Tibetan sheep have a high capacity to absorb and to regulate metabolism of SCFA in the rumen epithelium to adapt to low energy intake

Targeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces

Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922. More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.

Hepatic antioxidant capacity, immune response, and glycolysis of Tibetan sheep in response to dietary soluble protein levels

In recent years, the increasing cost of protein raw materials has significantly impacted feed expenses and presented challenges to the livestock industry. Ninety-two-month-old male Tibetan sheep (15.40±0.81 kg) were randomly divided into three groups based on protein levels in their diet: L group (12% protein), M group (14% protein), and H group (16% protein). The feeding experiment was performed for 100 days, including a 10-day adaption period. It was found that the liver cells of the M group exhibited a better uniform in cytoplasm. Additionally, group M sheep had higher levels of GSH-Px and T-AOC (P<0.05), as well as elevated IgM, IL-1β, IL-6, and SDH content compared to other groups (P<0.05). There were 577, 698, and 623 differentially expressed genes between groups H and L, groups H and M, and groups M and L, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that the DEGs regulated the activities of 56 pathways. Six liver-metabolism-related DEGs, SOD2, SOD1, CD19, IGF1, HK2, and PFKFB3, were expressed differently among the three sheep groups. In summary, a 14% protein level in the diet improved the hepatic antioxidant capacity, immune function, and glycolysis in Tibetan sheep through modulating the expression of functional genes.

Effects of dietary energy levels on production and absorption of hindgut short-chain fatty acids in two sheep breeds

Hindgut fermentation is a crucial process in the production of short-chain fatty acids (SCFAs) and the provision of energy for ruminants. However, hindgut fermentation is not well-researched and has only recently received more attention. Tibetan sheep (T-sheep), an indigenous sheep breed raised on the Qinghai-Tibetan Plateau (QTP), play a vital role in the livelihood of the residents and in ecosystem services in the region. They have adapted well to the fluctuating supply of energy and nutrition under the harsh environment of the QTP. As part of the same study as the present study, T-sheep produced more ruminal SCFAs and had a greater capacity to absorb SCFAs than Small-tailed Han sheep (H-sheep), a breed introduced to the QTP due to their high reproductive rate. These findings raised intriguing questions about whether T-sheep also produce and absorb a greater amount of hindgut SCFAs to adapt to the harsh QTP environment, and whether there is a link between rumen and hindgut dietary digestion. Twenty-four T-sheep and 24 H-sheep, all 1.5-year-old wethers, were divided randomly into four groups of six sheep in each breed, and each group received a diet of different energy yield, namely, 8.21, 9.33, 10.45 or 11.57 MJ digestible energy (DE)/kg DM. After 49 days of treatment, all sheep were slaughtered, and tissues and digesta from the cecum, colon, and rectum were collected. The morphology of tissues was examined, and the concentrations of SCFAs in digesta and the expressions of related genes involved in the absorption and metabolism of SCFAs were determined. The concentration of total SCFAs and the molar proportion of butyrate increased in each site as the dietary energy level increased, and the H-sheep produced greater yields of total SCFAs in both the colon and rectum than T-sheep. This indicated a greater production of SCFAs in the hindgut of H-sheep than T-sheep, compensating for their lesser production in the rumen. T-sheep had a greater absorption surface area of the hindgut and greater mRNA expressions of SCFA transporters, indicating a greater capacity to absorb SCFAs than H-sheep. However, T-sheep had lesser mRNA expressions of the rate-limiting enzymes and regulators in SCFAs metabolism, indicating a lesser capacity for metabolism of SCFAs in the hindgut than H-sheep. These characteristics confer T-sheep with an advantage in the absorption and metabolism of SCFAs in the hindgut, enabling them to adapt rapidly to the highly fluctuating energy intake on the harsh QTP.

Variations in HBA gene contribute to high-altitude hypoxia adaptation via affected O2 transfer in Tibetan sheep

Tibetan sheep are indigenous to the Qinghai-Xizang Plateau. Owing to the harsh hypoxic environment in this plateau, the hemoglobin (Hb) protein in Tibetan sheep has undergone adaptive changes over time. Hb is primarily responsible for transporting O2 and CO2 between the lungs and other tissues of the body. The α subunit of Hb, encoded by the HBA gene, is a crucial component of the protein. However, whether variations in the HBA gene sequence affect the adaptation of Tibetan sheep to high-altitude hypoxia remains unclear. In this study, we sequenced the HBA gene and identified three single nucleotide polymorphisms (SNPs). These SNPs were genotyped in Tibetan and Hu sheep using Kompetitive Allele-Specific PCR (KASP). The results showed that the frequencies of the AT genotype and H1H2 haplotype were higher in Tibetan sheep than in Hu sheep. Individuals with the AT genotype exhibited higher P50 levels, whereas those with the H1H2 haplotype exhibited lower PO2 and SaO2 levels. The higher P50 levels indicated that O2 was more readily released from oxygenated Hb into the tissues, with the lower PO2 and SaO2 levels facilitating this process. These findings indicate that variations in the HBA gene sequence contribute to enhancing O2 transfer efficiency in Tibetan sheep.

Large-scale metagenomic assembly provide new insights into the genetic evolution of gut microbiomes in plateau ungulates

Trillions of microbes colonize the ungulate gastrointestinal tract, playing a pivotal role in enhancing host nutrient utilization by breaking down cellulose and hemicellulose present in plants. Here, through large-scale metagenomic assembly, we established a catalog of 131,416 metagenome-assembled genomes (MAGs) and 11,175 high-quality species-level genome bins (SGBs) from 17 species of ungulates in China. Our study revealed the convergent evolution of high relative abundances of carbohydrate-active enzymes (CAZymes) in the gut microbiomes of plateau-dwelling ungulates. Notably, two significant factors contribute to this phenotype: structural variations in their gut microbiome genomes, which contain more CAZymes, and the presence of novel gut microbiota species, particularly those in the genus Cryptobacteroides, which are undergoing independent rapid evolution and speciation and have higher gene densities of CAZymes. Furthermore, these enrichment CAZymes in the gut microbiomes are highly enrichment in known metabolic pathways for short-chain fatty acid (SCFA) production. Our findings not only provide a valuable genomic resource for understanding the gut microbiomes of ungulates but also offer fresh insights into the interaction between gut microbiomes and their hosts, as well as the co-adaptation of hosts and their gut microbiomes to their environments.

