Multi-omics reveal the gut microbiota-mediated severe foraging environment adaption of small wild ruminants in the Three-River-Source National Park, China.

The Tibetan antelope (Pantholops hodgsonii), blue sheep (Pseudois nayaur), and Tibetan sheep (Ovis aries) are the dominant small ruminants in the Three-River-Source National Park (TRSNP). However, knowledge about the association between gut microbiota and host adaptability remains poorly understood. Herein, multi-omics sequencing approaches were employed to investigate the gut microbiota-mediated forage adaption in these ruminants. The results revealed that although wild ruminants (WR) of P. hodgsoni and P. nayaur were faced with severe foraging environments with significantly low vegetation coverage and nutrition, the apparent forage digestibility of dry matter, crude protein, and acid detergent fiber was significantly higher than that of O. aries. The 16s rRNA sequencing showed that the gut microbiota in WR underwent convergent evolution, and alpha diversity in these two groups was significantly higher than that in O. aries. Moreover, indicator species, including Bacteroidetes and Firmicutes, exhibited positive relationships with apparent forage digestibility, and their relative abundances were enriched in the gut of WR. Enterotype analysis further revealed that enterotype 1 belonged to WR, and the abundance of fatty acid synthesis metabolic pathway-related enzyme genes was significantly higher than enterotype 2, represented by O. aries. Besides, the metagenomic analysis identified 14 pathogenic bacterial species, among which 10 potentially pathogenic bacteria were significantly enriched in the gut microbiota of O. aries. Furthermore, the cellulolytic strains and genes encoding cellulase and hemicellulase were significantly enriched in WR. In conclusion, our results provide new evidence of gut microbiota to facilitate wildlife adaption in severe foraging environments of the TRSNP, China.

Targeted and untargeted metabolomics reveals meat quality in grazing yak during different phenology periods on the Qinghai-Tibetan Plateau.

Yak meat is more popular among consumers because of its high nutritional value, but little attention has been paid to its meat quality, which is affected by different phenology periods grass. We hypothesized that seasonal variations in grass composition influenced the ruminal bacteria community, and eventually affected the meat quality of yaks. This study aims to investigate the relationship of meat quality in grazing yak as well as the key rumen bacteria using targeted and untargeted metabolomics and 16S rRNA during different phenology periods. The main three altered metabolic pathways in grazing yak, including amino acids biosynthesis, glutathione metabolism, and fatty acids biosynthesis, were found in the grass period (GP) group compared to the regreen period (RP) and hay period (HP) groups. The GP group had higher concentrations of flavor amino acids (FAA), polyunsaturated fatty acids (PUFA), and a lower ratio of n-6/n-3 compared with the RP group. Correlation analysis results showed that Rikenellaceae_RC9_gut_group was positively correlated with fatty acids and lipid metabolites, which might be involved in lipid metabolism. Pediococcus had a positive correlation with biological peptides, which could be involved in the metabolism of bioactive compounds. In conclusion, grass in different phenology periods was associated with modified amino acids and fatty acids composition of yak meat as well as altered regulation of biological pathways, which was correlated with changes in rumen bacterial communities.

Effects of the alpine meadow in different phenological periods on rumen fermentation and gastrointestinal tract bacteria community in grazing yak on the Qinghai-Tibetan Plateau.

BACKGROUND: In this study, we investigated the effects of alpine meadow in different phenological periods on ruminal fermentation, serum biochemical indices, and gastrointestinal tract microbes in grazing yak on the Qinghai-Tibetan Plateau. A total of eighteen female freely grazing yaks with an average age of 3 years old and a body weight of 130 ± 19 kg were selected. According to the plant phenological periods, yaks were randomly allocated to one of three treatments: (1) regreen periods group (RP, n = 6); (2) grassy periods group (GP, n = 6); and (3) hay periods group (HP, n = 6). At the end of the experiment, the blood, rumen fluids, and rectal contents were collected to perform further analysis. RESULTS: The concentrations of total volatile fatty acid (TVFA), acetate, glucose (GLU), triglyceride (TG), cholesterol (CHO), high density lipoprotein (HDL), and low density lipoprotein (LDL) were higher in the GP group than in the HP group (P < 0.05). However, compared with the RP and GP groups, the HP group had higher concentrations of isobutyrate, isovalerate, valerate, and creatinine (CREA) (P < 0.05). The abundance of Prevotella in the rumen, and the abundances of Rikenellaceae_RC9_gut_group, Eubacterium_coprostanoligenes_group, and Prevotellaceae_UCG-004 in the gut were higher in the GP group compared with the HP group (P < 0.05). The HP had higher abundance of Eubacterium_coprostanoligenes_group in the rumen as well as the abundances of Romboutsia and Arthrobacter in the gut compared with the RP and GP groups (P < 0.05). CONCLUSIONS: Based on the results of rumen fermentation, serum biochemical, differential biomarkers, and function prediction, the carbohydrate digestion of grazing yak would be higher with the alpine meadow regreen and grassy due to the gastrointestinal tract microbes. However, the risk of microbe disorders and host inflammation in grazing yak were higher with the alpine meadow wither.

