9 results on '"Zhao, Shengguo"'
Search Results
2. Synergistic Responses of Tibetan Sheep Rumen Microbiota, Metabolites, and the Host to the Plateau Environment.
- Author
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Sha Y, Guo X, He Y, Li W, Liu X, Zhao S, Hu J, Wang J, Li S, Zhao Z, and Hao Z
- Subjects
- Animals, Sheep, Tibet, Metabolome, Amino Acids metabolism, Rumen chemistry, Microbiota
- Abstract
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.
- Published
- 2023
- Full Text
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3. Rumen Epithelial Development- and Metabolism-Related Genes Regulate Their Micromorphology and VFAs Mediating Plateau Adaptability at Different Ages in Tibetan Sheep.
- Author
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Sha Y, He Y, Liu X, Zhao S, Hu J, Wang J, Li S, Li W, Shi B, and Hao Z
- Subjects
- Sheep genetics, Animals, Tibet, Ruminants, Fermentation, Rumen chemistry, Microbiota
- Abstract
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.
- Published
- 2022
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- View/download PDF
4. Response of Ruminal Microbiota-Host Gene Interaction to High-Altitude Environments in Tibetan Sheep.
- Author
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Sha Y, Ren Y, Zhao S, He Y, Guo X, Pu X, Li W, Liu X, Wang J, and Li S
- Subjects
- Sheep, Animals, Propionates metabolism, RNA, Ribosomal, 16S genetics, RNA, Ribosomal, 16S metabolism, Altitude, Host Microbial Interactions, Tibet, Fatty Acids, Volatile metabolism, Acetates metabolism, Immunoglobulin A metabolism, Immunoglobulin G metabolism, Immunoglobulin M metabolism, Rumen chemistry, Microbiota
- Abstract
Altitude is the main external environmental pressure affecting the production performance of Tibetan sheep, and the adaptive evolution of many years has formed a certain response mechanism. However, there are few reports on the response of ruminal microbiota and host genomes of Tibetan sheep to high-altitude environments. Here, we conducted an integrated analysis of volatile fatty acids (VFAs), microbial diversity (16S rRNA), epithelial morphology, and epithelial transcriptome in the rumen of Tibetan sheep at different altitudes to understand the changes in ruminal microbiota−host interaction in response to high altitude. The differences in the nutritional quality of forage at different altitudes, especially the differences in fiber content (ADF/NDF), led to changes in rumen VFAs of Tibetan sheep, in which the A/P value (acetic acid/propionic acid) was significantly decreased (p < 0.05). In addition, the concentrations of IgA and IgG in Middle-altitude (MA) and High-altitude Tibetan sheep (HA) were significantly increased (p < 0.05), while the concentrations of IgM were significantly increased in MA (p < 0.05). Morphological results showed that the width of the rumen papilla and the thickness of the basal layer increased significantly in HA Tibetan sheep (p < 0.05). The 16S rRNA analysis found that the rumen microbial diversity of Tibetan sheep gradually decreased with increasing altitude, and there were some differences in phylum- and genus-level microbes at the three altitudes. RDA analysis found that the abundance of the Rikenellaceae RC9 gut group and the Ruminococcaceae NK4A214 group increased with altitudes. Furthermore, a functional analysis of the KEGG microbial database found the “lipid metabolism” function of HA Tibetan sheep to be significantly enriched. WGCNA revealed that five gene modules were enriched in “energy production and conversion”, “lipid transport and metabolism”, and “defense mechanisms”, and cooperated with microbiota to regulate rumen fermentation and epithelial immune barrier function, so as to improve the metabolism and immune level of Tibetan sheep at high altitude.
- Published
- 2022
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5. Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation.
- Author
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Liu S, Moon CD, Zheng N, Huws S, Zhao S, and Wang J
- Subjects
- Bacteria genetics, Genomics, Metagenomics methods, Metagenome genetics, Microbiota genetics
- Abstract
Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract., (© 2022. The Author(s).)
- Published
- 2022
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6. Activity- and Enrichment-Based Metaproteomics Insights into Active Urease from the Rumen Microbiota of Cattle.