Microbial dysbiosis in the gut–mammary axis as a mechanism for mastitis in dairy cows

Mastitis is a significant and costly disease in dairy cows, reducing milk production and affecting herd health. Recent research highlights the role of gastrointestinal microbial dysbiosis in the development of mastitis. This review focuses on how microbial imbalances in the rumen and intestines can compromise the integrity of the gastrointestinal barriers, allowing harmful bacteria and endotoxins, such as lipopolysaccharide, to enter the bloodstream and reach the mammary gland, triggering inflammation. This process links gastrointestinal health to mammary gland inflammation through the gut–mammary axis. Furthermore, disruptions in glucose metabolism and immune responses are implicated in the progression of mastitis. This review underscores the potential for non‐antibiotic interventions aimed at restoring microbial balance to reduce mastitis incidence, providing new insights into improving dairy cow health and farm productivity. Our findings emphasise the critical need to explore preventive measures targeting the rumen and intestinal microbiota for effective mastitis control.

Effect of supplementing lysins and methionine to low-protein diets on growth performance, hepatic antioxidant capacity, immune status, and glycolytic activity of tibetan sheep

Reducing the levels of dietary protein is an effective nutritional approach in lowering feed cost and nitrogen emissions in ruminants. The purpose of this study was to evaluate the effects of dietary Lys/Met ratio in a low protein diet (10%, dry matter basis) on the growth performance and hepatic function (antioxidant capacity, immune status, and glycolytic activity) in Tibetan lambs. Ninety two-month-old rams with an average weight of 15.37 ± 0.92 kg were randomly assigned to LP-L (dietary Lys/Met = 1:1), LP-M (dietary Lys/Met = 2:1) and LP-H (dietary Lys/Met = 3:1) treatments. The trial was conducted over 100 d, including 10 d of adaption to the diets. Hepatic phenotypes, antioxidant capacity, immune status, glycolytic activity and gene expression profiling was detected after the conclusion of the feeding trials. The results showed that the body weight was higher in the LP-L group when compared to those on the LP-M group (P < 0.05). In addition, the activities of the catalase (CAT) and glutathione peroxidase (GSH-Px) in the LP-L group were significantly increased compared with the LP-M group (P < 0.05), while the malondialdehyde (MDA) levels in LP-H group were significantly decreased (P < 0.05). Compared with LP-H group, both hepatic glycogen (P < 0.01) and lactate dehydrogenase (LDH) (P < 0.05) were significantly elevated in LP-L group. For the LP-L group, the hepatocytes were arranged radially with the central vein in the center, and hepatic plates exhibited tight arrangement. Transcriptome analysis identified 29, 179, and 129 differentially expressed genes (DEGs) between the LP-M vs. LP-L, LP-H vs. LP-M, and LP-H vs. LP-L groups, respectively (Q-values < 0.05 and |log2Fold Change| > 1). Gene Ontology (GO) and correlation analyses showed that in the LP-L group, core genes (C1QA and JUNB) enriched in oxidoreductase activity were positively correlated with antioxidant indicators, while the MYO9A core gene enriched in the immune response was positively associated with immune indicators, and core genes enriched in molecular function (PDK3 and PDP2) were positively correlated with glycolysis indicators. In summary, low-protein diet with a low Lys/Met ratio (1:1) could reduce the hepatic oxidative stress and improve the glycolytic activity by regulating the expression of related genes of Tibetan sheep.

Multi-omics revealed rumen microbiota metabolism and host immune regulation in Tibetan sheep of different ages

The rumen microbiota and metabolites play an important role in energy metabolism and immune regulation of the host. However, the regulatory mechanism of rumen microbiota and metabolite interactions with host on Tibetan sheep's plateau adaptability is still unclear. We analyzed the ruminal microbiome and metabolome, host transcriptome and serum metabolome characteristics of Tibetan sheep at different ages. Biomarkers Butyrivibrio, Lachnospiraceae_XPB1014_group, Prevotella, and Rikenellaceae_RC9_gut_group were found in 4 months, 1.5 years, 3.5 years, and 6 years Tibetan sheep, respectively. The rumen microbial metabolites were mainly enriched in galactose metabolism, unsaturated fatty acid biosynthesis and fatty acid degradation pathways, and had significant correlation with microbiota. These metabolites further interact with mRNA, and are co-enriched in arginine and proline metabolism, metabolism of xenobiotics by cytochrome P450, propanoate metabolism, starch and sucrose metabolism, gap junction pathway. Meanwhile, serum metabolites also have a similar function, such as chemical carcinogenesis - reactive oxygen species, limonene and pinene degradation, and cutin, suberine and wax biosynthesis, thus participating in the regulation of the body's immune and energy-related metabolic processes. This study systematically revealed that rumen microbiota, metabolites, mRNA and serum metabolites of Tibetan sheep were involved in the regulation of fermentation metabolic function and immune level of Tibetan sheep at different ages, which provided a new perspective for plateau adaptability research of Tibetan sheep at different ages.