Evaluation of the Longissimus Thoracis et Lumborum Muscle Quality of Chaka and Tibetan Sheep and the Analysis of Possible Mechanisms Regulating Meat Quality.

This study aimed to comprehensively evaluate the characteristics in the longissimus thoracis et lumborum (LTL) muscle of Chaka (CK) sheep and Tibetan (TB) sheep, and transcriptomics-metabolomics association analysis was used to find the possible genes, differential metabolites, and significant differential metabolic pathways that lead to meat quality differences. Based on the researched results, the nutritional quality of meat, including the contents of ether extract (11.95% vs. 10.56%), unsaturated fatty acid (51.20% vs. 47.69%), and polyunsaturated fatty acid (5.71% vs. 3.97%), were better in TB sheep than in CK sheep, while the CK sheep has better muscle fiber characteristics, such as the total number (62 vs. 45) and muscle fiber density (1426.54 mm2 vs. 1158.77 mm2) and flavor. Omics research has shown that the key differential metabolites and metabolic pathways were dominated by amino acid metabolism, particularly the glutathione metabolism, taurine and hypotaurine metabolism, and lipid metabolism-related pathways, such as glycerophospholipid metabolism and the sphingolipid signaling pathway. The intermediate metabolite sn-Glycerol 3-phosphoethanolamine played a key role in determining sheep meat quality, which was regulated by GPAT2, PLPP2, AGPAT1, PNPLA2, and GPAT4 and correlated with meat color, texture, and flavor. Overall, these results will provide effective information and more evidence to support further exploration of valuable biomarkers of meat quality.

Vegetation structural shift tells environmental changes on the Tibetan Plateau over 40 years.

Structural information of grassland changes on the Tibetan Plateau is essential for understanding alterations in critical ecosystem functioning and their underlying drivers that may reflect environmental changes. However, such information at the regional scale is still lacking due to methodological limitations. Beyond remote sensing indicators only recognizing vegetation productivity, we utilized multivariate data fusion and deep learning to characterize formation-based plant community structure in alpine grasslands at the regional scale of the Tibetan Plateau for the first time and compared it with the earlier version of Vegetation Map of China for historical changes. Over the past 40 years, we revealed that (1) the proportion of alpine meadows in alpine grasslands increased from 50% to 69%, well-reflecting the warming and wetting trend; (2) dominances of Kobresia pygmaea and Stipa purpurea formations in alpine meadows and steppes were strengthened to 76% and 92%, respectively; (3) the climate factor mainly drove the distribution of Stipa purpurea formation, but not the recent distribution of Kobresia pygmaea formation that was likely shaped by human activities. Therefore, the underlying mechanisms of grassland changes over the past 40 years were considered to be formation dependent. Overall, the first exploration for structural information of plant community changes in this study not only provides a new perspective to understand drivers of grassland changes and their spatial heterogeneity at the regional scale of the Tibetan Plateau, but also innovates large-scale vegetation study paradigm.

Copy number variations of the KAT6A gene are associated with body measurements of Chinese sheep breeds.