- Author
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Zhang X, Xiong Z, Li M, Zheng N, Zhao S, and Wang J
- Subjects
- Amino Acid Sequence, Animals, Cattle, Enzyme Activation, Models, Molecular, Protein Conformation, Structure-Activity Relationship, Urease chemistry, Metagenomics methods, Microbiota, Proteomics methods, Rumen microbiology, Urease metabolism
- Abstract
Regulation of microbial urease activity plays a crucial role in improving the utilization efficiency of urea and reducing nitrogen emissions to the environment for ruminant animals. Dealing with the diversity of microbial urease and identifying highly active urease as the target is the key for future regulation. However, the identification of active urease in the rumen is currently limited due to large numbers of uncultured microorganisms. In the present study, we describe an activity- and enrichment-based metaproteomic analysis as an approach for the discovery of highly active urease from the rumen microbiota of cattle. We conducted an optimization method of protein extraction and purification to obtain higher urease activity protein. Cryomilling was the best choice among the six applied protein extraction methods (ultrasonication, bead beating, cryomilling, high-pressure press, freeze-thawing, and protein extraction kit) for obtaining protein with high urease activity. The extracted protein by cryomilling was further enriched through gel filtration chromatography to obtain the fraction with the highest urease activity. Then, by using SDS-PAGE, the gel band including urease was excised and analyzed using LC-MS/MS, searching against a metagenome-derived protein database. Finally, we identified six microbial active ureases from 2225 rumen proteins, and the identified ureases were homologous to those of Fibrobacter and Treponema . Moreover, by comparing the 3D protein structures of the identified ureases and known ureases, we found that the residues in the β-turn of flap regions were nonconserved, which might be crucial in influencing the flexibility of flap regions and urease activity. In conclusion, the active urease from rumen microbes was identified by the approach of activity- and enrichment-based metaproteomics, which provides the target for designing a novel efficient urease inhibitor to regulate rumen microbial urease activity.
- Published
- 2022
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7. Substitution of residues in UreG to investigate UreE interactions and nickel binding in a predominant urease gene cluster from the ruminal metagenome.
- Author
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Zhang X, Zhao S, He Y, Zheng N, Yan X, and Wang J
- Subjects
- Amino Acid Sequence, Animals, Binding Sites, Gene Expression, Phylogeny, Protein Binding, Recombinant Proteins, Urease genetics, Metagenome, Metagenomics methods, Microbiota, Multigene Family, Nickel chemistry, Ruminants microbiology, Urease chemistry
- Abstract
Microbial ureases catalyze the hydrolysis of urea to ammonia, and inhibition of these enzymes in rumen has the potential to improve urea utilization efficiency and reduce urinary nitrogen excretion. Urease activity is catalyzed by a protein complex encoded by a gene cluster, and its accessory proteins (especially UreE and UreG) play important roles in transferring nickel to the active site for urease maturation. In this study, a predominant urease gene cluster (5290 bp) from the ruminal microbial metagenome was identified. Isothermal titration calorimetry (ITC) and analytical ultracentrifugation (AUC) analyses showed that the reaction of identified UreE with UreG was endothermic, and was dominated by a hydrophobic interaction, in which each UreE dimer bound 2 M equivalents of UreG monomer to form a UreE
2 -2UreG complex. Mutagenesis analyses showed that the UreG residues Glu-23, Asp-41, Glu-46, Glu-66, Cys-70, His-72, Asp-78, and Asp-118 were involved in the GTPase activity of UreG. Furthermore, variants of Cys-70 and His-72 involved in CPH motif of UreG, as well as the nearby Glu-66 and Asp-78, not only prevented interactions with UreE, but also prevented nickel binding. These data provide additional information regarding UreG residues that may be targeted for the design of new urease inhibitors., Competing Interests: Declaration of competing interest The authors declare no conflict of interest., (Copyright © 2020 Elsevier B.V. All rights reserved.)- Published
- 2020
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8. Impacts of Milking and Housing Environment on Milk Microbiota.