Ensiled diet improved the growth performance of Tibetan sheep by regulating the rumen microbial community and rumen epithelial morphology

The aim of this study was to investigate the effects of ensiled agricultural byproducts from Qinghai-Tibet plateau on growth performance, rumen microbiota, ruminal epithelium morphology, and nutrient transport-related gene expression in Tibetan sheep. Fourteen male Tibetan sheep were randomly assigned to one of two diets: an untreated diet (without silage inoculum, CON, n = 7) or an ensiled diet (with silage inoculum, ESD, n = 7). The total experimental period lasted for 84 d, including early 14 d as adaption period and remaining 70 d for data collection. The ESD increased average daily gain (P = 0.046), dry matter intake (P < 0.001), ammonia nitrogen (P = 0.045), microbial crude protein (P = 0.034), and total volatile fatty acids concentration (P < 0.001), and decreased ruminal pH value (P = 0.014). The proportion of propionate (P = 0.006) and the copy numbers of bacteria (P = 0.01) and protozoa (P = 0.002) were higher, while the proportion of acetate (P = 0.028) was lower in the sheep fed ESD compared to CON. Pyrosequencing of the 16S ribosomal RNA gene revealed that ESD increased the relative abundance of Firmicutes, Ruminococcus, Lachnospiraceae_AC2044_group, Lachnospiraceae_XPB1014_group, and Christensenellaceae_R-7_group in the rumen (P < 0.05), while decreased the relative abundance of Bacteroidota, Prevotellaceae_UCG-003, and Veillonellaceae_UCG-001 (P < 0.05). Analyses with PICRUSt2 and STAMP indicated that the propionate metabolism pathway was enriched in the sheep fed ESD (P = 0.026). The ESD increased the rumen papillae height (P = 0.012), density (P = 0.036), and surface area (P = 0.001), and improved the thickness of the total epithelia (P = 0.018), stratum corneum (P = 0.040), stratum granulosum (P = 0.042), and stratum spinosum and basale (P = 0.004). The relative mRNA expression of cyclin-dependent Kinase 2, CyclinA2, CyclinD2, zonula occludens-1, Occludin, monocarboxylate transporter isoform 1 (MCT1), MCT4, sodium/potassium pump, and sodium/hydrogen antiporter 3 were higher in the rumen epithelial of sheep fed ESD than CON (P < 0.05). Conversely, the relative mRNA expressions of Caspase 3 and B-cell lymphoma-2 were lower in the sheep fed ESD than CON (P < 0.05). In conclusion, compared with an untreated diet, feeding an ensiled diet altered the rumen microbial community, enhanced nutrient transport through rumen epithelium, and improved the growth performance of Tibetan sheep.

Meta-analysis identifying gut microbial biomarkers of Qinghai-Tibet Plateau populations and the functionality of microbiota-derived butyrate in high-altitude adaptation

The extreme environmental conditions of a plateau seriously threaten human health. The relationship between gut microbiota and human health at high altitudes has been extensively investigated. However, no universal gut microbiota biomarkers have been identified in the plateau population, limiting research into gut microbiota and high-altitude adaptation. 668 16s rRNA samples were analyzed using meta-analysis to reduce batch effects and uncover microbiota biomarkers in the plateau population. Furthermore, the robustness of these biomarkers was validated. Mendelian randomization (MR) results indicated that Tibetan gut microbiota may mediate a reduced erythropoietic response. Functional analysis and qPCR revealed that butyrate may be a functional metabolite in high-altitude adaptation. A high-altitude rat model showed that butyrate reduced intestinal damage caused by high altitudes. According to cell experiments, butyrate may downregulate hypoxia-inducible factor-1α (HIF-1α) expression and blunt cellular responses to hypoxic stress. Our research found universally applicable biomarkers and investigated their potential roles in promoting human health at high altitudes.

Effect of Different Feeds on the Fungi Microbiome of Suffolk Crossed with Tibetan Sheep

The gut microbiome plays an important role in the metabolism, nutrient absorption and immunocompetency of animals. The dynamics of the microbiota can be influenced by modulatory factors that involve nutrition, environment, health, diseases, etc. Few reports have been documented regarding the effects of different feeds on the fungi microbiome of Suffolk crossed with Tibetan sheep. A total of 30 Suffolk crossed with Tibetan sheep (ST sheep) were selected for the study and randomly divided into five equal groups (n = 6): AZ, BZ, CZ, DZ and EZ. Group AZ was fed with alfalfa and oat grass, whereas group BZ was fed with mixture of concentrated feed, alfalfa and oat grass. Groups CZ, DZ and EZ were fed with concentrated feed #1, #2 and #3, respectively. All experimental animals were fed twice a day for four months, and rectum samples were collected for microbiota analysis. Results revealed that 2,781,461 raw reads and 2,333,239 clean reads were achieved in the ST sheep. When compared with the sheep of groups AZ and BZ (164), the shared amplicon sequence variants (ASVs) between AZ and CZ (109), AZ (113) and DZ (118) as well as AZ along with EZ were fewer. Conspicuous different phyla (8) and genera (56) were examined and compared with free-range sheep in AZ. Genera including Xeromyces, Kazachstania, Cordyceps, Rhodotorula, Pichia, Spor, etc. were found higher in animals in the CZ, DZ and EZ groups. The results of this study provide new insights regarding the effects of different feeds on the fungi microbiome of sheep farmed on the plateau. We concluded that the differences in feed in Suffolk crossed with Tibetan sheep altered their gut microbiota.

Synergistic Responses of Tibetan Sheep Rumen Microbiota, Metabolites, and the Host to the Plateau Environment

Plateau adaptation in animals involves genetic mechanisms as well as coevolutionary mechanisms of the microbiota and metabolome of the animal. Therefore, the characteristics of the rumen microbiome and metabolome, transcriptome, and serum metabolome of Tibetan sheep at different altitudes (4500 m, 3500 m, and 2500 m) were analyzed. The results showed that the rumen differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and carbohydrate metabolism, and there was a significant correlation with microbiota. The differentially expressed genes and metabolites at middle and high altitudes were coenriched in asthma, arachidonic acid metabolism, and butanoate and propanoate metabolism. In addition, the serum differential metabolites at 3500 m and 4500 m were mainly enriched in amino acid metabolism, lipid metabolism, and metabolism of xenobiotics by cytochrome P450, and they were also related to microbiota. Further analysis revealed that rumen metabolites accounted for 7.65% of serum metabolites. These common metabolites were mainly enriched in metabolic pathways and were significantly correlated with host genes (p < 0.05). This study found that microbiota, metabolites, and epithelial genes were coenriched in pathways related to lipid metabolism, energy metabolism, and immune metabolism, which may be involved in the regulation of Tibetan sheep adaptation to plateau environmental changes.