Copy number variation (CNV) is one kind of genomic structure variations and presents as gains and losses of genomic fragments. More recently, we have made an atlas of CNV maps for livestock. In the future, it is a primary focus to determine the phenotypic effects of candidate CNVs. Lysine Acetyltransferase 6 A (KAT6A) is a protein coding gene and plays a critical role in many cellular processes. However, the effects of KAT6A CNVs on sheep body measurements remains unknown. In this study, we performed quantitative polymerase chain reaction (qPCR) to detect the presences and distributions of three CNV regions within KAT6A gene in 672 sheep from four Chinese breeds. Association analysis indicated that the three CNVs of KAT6A gene were significantly associated with body measurement(s) in Small-tailed Han sheep (STH) and Hu sheep (HU) (p < 0.05), while no effects on Large-tailed Han sheep (LTH) were observed (p > 0.05) were observed. Additionally, only one CNV was significantly associated with body measurement (body length) in Chaka sheep (CK) (p < 0.05). Our study provided evidence that the CNV(s) of KAT6A gene could be used as candidate marker(s) for molecular breedings of STH, HU, and CK breeds.

Nardosinone suppresses monoiodoacetate-induced osteoarthritis in rats: The key role of the miR-218-5p/NUMB axis.

Nardosinone is a bioactive compound with a sesquiterpenoid structure isolated from Nardostachys jatamansi. The compound has shown treatment effects against skeletal disorders. In the current study, the effects of nardosinone on osteoarthritis (OA) were first assessed and the mechanism underlying the effects was explored by detecting changes in the miR-218-5p/NUMB axis. The miR, as a potential target mediating the effects of nardosinone on OA, was first determined with microarray and RT-qPCR detections. Then, OA symptoms were induced in rats using monoiodoacetate (MIA) and treated with nardosinone. The anti-OA effects of nardosinone were assessed via the detection of the histological structure and inflammation. The role of miR-218-5p was delineated by modulating its levels in OA-affected rats. Based on the results of microarray and RT-qPCR detections, miR-218-5p was selected as the therapeutic target for nardosinone. The induction of OA resulted in tissue destruction and the production of cytokines in rat joint tissues, which was associated with the up-regulation of miR-218-5p and the downregulation of NUMB. For OA-affected rats treated with nardosinone, the joint structure was improved and the inflammatory response was suppressed, along with the restored expression levels of miR-218-5p and NUMB. The re-induced level of miR-218-5p compromised the anti-OA effects of nardosinone, indicating that the inhibition of the miR played an indispensable role in the anti-OA function of nardosinone. Collectively, the findings of our study demonstrated that nardosinone exerts treatment effects against OA by modulating the miR-218-5p/NUMB axis. Future studies will provide more detailed information on the interaction between nardosinone and miR in the attenuation of OA.

Rumen Microbiome Reveals the Differential Response of CO2 and CH4 Emissions of Yaks to Feeding Regimes on the Qinghai-Tibet Plateau.

Shifts in feeding regimes are important factors affecting greenhouse gas (GHG) emissions from livestock farming. However, the quantitative values and associated drivers of GHG emissions from yaks (Bos grunniens) following shifts in feeding regimes have yet to be fully described. In this study, we aimed to investigate CH4 and CO2 emissions differences of yaks under different feeding regimes and their potential microbial mechanisms. Using static breathing chamber and Picarro G2508 gas concentration analyzer, we measured the CO2 and CH4 emissions from yaks under traditional grazing (TG) and warm-grazing and cold-indoor feeding (WGCF) regimes. Microbial inventories from the ruminal fluid of the yaks were determined via Illumina 16S rRNA and ITS sequencing. Results showed that implementing the TG regime in yaks decreased their CO2 and CH4 emissions compared to the WGCF regime. The alpha diversity of ruminal archaeal community was higher in the TG regime than in the WGCF regime. The beta diversity showed that significant differences in the rumen microbial composition of the TG regime and the WGCF regime. Changes in the rumen microbiota of the yaks were driven by differences in dietary nutritional parameters. The relative abundances of the phyla Neocallimastigomycota and Euryarchaeota and the functional genera Prevotella, Ruminococcus, Orpinomyces, and Methanobrevibacter were significantly higher in the WGCF regime than in the TG regime. CO2 and CH4 emissions from yaks differed mainly because of the enrichment relationship of functional H2- and CO2-producing microorganisms, hydrogen-consuming microbiota, and hydrogenotrophic methanogenic microbiota. Our results provided a view that it is ecologically important to develop GHG emissions reduction strategies for yaks on the Qinghai-Tibet Plateau based on traditional grazing regime.

Comparative Analysis of the Composition of Fatty Acids and Metabolites between Black Tibetan and Chaka Sheep on the Qinghai-Tibet Plateau.