- Author
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Du, Bingyao, Meng, Lu, Liu, Huimin, Zheng, Nan, Zhang, Yangdong, Guo, Xiaodong, Zhao, Shengguo, Li, Fadi, and Wang, Jiaqi
- Subjects
ANIMAL herds ,RAW milk ,FARM management ,MILKING ,DAIRY processing ,MILK quality - Abstract
Simple Summary: Microbiota can enter and persist in raw milk at several stages of the farming chain. The development of culture-independent methods and high-throughput DNA sequencing techniques have improved the approach to study microbiota communities in milk and milk products. This work aimed to determine the effects of farming environments on milk microbiota using the high-throughput DNA sequencing technique, and to elucidate the relationship among the microbiota. The effects of the farming environment on the microbiota in milk can guide farm and management practices to ensure that the milk is not contaminated with bacteria during milking and processing, thereby improving the quality of the milk. The aim of the present study was to determine the effects of farming environments on microbiota in raw milk and to assess the relationship among microbes by 16S rRNA sequencing methods. Samples of raw milk, cow trough water, teat dip cup, teat, teat liner, dairy hall air, cowshed air, feces, feed, and bedding from two farms were collected. The two highest abundant bacterial groups of Moraxellaceae and Staphylococcaceae were found in milk and teat liner samples, respectively, at Zhengzhou farm, Henan Province. Moreover, the two highest abundant bacterial groups of Enterobacteriaceae and Moraxellaceae were found in milk and teat dip cup samples, respectively, at Qiqihar farm, Heilongjiang Province. Source Tracker analysis revealed that the teat liner and teat dip cup were the most important contributors of microbes in milk samples at Zhengzhou farm and Qiqihar farm, respectively, which could be attributed to the management level of the farm. Therefore, disinfection and cleaning procedures should be developed to improve the quality of raw milk. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
9. A Novel Urease Inhibitor of Ruminal Microbiota Screened through Molecular Docking.
- Author
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Zhang, Zhenyu, Li, Ming, Zhang, Xiaoyin, Zheng, Nan, Zhao, Shengguo, and Wang, Jiaqi
- Subjects
MOLECULAR docking ,UREASE ,UREA as fertilizer ,URINARY tract infections ,PROPIONIC acid ,NITROGEN fertilizers - Abstract
Inhibition of the urease activity of ruminal microbiota is not only beneficial for increasing dietary and endogenic urea-N utilization efficiency in ruminants but also might be applicable for the preservation of nitrogen fertilizer in soil and treatment of gastrointestinal and urinary tract infections caused by ureolytic bacteria. To discover urease inhibitors to efficiently target ruminal microbiota, the identified ruminal microbial metagenomic urease gene was used to construct a homology model to virtually screen urease inhibitors from the ChemDiv database by molecular docking. The GMQE and QMEAN values of the homology model were 0.85 and −0.37, respectively, indicating a good model quality. The inhibition effect of the screened urease inhibitor for ruminal urea degradation was assessed by ruminal microbial fermentation in vitro. The toxic effect of the candidate inhibitor was performed using gut Caco-2 cells in vitro. The results showed that compound 3-[1-[(aminocarbonyl)amino]-5-(4-methoxyphenyl)-1H-pyrrol-2-yl] propanoic acid (ChemDiv_ID: 6238-0047, IC
50 = 65.86 μM) was found to be the most effective urease inhibitor among the candidate compounds. Compound 6238-0047 significantly lowered the amount of urea degradation and ammonia production in ruminal microbial fermentation. The 24 h degradation rate of compound 6238-0047 in ruminal microbial fermentation was 3.32%–16.00%. In addition, compound 6238-0047 (10–100 μM) had no significant adverse effect on the cell viability of Caco-2 cells. Molecular docking showed that compound 6238-0047 could interact with Asp359 in the active site and Cys318 in the flap region by the hydrogen bond and Pi-Alkyl interaction, respectively. Compound 6238-0047 could be used as a novel inhibitor for decreasing the urease activity of ruminal microbiota. [ABSTRACT FROM AUTHOR]- Published
- 2020
- Full Text
- View/download PDF
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