Interaction between Rumen Epithelial miRNAs-Microbiota-Metabolites in Response to Cold-Season Nutritional Stress in Tibetan Sheep

Tibetan sheep are already well adapted to cold season nutrient stress on the Tibetan Plateau. Rumen, an important nutrient for metabolism and as an absorption organ in ruminants, plays a vital role in the cold stress adaptations of Tibetan sheep. Ruminal microbiota also plays an indispensable role in rumen function. In this study, combined multiomics data were utilized to comprehensively analyze the interaction mechanism between rumen epithelial miRNAs and microbiota and their metabolites in Tibetan sheep under nutrient stress in the cold season. A total of 949 miRNAs were identified in the rumen epithelium of both cold and warm seasons. A total of 62 differentially expressed (DE) miRNAs were screened using FC > 1.5 and p value < 0.01, and a total of 20,206 targeted genes were predicted by DE miRNAs. KEGG enrichment analysis revealed that DE miRNA-targeted genes were mainly enriched in axon guidance(ko04360), tight junction(ko04530), inflammatory mediator regulation of TRP channels(ko04750) and metabolism-related pathways. Correlation analysis revealed that rumen microbiota, rumen VFAs and DE miRNAs were all correlated. Further study revealed that the targeted genes of cold and warm season rumen epithelial DE miRNAs were coenriched with differential metabolites of microbiota in glycerophospholipid metabolism (ko00564), apoptosis (ko04210), inflammatory mediator regulation of TRP channels (ko04750), small cell lung cancer (ko05222), and choline metabolism in cancer (ko05231) pathways. There are several interactions between Tibetan sheep rumen epithelial miRNAs, rumen microbiota, and microbial metabolites, mainly through maintaining rumen epithelial barrier function and host homeostasis of choline and cholesterol, improving host immunity, and promoting energy metabolism pathways, thus enabling Tibetan sheep to effectively respond to cold season nutrient stress. The results also suggest that rumen microbiota have coevolved with their hosts to improve the adaptive capacity of Tibetan sheep to cold season nutrient stress, providing a new perspective for the study of cold season nutritional stress adaptation in Tibetan sheep.

Shift of Feeding Strategies from Grazing to Different Forage Feeds Reshapes the Rumen Microbiota To Improve the Ability of Tibetan Sheep (Ovis aries) To Adapt to the Cold Season

The dynamics of ruminant-rumen microbiome symbiosis associated with feeding strategies in the cold season were examined. Twelve pure-grazing adult Tibetan sheep (Ovis aries) (18 months old; body weight, 40 ± 0.23 kg) were transferred from natural pasture to two indoor feedlots and fed either a native-pasture diet (NPF group) or an oat hay diet (OHF group) (n = 6 per treatment), and then the flexibility of rumen microbiomes to adapt to these compositionally different feeding strategies was examined. Principal-coordinate analysis and similarity analysis indicated that the rumen bacterial composition correlated with altered feeding strategies. Microbial diversity was higher in the grazing group than in those fed with native pasture and an oat hay diet (P < 0.05). The dominant microbial phyla were Bacteroidetes and Firmicutes, and the core bacterial taxa comprised mostly (42.49% of shared operational taxonomic units [OTUs]) Ruminococcaceae (408 taxa), Lachnospiraceae (333 taxa), and Prevotellaceae (195 taxa), which were relatively stable across different treatments. Greater relative abundances of Tenericutes at the phylum level, Pseudomonadales at the order level, Mollicutes at the class level, and Pseudomonas at the genus level were observed in a grazing period than in the other two treatments (NPF and OHF) (P < 0.05). In the OHF group, due to the high nutritional quality of the forage, Tibetan sheep can produce high concentrations of short-chain fatty acids (SCFAs) and NH3-N by increasing the relative abundances of key bacteria in the rumen, such as Lentisphaerae, Negativicutes, Selenomonadales, Veillonellaceae, Ruminococcus 2, Quinella, Bacteroidales RF16 group, and Prevotella 1, to aid in nutrients degradation and energy utilization. The levels of beneficial bacteria were increased by the oat hay diet; these microbiotas are likely to help improve and maintain host health and metabolic ability in Tibetan sheep to adapt to cold environments. The rumen fermentation parameters were significantly influenced by feeding strategy in the cold season (P < 0.05). Overall, the results of this study demonstrate the strong effect of feeding strategies on the rumen microbiota of Tibetan sheep, which provided a new idea for the nutrition regulation of Tibetan sheep grazing in the cold season on the Qinghai-Tibetan Plateau. IMPORTANCE During the cold season, like other high-altitude mammals, Tibetan sheep have to adapt their physiological and nutritional strategies, as well as the structure and function of their rumen microbial community, to the seasonal variation of lower food availability and quality. This study focused on the changes and adaptability in the rumen microbiota of Tibetan sheep when they adapted from grazing to a high-efficiency feeding strategy during the cold season by analyzing the rumen microbiota of Tibetan sheep raised under the different management systems, and it shows the linkages among the rumen core and pan-bacteriomes, nutrient utilization, and rumen short-chain fatty acids. The findings from this study suggest that the feeding strategies potentially contribute to variations in the pan-rumen bacteriome, together with the core bacteriome. Fundamental knowledge on the rumen microbiomes and their roles in nutrient utilization furthers our understanding of how rumen microbial adaptation to harsh environments may function in hosts. The facts obtained from the present trial clarified the possible mechanisms of the positive effects of feeding strategy on nutrient utilization and rumen fermentation in harsh environments.