The objective of this study was to investigate and compare fatty acids and metabolites in the longissimus dorsi muscle between Black Tibetan and Chaka sheep grazing in a highly saline environment. A total of eight castrated sheep (14 months old) with similar body weights (25 ± 2.2 kg) were selected. The experimental treatments included Black Tibetan (BT) and Chaka sheep (CK) groups, and each group had four replications. The experiment lasted for 20 months. All sheep grazed in a highly saline environment for the whole experimental period and had free access to water. The results showed that the diameter (42.23 vs. 51.46 µm), perimeter (131.78 vs. 166.14 µm), and area of muscle fibers (1328.74 vs. 1998.64 µm2) were smaller in Chaka sheep than in Black Tibetan sheep. The ash content in the longissimus dorsi was lower in Chaka sheep than in Black Tibetan sheep (p = 0.010), and the contents of dry matter (DM), ether extract (EE), and crude protein (CP) in the longissimus dorsi showed no differences (p > 0.05). For fatty acids, the proportions of C10:0, C15:0, and tC18:1 in the longissimus dorsi were higher in Chaka sheep than in Black Tibetan sheep (p < 0.05). However, all other individual fatty acids were similar among treatments, including saturated fatty acids (SFAs), unsaturated fatty acids (UFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), and the ratios of n-6 PUFAs to n-3 PUFAs and PUFAs to SFAs (p > 0.05). A total of 65 biomarkers were identified between the two breeds of sheep. Among these metabolites, 40 metabolic biomarkers were upregulated in the CK group compared to the BT group, and 25 metabolites were downregulated. The main metabolites include 30 organic acids, 9 amino acids, 5 peptides, 4 amides, 3 adenosines, 2 amines, and other compounds. Based on KEGG analysis, eight pathways, namely, fatty acid biosynthesis, purine metabolism, the biosynthesis of unsaturated fatty acids, renin secretion, the regulation of lipolysis in adipocytes, neuroactive ligand−receptor interaction, the cGMP-PKG signaling pathway, and the cAMP signaling pathway, were identified as significantly different pathways. According to the results on fatty acids and metabolites, upregulated organic acid and fatty acid biosynthesis increased the meat quality of Chaka sheep.

Genome-wide analysis of CNVs in three populations of Tibetan sheep using whole-genome resequencing.

Copy number variation (CNV), an important source of genomic structural variation, can disturb genetic structure, dosage, regulation and expression, and is associated with phenotypic diversity and adaptation to local environments in mammals. In the present study, 24 resequencing datasets were used to characterize CNVs in three ecotypic populations of Tibetan sheep and assess CNVs related to domestication and adaptation in Qinghai-Tibetan Plateau. A total of 87,832 CNV events accounting for 0.3% of the sheep genome were detected. After merging the overlapping CNVs, 2777 CNV regions (CNVRs) were obtained, among which 1098 CNVRs were shared by the three populations. The average length of these CNVRs was more than 3 kb, and duplication events were more frequent than deletions. Functional analysis showed that the shared CNVRs were significantly enriched in 56 GO terms and 18 KEGG pathways that were mainly concerned with ABC transporters, olfactory transduction and oxygen transport. Moreover, 188 CNVRs overlapped with 97 quantitative trait loci (QTLs), such as growth and carcass QTLs, immunoglobulin QTLs, milk yield QTLs and fecal egg counts QTLs. PCDH15, APP and GRID2 overlapped with body weight QTLs. Furthermore, Vst analysis showed that RUNX1, LOC101104348, LOC105604082 and PAG11 were highly divergent between Highland-type Tibetan Sheep (HTS) and Valley-type Tibetan sheep (VTS), and RUNX1 and LOC101111988 were significantly differentiated between VTS and Oura-type Tibetan sheep (OTS). The duplication of RUNX1 may facilitate the hypoxia adaptation of OTS and HTS in Qinghai-Tibetan Plateau, which deserves further research in detail. In conclusion, for the first time, we represented the genome-wide distribution characteristics of CNVs in Tibetan sheep by resequencing, and provided a valuable genetic variation resource, which will facilitate the elucidation of the genetic basis underlying the distinct phenotypic traits and local adaptation of Tibetan sheep.

Polydatin inhibits IL-1ß-mediated chondrocyte inflammation and ameliorates cartilage degradation: Involvement of the NF-κB and Wnt/ß-catenin pathways.

