they were clustered into T. sinensis or T. ovis.

CONCLUSION

To our knowledge, this is the first report of T. sinensis in Qinghai region. In addition, high prevalence of the generally sub-clinical T. ovis in sheep indicates extensive exposure to ticks and transmission of tick-borne pathogens with a significant economic impact. This study provides insights into the distribution and genetic diversity of Theileria in China.

Effect of high proportion concentrate dietary on Ashdan Yak jejunal barrier and microbial function in cold season

The intestinal health of ruminants plays a vital role in absorbing and metabolizing nutrients. In order to explore the jejunal barrier and microbiota dysfunction of Ashdan yaks, animals were fed with a high proportion of concentrated feeds in cold season. In present study, twelve Ashdan male yaks were arbitrarily separated into two categories, namely FF and CF. Compositional and functional differences in their jejunum barrier and microbiota between the FF and CF yaks were compared using metagenomics and proteomics methods. The results showed that the activity of jejunum digestive protease and microbe metabolite of forage-fed yaks were more conducive to healthy cultivation than the concentrate-fed yaks. 57 differentially expressed proteins (DEPs) were recognized using label-free MS, those could conclude to 2 principal classes: structural proteins and inflammatory factors, and 14 proteins were relatively active in those principal classes. Firmicutes were the dominant bacterial phylum in the jejunum microbiota of both the forage-fed group (24.33%) and concentrate-fed group (23.16%). As compared to forage-fed group, the concentrate-fed group showed enhanced alpha diversity and reduced beta diversity of the jejunal microbiota. The long-term high-proportion concentrate feeding inhibited the growth of Actinobacteria, Proteo-bacteria, Ascomycota, Bacteroidetes and stimulated the growth of Streptophyta, Cyanobacteria, Fusobacteria and Chlamydiae. The concentrate-fed group showed increase in the abundance of immune system process, along with decrease in the metabolic process, especially the binding process. Interestingly, the proteomics and metagenomics results were both inclined to the enrichment of jejunum mechanical barrier and inflammatory response. Overall, the study suggested that the long-term high-proportion concentrate feeding affected the expressions of specific jejunum proteins and composition of microbiota, which damaged the jejunum barrier and the function of microbiota in yaks.

Selenium Yeast Dietary Supplement Affects Rumen Bacterial Population Dynamics and Fermentation Parameters of Tibetan Sheep (Ovis aries) in Alpine Meadow

Selenium (Se) deficiency is a widespread and seasonally chronic phenomenon observed in Tibetan sheep (Ovis aries) traditionally grazed on the Qinghai-Tibet Plateau (QTP). Effects of the dietary addition of Se-enriched yeast (SeY) on the bacterial community in sheep rumen and rumen fermentation were evaluated with the aim of gaining a better understanding of the rumen prokaryotic community. Twenty-four yearling Tibetan rams [initial average body weight (BW) of 31.0 ± 0.64 kg] were randomly divided into four treatment groups, namely, control (CK), low Se (L), medium Se (M), and high Se (H). Each group comprised six rams and was fed a basic diet of fresh forage cut from the alpine meadow, to which SeY was added at prescribed dose rates. This feed trial was conducted for over 35 days. On the final day, rumen fluid was collected using a transesophageal sampler for analyzing rumen pH, NH3-N content, volatile fatty acid (VFA) level, and the rumen microbial community. Our analyses showed that NH3-N, total VFA, and propionate concentrations in the M group were significantly higher than in the other groups (P < 0.05). Both the principal coordinates analysis (PCoA) and the analysis of similarities revealed that the bacterial population structure of rumen differed among the four groups. The predominant rumen bacterial phyla were found to be Bacteroidetes and Firmicutes, and the three dominant genera in all the samples across all treatments were Christensenellaceae R7 group, Rikenellaceae RC9 gut group, and Prevotella 1. The relative abundances of Prevotella 1, Rikenellaceae RC9 gut group, Ruminococcus 2, Lachnospiraceae XPB1014 group, Carnobacterium, and Hafnia-Obesumbacterium were found to differ significantly among the four treatment groups (P < 0.05). Moreover, Tax4fun metagenome estimation revealed that gene functions and metabolic pathways associated with carbohydrate and other amino acids were overexpressed in the rumen microbiota of SeY-supplemented sheep. To conclude, SeY significantly affects the abundance of rumen bacteria and ultimately affects the rumen microbial fermentation.

Effect of high proportion concentrate dietary on Yak jejunal structure, physiological function and protein composition during cold season

The current study aimed to investigate the damage of long-term high concentrate diet feeding pattern on Yak jejunal structure, physiological function and protein composition during cold season. Twelve Datong male Yak (Bos grunniens) with the same age from cold season were randomly selected and slaughtered to determine Yak jejunal digestive enzyme activity, morphology and protein composition on different feeding patterns in Tibetan Plateau. The results showed that Yak jejunum digestive enzyme activity and morphology of grazing reared group were better than those in the intensively reared group. A total of 96 differentially expressed proteins were identified by label-free Mass Spectrometry (MS), which could be concluded to two predominant themes: protein structure and inflammatory response. Nine differentially expressed proteins were correlated in Yak jejunum damage in different feeding patterns. According to this research, we found that feeding pattern resulted the differences in Yak jejunum physiological function, morphology and protein composition. This fact was confirmed long-term high dietary concentrate feeding could damage the jejunum epithelial morphology and function.

Exploration of the effects of altitude change on bacteria and fungi in the rumen of yak (Bos grunniens)

The yak (Bos grunniens) is a ruminant animal with strong regional adaptability. However, little is known about the adaptation of the rumen microbial community of yaks at different altitudes and the adaptation mechanism of the host and intestinal microorganisms to the habitat. We investigated the adaptability of the rumen microorganisms of yaks at high and low altitudes. We also compared and analyzed the abundance and diversity of core microorganisms and those that varied between different animals. The aim was to compare the rumen bacterial and fungal communities of grazing yak living at two elevations. Bacteroidetes, Firmicutes, Ascomycota, and Chytridiomycota were the dominant bacteria in the plateau and low-altitude regions. Significant differences between the dominant microorganisms in the rumen of yaks were evident in the two regions. The proportion of fiber-degrading bacteria was significantly different between yaks dwelling at high-altitude and low-altitude regions. The abundance of starch-degrading bacteria was not significantly different with altitude. Species clustering similarity analysis showed that the rumen microorganisms in the two areas were obviously isolated and clustered into branches. Functional prediction showed significant differences in rumen microbial methane metabolism, starch and sucrose metabolism, ion-coupled transporter and bacterial secretion system at different altitudes. Overall, the results of this study improved our understanding of the abundance and composition of microorganisms in the rumen of yak at different altitudes.