Rumen Epithelial Development- and Metabolism-Related Genes Regulate Their Micromorphology and VFAs Mediating Plateau Adaptability at Different Ages in Tibetan Sheep

The rumen is an important hallmark organ of ruminants and plays an important role in the metabolism and immune barrier of Tibetan sheep on the Plateau. However, there are few studies on rumen development and metabolism regulation in Tibetan sheep at different ages. Here, we comprehensively analyzed the immune function, fermentation function, rumen epithelial micromorphology and transcriptome profile of Tibetan sheep at different ages. The results showed that the concentration of IgG decreased and the concentration of IgM increased with age (p < 0.05), and the highest concentration of IgA was observed at 1.5 and 3.5 years of age. In terms of rumen fermentation characteristics, VFAs of 4-month-old lambs were the highest, followed by VFAs and NH3-N of Tibetan sheep at 3.5 years of age. Hematoxylin-eosin staining and transmission electron microscopy section examination of rumen epithelial tissue showed that the rumen papilla width increased with age (p < 0.001), the thickness of the stratum corneum decreased, the cells in the stratum corneum showed accelerated migration and the thickness of the rumen muscle layer increased (p < 0.001). Desmosomal junctions between the layers of rumen epithelium increased at 1.5 and 3.5 years old, forming a compact barrier structure, and the basal layer had more mitochondria involved in the regulation of energy metabolism. RNA-seq analysis revealed that a total of 1006 differentially expressed genes (DEGs) were identified at four ages. The DEGs of Tibetan sheep aged 4 months and 6 years were mainly enriched in the oxidation−reduction process and ISG15-protein conjugation pathway. The 1.5 and 3.5-year-olds were mainly enriched in skeletal muscle thin filament assembly, mesenchyme migration and the tight junction pathway. WGCNA showed that DEGs related to rumen microbiota metabolite VFAs and epithelial morphology were enriched in “Metabolism of xenobiotics by cytochrome P450, PPAR signaling pathway, Butanoate metabolism pathways” and participated in the regulation of rumen epithelial immune and fermentation metabolism functions of Tibetan sheep at different ages. This study systematically revealed the regulatory mechanism of rumen epithelial development and metabolism in the plateau adaptation of Tibetan sheep, providing a new approach for the study of plateau adaptation.

A comparison of average daily gain, apparent digestibilities, energy balance, rumen fermentation parameters, and serum metabolites between yaks (Bos grunniens) and Qaidam cattle (Bos taurus) consuming diets differing in energy level

Yaks (Bos grunniens), indigenous to the harsh Qinghai-Tibetan Plateau, are well adapted to the severe conditions, and graze natural pasture without supplements all year round. Qaidam cattle (Bos taurus), introduced to the Qinghai-Tibetan Plateau 1,700 years ago, are raised at a lower altitude than yaks, provided with shelter at night and offered supplements in winter. Based on their different backgrounds, we hypothesized that yaks have lower energy requirements for maintenance than cattle. To test this hypothesis, we measured average daily gain (ADG), apparent digestibilities, energy balance, rumen fermentation parameters, and serum metabolites in growing yaks and cattle offered diets differing in metabolizable energy (ME) levels (6.62, 8.02, 9.42 and 10.80 MJ/kg), but with the same crude protein concentration. Six castrated yaks (155 ± 5.8 kg) and 6 castrated Qaidam cattle (154 ± 8.0 kg), all 2.5 years old, were used in 2 concurrent 4 × 4 Latin square designs. Neutral and acid detergent fiber digestibilities were greater (P < 0.05) in yaks than in cattle, and decreased linearly (P < 0.05) with increasing dietary energy level; whereas, digestibilities of dry matter, organic matter, crude protein and ether extract increased (P < 0.05) linearly with increasing energy level. The ADG was greater (P < 0.001) in yaks than in cattle, and increased (P < 0.05) linearly with increasing energy levels. From the regressions of ADG on ME intake, the estimated ME requirement for maintenance was lower (P < 0.05) in yaks than in cattle (0.43 vs. 0.57 MJ/kg BW^0.75). The ratios of digestible energy (DE):gross energy and ME:DE were higher (P < 0.05) in yaks than in cattle, and increased (P < 0.05) linearly with increasing dietary energy level. Ruminal pH decreased (P < 0.05), whereas concentrations of total volatile fatty acids (VFAs) and ammonia increased (P < 0.01) with increasing dietary energy level, and all were greater (P < 0.05) in yaks than in cattle. Concentrations of ruminal acetate and iso-VFAs were greater (P < 0.05), whereas propionate was lower (P < 0.05) in yaks than in cattle; acetate decreased (P < 0.001), whereas butyrate and propionate increased (P < 0.001) linearly with increasing dietary energy level. Serum concentrations of β-hydroxybutyrate were lower (interaction, P < 0.001) in yaks than in cattle fed diets of 9.42 and 10.80 MJ/kg, whereas non-esterified fatty acids were greater (interaction, P < 0.01) in yaks than in cattle fed diets of 6.62 and 8.02 MJ/kg. Concentrations of serum leptin and growth hormone were greater in yaks than in cattle and serum insulin and growth hormone increased (P < 0.01) linearly with increasing dietary energy level. Our hypothesis that yaks have lower energy requirements for maintenance than cattle was supported. This lower requirement confers an advantage to yaks over Qaidam cattle in consuming low energy diets during the long winter on the Qinghai-Tibetan Plateau.

Monensin supplementation downregulated the expression signature of genes involved in cholesterol synthesis in the ruminal epithelium and adipose tissue of lambs

To understand the metabolic mechanisms regulating lipid metabolism by monensin, Afshari male lambs (n = 16) with 41.0 ± 2.4 kg body weight (BW, mean ± SD) at approximately 180 days of age were randomly assigned equally to two dietary treatments. After a 21-day pre-adaptation period, all animals in two groups continued to receive the basal diet, but one group received no monensin supplementation (control) while the other group received 30 mg/day of monensin per animal. Individual BW was recorded weekly to determine the average daily body weight gain (ADG). At the end of the 56-day experimental period, lambs were weighed and slaughtered. Monensin supplementation did not affect BW, ADG, and rumen fermentation characteristics. However, monensin significantly downregulated the sterol regulatory element-binding protein (SREBP)-2 gene expression in all sample tissues (p < 0.05). Also, monensin downregulated expressions of SREBP-1c and peroxisome proliferator-activated receptor (PPAR)-γ in back fat tissues. Monensin increased the expression of 3-hydroxy-3-methylglutaryl-CoA synthase (HMGCS)-2, but it decreased the mRNA abundance of HMGCS-1 in the rumen epithelial tissues (p < 0.05). Our data suggest that monensin downregulates cholesterol synthesis via inhibition of HMGCS-1 and impairment of the SREBP pathway, probably due to a crosstalk among different tissues to control energy metabolism.