Osteoarthritis (OA) is a highly prevalent chronic joint disease that involves extracellular matrix (ECM) degradation and articular cartilage inflammation. Polydatin (PD) can alleviate inflammatory reactions in numerous diseases. The present study aimed to investigate the chondroprotective and anti-inflammatory effects of PD on interleukin (IL)- 1ß-treated chondrocytes in vitro and anterior cruciate ligament transection-induced rat OA models in vivo. Primary chondrocytes were isolated from SD rats and cultured. Only second-passage cells were used for subsequent experiments. Counting kit-8, quantitative real-time polymerase chain reaction, western blotting, enzyme-linked immunosorbent assay, and immunofluorescence were used to detect relevant indices. Rat OA models were established to obtain in vivo data. PD treatment decreased the production of nitric oxide (NO), prostaglandin E2 (PGE2), inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), tumor necrosis factor-α (TNF-α), and IL-6 during IL-1ß-stimulated chondrocyte inflammation. Moreover, PD upregulated aggrecan and collagen II expression, whereas downregulated a disintegrin and metalloproteinase with thrombospondin motifs 5 (ADAMTS5) and matrix metalloproteinase-13 (MMP-13) expression on IL-1ß-mediated chondrocytes. Additionally, PD reduced IL-1ß-stimulated NF-κB and Wnt/ß-catenin activation and nuclear translocation. The results of histological analysis and scoring revealed that OA in the rat models was effectively ameliorated by the intra-articular injection of PD. PD suppressed IL-1ß-stimulated iNOS, COX-2, NO, and PGE2 production, TNF-α, IL-6, collagen X, MMP-13, and ADAMTS-5 expression, collagen II and aggrecan degeneration by inhibiting NF-κB and Wnt/ß-catenin signaling in vitro. PD also mitigated OA progression in the rat models, thereby providing reliable data that PD could serve as a promising candidate for OA therapy.

The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau.

It was acknowledged long ago that microorganisms have played critical roles in animal evolution. Tibetan wild asses (TWA, Equus kiang) are the only wild perissodactyls on the Qinghai-Tibet Plateau (QTP) and the first national protected animals; however, knowledge about the relationships between their gut microbiota and the host's adaptability remains poorly understood. Herein, 16S rRNA and meta-genomic sequencing approaches were employed to investigate the gut microbiota-host associations in TWA and were compared against those of the co-resident livestock of yak (Bos grunnies) and Tibetan sheep (Ovis aries). Results revealed that the gut microbiota of yak and Tibetan sheep underwent convergent evolution. By contrast, the intestinal microflora of TWA diverged in a direction enabling the host to subsist on sparse and low-quality forage. Meanwhile, high microbial diversity (Shannon and Chao1 indices), cellulolytic activity, and abundant indicator species such as Spirochaetes, Bacteroidetes, Prevotella_1, and Treponema_2 supported forage digestion and short-chain fatty acid production in the gut of TWA. Meanwhile, the enterotype identification analysis showed that TWA shifted their enterotype in response to low-quality forage for a better utilization of forage nitrogen and short-chain fatty acid production. Metagenomic analysis revealed that plant biomass degrading microbial consortia, genes, and enzymes like the cellulolytic strains (Prevotella ruminicola, Ruminococcus flavefaciens, Ruminococcus albus, Butyrivibrio fibrisolvens, and Ruminobacter amylophilus), as well as carbohydrate metabolism genes (GH43, GH3, GH31, GH5, and GH10) and enzymes (ß-glucosidase, xylanase, and ß-xylosidase, etc.) had a significantly higher enrichment in TWA. Our results indicate that gut microbiota can improve the adaptability of TWA through plant biomass degradation and energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies and also provide a strong rationale for understanding the roles of gut microbiota in the adaptation of QTP wildlife when facing harsh feeding environments.

The Response of Ruminal Microbiota and Metabolites to Different Dietary Protein Levels in Tibetan Sheep on the Qinghai-Tibetan Plateau.