Nutritional Modulation, Gut, and Omics Crosstalk in Ruminants

Simple Summary

Over the last decade, animal nutrition science has been significantly developed, supported by the great advancements in molecular technologies. For scientists, the present "feedomics and nutrigenomics" era continues to evolve and shape how research is designed, performed, and understood. The new omics interpretations have established a new point of view for the nutrition–gene interaction, integrating more comprehensive findings from animal physiology, molecular genetics, and biochemistry. In the ruminant model, this modern approach addresses rumen microbes as a critical intermediate that can deepen the studies of diet–gut interaction with host genomics. The present review discusses nutrigenomics’ and feedomics’ potential contribution to diminishing the knowledge gap about the DNA cellular activities of different nutrients. It also presents how nutritional management can influence the epigenetic pathway, considering the production type, life stage, and species for more sustainable ruminant nutrition strategies.

Abstract

Ruminant nutrition has significantly revolutionized a new and prodigious molecular approach in livestock sciences over the last decade. Wide-spectrum advances in DNA and RNA technologies and analysis have produced a wealth of data that have shifted the research threshold scheme to a more affluent level. Recently, the published literature has pointed out the nutrient roles in different cellular genomic alterations among different ruminant species, besides the interactions with other factors, such as age, type, and breed. Additionally, it has addressed rumen microbes within the gut health and productivity context, which has made interpreting homogenous evidence more complicated. As a more systematic approach, nutrigenomics can identify how genomics interacts with nutrition and other variables linked to animal performance. Such findings should contribute to crystallizing powerful interpretations correlating feeding management with ruminant production and health through genomics. This review will present a road-mapping discussion of promising trends in ruminant nutrigenomics as a reference for phenotype expression through multi-level omics changes.

Small intestinal morphology and sugar transporters expression when consuming diets of different energy levels: comparison between Tibetan and small-tailed Han sheep

Some non-structural carbohydrates, especially starch, escape ruminal fermentation, are converted into glucose, and are absorbed from the small intestine. This glucose provides an important source of energy, and its usage is more efficient than glucose from carbohydrates which are fermented as short chain fatty acids in the rumen and, subsequently, undergo hepatic gluconeogenesis. Tibetan sheep graze on the harsh Qinghai-Tibetan Plateau (QTP) all year round and their carbohydrate and energy intakes fluctuate greatly with seasonal forage availability. Consequently, a high capacity to absorb glucose from the small intestine would be particularly beneficial for Tibetan sheep to allow them to cope with the inconsistent dietary intakes. This study examined how the small intestinal morphology and sugar transporters' expression of Tibetan and Small-tailed Han (Han) sheep respond to fluctuating energy intakes under the harsh conditions of the QTP. Han sheep graze on the QTP only in summer and are generally raised in feedlots. Twenty-four Tibetan sheep and 24 Han sheep, all wethers, were assigned randomly to four groups (n = 6 per breed/group), with each group offered a diet differing in digestible energy content: 8.21, 9.33, 10.45 and 11.57 MJ/kg DM. After 49 d, all sheep were slaughtered, tissues of the small intestine were collected, and measurements were made of the morphology and glucose transporters and the related regulation gene expressions. At intakes of low energy levels, Tibetan sheep had a greater villus surface area in the duodenum, jejunum and ileum and higher mRNA expression of sodium-dependent glucose transporter 1 in the duodenum and ileum (P < 0.05) than Han sheep. In the glucose transporter 2 (GLUT2) mediated glucose absorption pathway, Tibetan sheep had higher GLUT2 and taste receptor family 1 member 2 and 3 mRNA expressions than Han sheep in the duodenum, jejunum and ileum (P < 0.05). We concluded that the differences between breeds indicated a greater glucose absorption capacity in the small intestine of Tibetan than Han sheep, which would confer an advantage to Tibetan over Han sheep to an inconsistent energy intake on the harsh QTP. These findings suggested that ruminants raised under harsh environmental conditions with highly fluctuating dietary intakes, as is often the case in grazing ruminants worldwide, are able to absorb glucose from the small intestine to a greater extent than ruminants raised under more moderate conditions.

Astragalus membranaceus Alters Rumen Bacteria to Enhance Fiber Digestion, Improves Antioxidant Capacity and Immunity Indices of Small Intestinal Mucosa, and Enhances Liver Metabolites for Energy Synthesis in Tibetan Sheep

Simple Summary

Astragalus membranaceus is a widely used traditional Chinese herb that has been used by humans for hundreds of years. The Qinghai-Tibetan plateau (QTP) is regarded as one of the remaining ‘Green’ places in the world. With the fast-developing intensive livestock production, sustainable and environmentally-friendly practices are required urgently on the QTP. In the current study, Tibetan sheep were supplemented with the root of Astragalus membranaceus (AMT) to reduce the use of chemical veterinary drugs and antibiotics, and to examine the effect on rumen bacteria, the antioxidant capacities and immunity indices of small intestinal mucosa and meat tissue, and the liver metabolome responses.