Ruminal microbiota and metabolites play crucial roles in animal health and productivity. Exploring the dynamic changes and interactions between microbial community composition and metabolites is important for understanding ruminal nutrition and metabolism. Tibetan sheep (Ovis aries) are an important livestock resource on the Qinghai-Tibetan Plateau (QTP), and the effects of various dietary protein levels on ruminal microbiota and metabolites are still unknown. The aim of this study was to investigate the response of ruminal microbiota and metabolites to different levels of dietary protein in Tibetan sheep. Three diets with different protein levels (low protein 10.1%, medium protein 12.1%, and high protein 14.1%) were fed to Tibetan sheep. 16S rRNA gene sequencing and gas chromatography coupled with time-of-flight mass spectrometry (GC-TOF-MS) were used to study the profile changes in each group of ruminal microbes and metabolites, as well as the potential interaction between them. The rumen microbiota in all groups was dominated by the phyla Bacteroidetes and Firmicutes regardless of the dietary protein level. At the genus level, Prevotella_1, Rikenellaceae_RC9_gut_group and Prevotellaceae_UCG-001 were dominant. Under the same forage-to-concentrate ratio condition, the difference in the dietary protein levels had no significant impact on the bacterial alpha diversity index and relative abundance of the major phyla and genera in Tibetan sheep. Rumen metabolomics analysis revealed that dietary protein levels altered the concentrations of ruminal amino acids, carbohydrates and organic acids, and significantly affected tryptophan metabolism (p < 0.05). Correlation analysis of the microbiota and metabolites revealed positive and negative regulatory mechanisms. Overall, this study provides detailed information on rumen microorganisms and ruminal metabolites under different levels of dietary protein, which could be helpful in subsequent research for regulating animal nutrition and metabolism through nutritional interventions.

Cropping practices manipulate soil bacterial structure and functions on the Qinghai-Tibet Plateau.

There is an increasing awareness of the adverse environmental effects of the intensive practices used in modern crop farming, such as those that cause greenhouse gas emissions and nutrient leaching. Harnessing beneficial microbes by changing planting practices presents a promising strategy for optimizing plant growth and agricultural sustainability. However, the characteristics of soil microorganisms under different planting patterns remain uncertain. We conducted a study of soil bacterial structure and function under monoculture vs. polyculture planting regimes using 16S rRNA gene sequencing on the Qinghai-Tibet Plateau. We observed substantial variations in bacterial richness, diversity, and relative abundances of taxa between gramineous and leguminous monocultures, as well as between gramineae-legume polycultures. The number of operational taxonomic units and alpha and beta diversity were markedly higher in the leguminous monocultures than in the gramineous monocultures; conversely, network analysis revealed that the interactions among the bacterial genera in the gramineous monocultures were more complex than those in the other two planting regimes. Moreover, nitrogen fixation, soil detoxification, and productivity were increased under the gramineous monocultures; more importantly, low soil-borne diseases (e.g., animals parasitic or symbiont) also facilitated strongly suppressive effects toward soil-borne pathogens. Nevertheless, the gramineae-legume polycultures were prone to nitrate seepage contamination, and leguminous monocultures exhibited strong denitrification effects. These results revealed that the gramineous monoculture is a more promising cropping pattern on the Qinghai-Tibetan Plateau. Understanding the bacterial distribution patterns and interactions of crop-sensitive microbes presents a basis for developing microbial management strategies for smart farming.

Copy number variation of the CCDC39 gene is associated with growth traits in Chinese cattle.

BACKGROUND: Copy number variation (CNV) has become an essential part of genetic structural variation. Coiled-coil domain containing 39 (CCDC39) is a gene that related to the growth and development of organs and tissues. It is identified that it has a CNV region by animal genome resequencing. OBJECTIVE: In this study, we detected the phenotypic traits and different distributions of CCDC39 gene copy numbers in five Chinese cattle breeds (Qinchuan (QC) cattle, Yunling (YL) cattle, Xianan (XN) cattle, Pinan (PN) cattle and Jiaxian (JX) cattle). METHODS: Five hundred and six cattle were randomly selected for CNV distribution detection. Blood samples were taken and genomic DNA was extracted. Different tissues were obtained from adult (n = 3) XN cattle, including heart, liver, kidney, skeletal muscle and lung. The genome qPCR experiment was performed with SYBR Green in triplicate. CDNA qPCR was used to detect the expression level of CCDC39 in different tissues and varieties. Using SPSS v20.0 software, the relationship between CCDC39 CNV and the growth traits of PN, XN, QC, NY and YL cattle breeds was analyzed by one-way analysis of variance (ANOVA). RESULTS: The results showed that the expression of CCDC39 in lung was higher than that in other tissues. The expression in liver and kidney was similar, but the expression in heart and muscle was less. It can be seen that the duplication type of QC cattle CCDC39 CNV is higher than the deletion or normal in the height at hip cross. The normal type of PN cattle in body length and hip width was better than duplication and deletion (p < 0.05). In XN cattle, the deletion type of CNV had superior growth characteristics in heart girth and cannon bone circumference compared with the duplication type and the normal type (p < 0.05). CONCLUSION: The study revealed a significant association between CNV of CCDC39 gene and growth traits in different Chinese cattle breeds.

Copy number variations of TOP2B gene are associated with growth traits in Chinese sheep breeds.

Copy number variations are primary source of genetic variations, which are associated with essential traits in many organisms. During recent years, there have been numerous research works that reveal functions of CNV. However, these studies provide only several references about copy number variations in the sheep genome. In this study, we examined the copy number variation of the TOP2B gene in three Chinese sheep breeds (Chaka sheep, Hu sheep, Small-tailed Han sheep) and performed correlation analysis with growth traits, to detect the influence of CNVs. TOP2B copy numbers were divided into three distribution groups (gain, median, loss) in three Chinese sheep breeds. The distribution amount of copy number < 2 of TOP2B CNVs was dominant in all sheep breeds. The statistical analysis showed that TOP2B CNV had a significant effect on body length in CK sheep (p < 0.05), and effects on chest circumference, canon circumference (p < 0.05) in HU sheep. CNVs in STH sheep breed were relevant to chest circumference and height of hip cross (p < 0.05). These results confirmed the relationship between CNV of TOP2B gene and growth traits in three sheep breeds, and provide a reliable reference for sheep breeding.

Effect of Dietary Protein Levels on Dynamic Changes and Interactions of Ruminal Microbiota and Metabolites in Yaks on the Qinghai-Tibetan Plateau.

To improve performance and optimize rumen function in yaks (Bos grunniens), further knowledge on the appropriate dietary protein levels for ruminal microbiota and the metabolite profiles of yaks in feedlot feeding is necessary. Current understanding of dietary protein requirements, ruminal microbiota, and metabolites is limited. In this study, yaks were fed a low-protein diet (L; 9.64%), middle low-protein diet (ML; 11.25%), middle high-protein diet (MH; 12.48%), or a high-protein diet (H; 13.87%), and the effects of those diets on changes and interactions in ruminal microbiota and metabolites were investigated. Twenty-four female yaks were selected, and the effects on ruminal microbiota and metabolites were investigated using 16s rRNA gene sequencing and gas chromatography time-of-flight/mass spectrometry (GC-TOF/MS). Diets containing different protein levels changed the composition of the rumen bacterial community, the H group significantly reduced the diversity of ruminal microbiota (p < 0.05), and the number of shared amplicon sequence variants (ASVs) between the H group and the other three groups was lower, suggesting that the ruminal microbiota community fluctuated more with a high-protein diet. In rumen, Bacteroidetes, Firmicutes, and Proteobacteria were the most abundant bacteria at the phylum level, and Bacteroidetes was significantly less abundant in the MH group than in the L and ML groups (p < 0.05). Prevotella_1, Rikenellaceae_RC9_gut_group, and Christensenellaceae_R-7_group had the highest abundance at the genus level. Prevotellaceae was enriched in the low-protein groups, whereas Bacteroidales_BS11_gut_group was enriched in the high-protein groups. Rumen metabolite concentrations and metabolic patterns were altered by dietary protein levels: organic acid metabolites, antioxidant-related metabolites, and some plant-derived metabolites showed variation between the groups. Enrichment analysis revealed that significant changes were concentrated in six pathways, including the citrate cycle (TCA cycle), glyoxylate and dicarboxylate metabolism, and butanoate metabolism. Network analysis showed promotion or restraint relationships between different rumen microbiota and metabolites. Overall, the rumen function was higher in the MH group. This study provides a reference for appropriate dietary protein levels and improves understanding of rumen microbes and metabolites.

Bacterial Community Characteristics in the Gastrointestinal Tract of Yak (Bos grunniens) Fully Grazed on Pasture of the Qinghai-Tibetan Plateau of China.