Abstract

Natural, non-toxic feed additives can potentially replace chemical medications and antibiotics that are offered sheep to improve performance. In the present study, Tibetan sheep were supplemented with the root of Astragalus membranaceus (AMT), a traditional herb used widely in China. Twenty-four male Tibetan sheep (31 ± 1.4 kg; 9-month-old) were assigned randomly to one of four levels of supplementary AMT: 0 g/kg (A₀), 20 g/kg (A₂₀), 50 g/kg (A₅₀) and 80 g/kg (A₈₀) dry matter intake (DMI). The A₅₀ and A₈₀ groups increased the diversity of rumen bacteria on d 14 and the relative abundances of fiber decomposing bacteria. Supplementary AMT upregulated the metabolism of vitamins, nucleotides, amino acids and glycan, and downregulated the metabolism of lipids and carbohydrates. In addition, supplementary AMT enriched rumen bacteria for drug resistance, and reduced bacteria incurring cell motility. In general, AMT supplementation increased the concentrations of catalase (CAT), superoxide dismutase (SOD) total antioxidant capacity (T-AOC) and secretory immunoglobulin A (sIgA) in the small intestinal mucosa and CAT and SOD in meat tissue. The liver tissue metabolome response showed that AMT in the A₈₀ lambs compared to the A₀ lambs upregulated the metabolites for energy synthesis. It was concluded that supplementary A. membranaceus increased the relative abundances of fiber decomposing bacteria and improved the antioxidant capacities and immunity indices of small intestinal mucosa and meat tissue in Tibetan sheep.

Hypothalamic regulation of energy homoeostasis when consuming diets of different energy concentrations: comparison between Tibetan and Small-tailed Han sheep

Seasonal energy intake of Tibetan sheep on the harsh Qinghai-Tibetan Plateau (QTP) fluctuates greatly and is often well below maintenance requirements. The aim of this study was to gain insight into how the hypothalamus regulates energy homoeostasis in Tibetan sheep. We compared Tibetan and Small-tailed Han sheep (n 24 of each breed), which were each allocated randomly into four groups and offered one of four diets that differed in digestible energy densities: 8·21, 9·33, 10·45 and 11·57 MJ/kg DM. Sheep were weighed every 2 weeks, and it was assumed that the change in body weight (BW) reflected the change in energy balance. The arcuate nucleus of the hypothalamus in Tibetan sheep had greater protein expressions of neuropeptide Y (NPY) and agouti-related peptide (AgRP) when in negative energy balance, but lesser protein expressions of proopiomelanocortin (POMC) and cocaine and amphetamine-regulated transcript (CART) when in positive energy balance than Small-tailed Han sheep. As a result, Tibetan sheep had a lesser BW loss when in negative energy balance and stored more energy and gained more BW when in positive energy balance than Small-tailed Han sheep with the same dietary intake. Moreover, in the hypothalamic adenosine monophosphate-activated protein kinase (AMPK) regulation pathway, Tibetan sheep had greater adenosine monophosphate-activated protein kinase-α 2 protein expression than Small-tailed Han sheep, which supported the premise of a better ability to regulate energy homoeostasis and better growth performance. These differences in the hypothalamic NPY/AgRP, POMC/CART and AMPK pathways between breeds conferred an advantage to the Tibetan over Small-tailed Han sheep to cope with low energy intake on the harsh QTP.

Integrating miRNA and mRNA Profiling to Assess the Potential miRNA-mRNA Modules Linked With Testicular Immune Homeostasis in Sheep

Beyond its well-known role in spermatogenesis and androgen production, mammalian testes are increasingly recognized as an immune-privileged organ for protecting autoantigenic germ cells, especially meiotic and postmeiotic germ cells, from systemic immune responses. Despite its importance, the molecular mechanisms underlying this regulation in mammals, including sheep, are far from known. In this study, we searched for the genes associated with testicular immune privilege and assessed their possible modulating mechanisms by analyzing systematic profiling of mRNAs and miRNAs on testicular tissues derived from prepubertal and postpubertal Tibetan sheep acquired by RNA sequencing. We identified 1,118 differentially expressed (DE) mRNAs associated with immunity (245 increased mRNAs and 873 decreased mRNAs) and 715 DE miRNAs (561 increased miRNAs and 154 decreased miRNAs) in postpubertal testes compared with prepuberty. qPCR validations for 20 DE mRNAs and 16 miRNAs showed that the RNA-seq results are reliable. By using Western blot, the postpubertal testes exhibited decreased protein abundance of CD19 and TGFBR2 (two proteins encoded by DE mRNAs) when compared with prepuberty, consistent with mRNA levels. The subsequent immunofluorescent staining showed that the positive signals for the CD19 protein were observed mainly in Sertoli cells and the basement membrane of pre- and postpubertal testes, as well as the prepubertal testicular vascular endothelium. The TGFBR2 protein was found mostly in interstitial cells and germ cells of pre- and postpubertal testes. Functional enrichment analysis indicated that DE mRNAs were mainly enriched in biological processes or pathways strongly associated with the blood–testis barrier (BTB) function. Many decreased mRNAs with low expression abundance were significantly enriched in pathways related to immune response. Also, multiple key miRNA-target negative correlation regulatory networks were subsequently established. Furthermore, we verified the target associations between either oar-miR-29b or oar-miR-1185-3p and ITGB1 by dual-luciferase reporter assay. Finally, a putative schematic model of the miRNA-mRNA-pathway network mediated by immune homeostasis-related genes was proposed to show their potential regulatory roles in sheep testicular privilege. Taken together, we conclude that many immune-related genes identified in this study are negatively regulated by potential miRNAs to participate in the homeostatic regulation of testicular immune privilege of sheep by sustaining BTB function and inhibiting immune responses under normal physiological conditions. This work offers the first global view of the expression profiles of miRNAs/mRNAs involved in sheep testicular immune privilege and how the genes potentially contribute to immune-homeostatic maintenance.