In the current research, samples of yak gastrointestinal tracts (GITs) were used to profile the bacterial compositional characteristics using high through-put sequencing technology of 16S RNA amplicon. A total of 6959 OTUs was obtained from 20,799,614 effective tags, among which 751 OTUs were shared by ten sections. A total of 16 known phyla were obtained in all samples-the most abundant phyla were Firmicutes (34.58%), Bacteroidetes (33.96%) and Verrucomicrobia (11.70%). At the genus level, a total of 66 genera were obtained-Rikenellaceae_RC9_gut_group (7.24%), Akkermansia (6.32%) and Ruminococcaceae_UCG-005 (6.14%) were the most abundant. Species of Observed (Sob), Shannon and Chao values of the Stomach were the greatest, followed by the large intestine, while small intestine had the lowest diversity (p < 0.05). Bacteroidete were more abundant in sections from rumen to duodenum; while Firmicutes were the most abundant in sections from jejunum. ABC transporters (7.82%), Aminoacyl-tRNA biosynthesis (4.85%) and Purine metabolism (3.77%) were the most abundant level-3 pathways in all samples. The results of associated correlation analysis indicated that rectum samples might be used as an estimator of rumen bacterial communities and fermentation. The results of this research enrich the current knowledge about the unique animals of the QTP and extend our insight into GITs microecology of various animals.

Characterization of the bacterial microbiota across the different intestinal segments of the Qinghai semi-fine wool sheep on the Qinghai-Tibetan Plateau.

OBJECTIVE: The intestinal microbiota enhances nutrient absorption in the host and thus promotes heath. Qinghai semi-fine wool sheep is an important livestock raised in the Qinghai-Tibetan Plateau; however, little is known about the bacterial microbiota of its intestinal tract. The aim of this study was to detect the microbial characterization in the intestinal tract of the Qinghai semi-fine wool sheep. METHODS: The bacterial profiles of the six different intestinal segments (duodenum, jejunum, ileum, cecum, colon and rectum) of Qinghai semi-fine wool sheep were studied using 16S rRNA V3-V4 hypervariable amplicon sequencing. RESULTS: A total of 2,623,323 effective sequences were obtained, and 441 OTUs shared all six intestinal segments. The bacterial diversity was significantly different among the different intestinal segments, and the large intestine exhibited higher bacterial diversity than the small intestine. Firmicutes, Bacteroidetes, and Patescibacteria were the dominant phyla in these bacterial communities. Additionally, at the genus level, Prevotella_1, Candidatus_ Saccharimonas, and Ruminococcaceae_UCG-005 were the most predominant genus in duodenal segment, jejunal and ileal segments, and cecal, colonic, and rectal segments, respectively. We predicted that the microbial functions and the relative abundance of the genes involved in carbohydrate metabolism were overrepresented in the intestinal segments of Qinghai semi-fine wool sheep. CONCLUSION: The bacterial communities and functions differed among different intestinal segments. Our study is the first to provide insights into the composition and biological functions of the intestinal microbiota of Qinghai semi-fine wool sheep. Our results also provide useful information for the nutritional regulation and production development in Qinghai semi-fine wool sheep.

MiR-452 Regulates C2C12 Myoblast Proliferation and Differentiation via Targeting ANGPT1.

microRNAs are a kind of endogenous, non-coding, single-strand small RNA. They have been reported as an important regulatory factor in skeletal myogenesis. In this study, miR-452 was selected from RNA high-throughput sequencing data to explore its regulatory role in myogenesis. Functionally, miR-452 overexpression could promote C2C12 myoblast proliferation while inhibiting myogenic differentiation. On the contrary, inhibition of miR-452 could suppress C2C12 myoblast proliferation but accelerate myogenic differentiation. Bioinformatics analysis and dual luciferase report assays showed that Angiopoietin 1 (ANGPT1), RB1, and CACNB4 were the potential target genes of miR-452. To further confirm the target relationship between ANGPT1, RB1, and CACNB4 with miR-452, the mRNA level and protein level of these genes were detected by using RT-qPCR and Western blot, respectively. Result analysis indicated that ANGPT1 was a target gene of miR-452. In addition, knockdown of ANGPT1 could obviously promote C2C12 myoblast proliferation but block their differentiation. In summary, these results demonstrated that miR-452 promoted C2C12 myoblast proliferation and inhibited their differentiation via targeting ANGPT1.