Unraveling Stage-Dependent Expression Patterns of Circular RNAs and Their Related ceRNA Modulation in Ovine Postnatal Testis Development

Circular RNAs (circRNAs) have been shown to function in the reproductive systems including testis. However, their expression, as well as function in testicular development of sheep remain undefined. Herein, we performed RNA sequencing to reveal circRNA temporal expression patterns in testes of Tibetan sheep from different stages of maturation (3M, 3-month-old; 1Y, 1-year-old; 3Y, 3-year-old). A total of 3,982, 414, and 4,060 differentially expressed (DE) circRNAs were uncovered from 3M vs 1Y, 1Y vs 3Y, and 3M vs 3Y, respectively. Functional enrichment assessment indicated that the source genes of DE circRNAs were primarily engaged in spermatogenesis and testicular immune privilege including blood-testis barrier (BTB). We subsequently constructed the core circRNA-miRNA-mRNA interaction network for genes related to testicular function, such as spermatogenesis, germ cell development, BTB, and cell cycle/meiosis. Furthermore, we validated the target associations between either circ_024949, circ_026259 or IGF1, and oar-miR-29b in this network, and revealed their similar expression signatures in developmental testes that they were extensively expressed in germ cells, Leydig cells, and Sertoli cells, thus suggesting their broad functions in the functional maintenance of Leydig cells and Sertoli cells, as well as the development and maturation of male germ cells. Meanwhile, circ_026259 was shown to promote IGF1 expression through inhibition of oar-miR-29b in sheep Sertoli cells. This work gives the first global view for the expression and regulation of circRNAs in sheep testis, which will be helpful for providing new insights into the molecular mechanism of ovine testis function.

Genetic diversity and population structure of Tibetan sheep breeds determined by whole genome resequencing

Tibetan sheep is one of primitive Chinese sheep breeds, which achieved the divergence about 2500 years ago in Qinghai plateau region. According to different geographic conditions, especially altitudes, Tibetan sheep evolved into different breeds. In this study, we performed whole genome resequencing of 5 representative Tibetan sheep breeds. Comparative genomic analysis showed that they can be divided into different clades with a close genetic relationship. However, some genes with common selective regions were enriched for hypoxic adaptability in different breeds living at higher altitude, including GHR, BMP15, and CPLANE1. Furthermore, breed-specific selective regions about physical characteristics, especially wool growth, were found in genes such as BSND, USP24, NCAPG, and LCORL. This study could contribute to our understanding about trait formation and offer a reference for breeding of Tibetan sheep.

Energy substrate metabolism in skeletal muscle and liver when consuming diets of different energy levels: comparison between Tibetan and Small-tailed Han sheep

The energy intake of Tibetan sheep on the harsh Qinghai-Tibetan Plateau (QTP) varies greatly with seasonal forage fluctuations and is often below maintenance requirements, especially during the long, cold winter. The liver plays a crucial role in gluconeogenesis and skeletal muscle is the primary tissue of energy expenditure in mammals. Both play important roles in energy substrate metabolism and regulating energy metabolism homeostasis of the body. This study aimed to gain insight into how skeletal muscle and liver of Tibetan sheep regulate energy substrate metabolism to cope with low energy intake under the harsh environment of the QTP. Tibetan sheep (n = 24; 48.5 ± 1.89 kg BW) were compared with Small-tailed Han sheep (n = 24; 49.2 ± 2.21 kg BW), which were allocated randomly into one of four groups that differed in dietary digestible energy densities: 8.21, 9.33, 10.45 and 11.57 MJ /kg DM. The sheep were slaughtered after a 49-d feeding period, skeletal muscle and liver tissues were collected and measurements were made of the activities of the key enzymes of energy substrate metabolism and the expressions of genes related to energy homeostasis regulation. Compared with Small-tailed Han sheep, Tibetan sheep exhibited higher capacities of propionate to glucose conversion and fatty acid oxidation and ketogenesis in the liver, higher glucose utilization efficiency in both skeletal muscle and liver, but lower activities of fatty acid oxidation and protein mobilization in skeletal muscle, especially when in negative energy balance. However, the Small-tailed Han sheep exhibited higher capacities to convert amino acids and lactate to glucose and higher levels of glycolysis and lipogenesis in the liver than Tibetan sheep. These differences in gluconeogenesis and energy substrate metabolism conferred the Tibetan sheep an advantage over Small-tailed Han sheep to cope with low energy intake and regulate whole-body energy homeostasis under the harsh environment of the QTP.

Comparison of MicroRNA Transcriptomes Reveals the Association between MiR-148a-3p Expression and Rumen Development in Goats

Simple Summary

In ruminants, the rumen epithelium plays an important role in nutrient absorption, metabolism and transport. MicroRNAs (miRNAs) have been reported to regulate the proliferation of diverse epithelial cells. In this study, we profiled the miRNA transcriptomes of goat rumens at four development stages and screened for candidate miRNAs related to rumen development. MiR-148a-3p was found to be highly expressed in the rumen tissues and induced the proliferation of GES-1 cells by targeting QKI. Our findings provide some insights into the functional roles of miRNAs in rumen growth and functional development in ruminants.

Abstract

The rumen is an important digestive organ of ruminants. From the fetal to adult stage, the morphology, structure and function of the rumen change significantly. However, the knowledge of the intrinsic genetic regulation of these changes is still limited. We previously reported a genome-wide expression profile of miRNAs in pre-natal goat rumens. In this study, we combined and analyzed the transcriptomes of rumen miRNAs during pre-natal (E60 and E135) and post-natal (D30 and D150) stages. A total of 66 differentially expressed miRNAs (DEMs) were identified in the rumen tissues from D30 and D150 goats. Of these, 17 DEMs were consistently highly expressed in the rumens at the pre-weaning stages (E60, E135 and D30), while down-regulated at D150. Noteworthy, annotation analysis revealed that the target genes regulated by the DEMs were mainly enriched in MAPK signaling pathway, Jak-STAT signaling pathway and Ras signaling pathway. Interestingly, the expression of miR-148a-3p was significantly high in the embryonic stage and down-regulated at D150. The potential binding sites of miR-148a-3p in the 3′-UTR of QKI were predicted by the TargetScan and verified by the dual luciferase report assay. The co-localization of miR-148a-3p and QKI through in situ hybridization was observed in the rumen tissues but not in the intestinal tracts. Moreover, the expression of miR-148a-3p in the epithelium was significantly higher than that in the other layers of the rumen, suggesting that miR-148a-3p is involved in the development of the rumen epithelial cells by targeting QKI. Subsequently, miR-148a-3p inhibitor was found to induce the proliferation of GES-1 cells. Taken together, our study identified DEMs involved in the development of the rumen and provides insights into the regulation mechanism of rumen development in goats.