溶糊精琥珀酸弧菌（Succinivibrio dextrinosolvens）屬于革蘭氏陰性厭氧細(xì)菌,是反芻動物瘤胃中的常見棲息細(xì)菌,并且在高谷物日糧條件下數(shù)量較多。溶糊精琥珀酸弧菌能發(fā)酵淀粉水解產(chǎn)物糊精和麥芽糖,某些溶糊精琥珀酸弧菌菌株能產(chǎn)生高活性脲酶。因此,研究瘤胃溶糊精琥珀酸弧菌的基因組特征及其代謝尿素氮機(jī)制,對于豐富瘤胃微生物氮代謝研究具有重要補(bǔ)充作用。通過厭氧細(xì)菌分離技術(shù),從奶牛瘤胃中分離獲得一株溶糊精琥珀酸弧菌,命名為SD-Z6菌株。通過三代Oxford高通量測序,分析溶糊精琥珀酸弧菌SD-Z6的全基因組序列,并且與該菌種中其他菌株基因組進(jìn)行比較。同時(shí),檢測溶糊精琥珀酸弧菌SD-Z6的形態(tài)特征和生理生化。利用尿素、氨基酸和硫酸銨三種氮源,分析溶糊精琥珀酸弧菌SD-Z6的氮代謝,并利用轉(zhuǎn)錄組方法分析溶糊精琥珀酸弧菌SD-Z6功能基因的變化。結(jié)果表明,溶糊精琥珀酸弧菌SD-Z6的全基因組大小為3.47 Mbp,G+C含量為38.9%�？偣埠�2993個(gè)編碼序列,占98%,其中鑒定出21個(gè)rRNA基因和69個(gè)tRNA。COG功能注釋表明,調(diào)節(jié)碳水化合物（10.6%）和氨基酸（9%）... 

【文章來源】：中國農(nóng)業(yè)科學(xué)院北京市

【文章頁數(shù)】：116 頁

【學(xué)位級別】：博士

【文章目錄】：
摘要
Abstract
Abbreviations
Chapter1.Literature Review
    1.1.Introduction
    1.2.True protein as nitrogen sources for ruminants
        1.2.1.Degradation of protein in the rumen
    1.3.Non– protein nitrogen containing compound for ruminants
    1.4.Urea as protein sources for ruminants
    1.5.Metabolism of Urea/Non-protein nitrogen compound in ruminants
    1.6.Ammonia assimilation and emission
        1.6.1.Glutamate dehydrogenase
        1.6.2.Glutamine synthetase
        1.6.3.Glutamate synthase
    1.7.Factors affecting urea utilization and ammonia assimilation
        1.7.1.Effects of nitrogen Sources
        1.7.2.Effects of nitrogen concentration
        1.7.3.Effect of Energy on ammonia assimilation and NPN utilization
        1.7.4.Effects of enzyme activity inhibitors on Nitrogen metabolism
    1.8.Isolation,identification and characterization of ruminal bacteria
        1.8.1.Culture-dependent methods
        1.8.2.Culture-independent methods
        1.8.3.MALDI-TOF mass spectrometry methods
    1.9.Phenotypic characteristics and importance of Succinivibrio dextrinosolvens
Chapter2.Enrichment,Isolation and Characterization of a ureolytic Succinivibrio dextrinosolvens strain Z6 from rumen of dairy cows
    2.1.Summary
    2.2.Introduction
    2.3.Material Methods
        2.3.1.Media components and Preparation
        2.3.2.Rumen fluid sample collection
        2.3.3.Enrichment and isolation cultures
        2.3.4.DNA isolation and PCR Amplification
        2.3.5.Matrix assisted laser desorption ionization time of flight mass spectrometry(MALDI-TOF MS)analysis
        2.3.6.Phenotypic and Chemotaxonomic Characterization
    2.4.Result
        2.4.1.Isolation and enrichment
        2.4.2.Phenotypic and chemotaxonomic characterization
    2.5.Discussion
    2.6.Conclusion
Chapter3.Complete genome sequence and identification of gene related to nitrogen metabolism of Succinivibrio dextrinosolvens strain Z6
    3.1.Summary
    3.2.Introduction
    3.3.Material and methods
        3.3.1.Bacterial Culture Conditions
        3.3.2.Genomic DNA Extraction
        3.3.3.Whole genome sequencing and analysis
    3.4.Results
        3.4.1.Complete genome of S.dextrinosolvens Z6
        3.4.2.Comparative Genome Analysis of S.dextrinosolvens strains
        3.4.3.Genes involved in nitrogen metabolism in S.dextrinosolvens Z6
    3.5.Discussion
    3.6.Conclusion
Chapter4.Effects of different nitrogen sources on the transcriptional regulation of nitrogen metabolism and the corresponding expression of genes to enzymatic activities in Succinivibrio dextrinosolvens strain Z6
    4.1.Summary
    4.2.Introduction
    4.3.Material and methods
        4.3.1.Bacteria and culture conditions
        4.3.2.Experimental design
        4.3.3.Nitrogen Metabolism
        4.3.4.Sampling technique
        4.3.5.Chemical and Enzyme activity analysis
        4.3.6.Transcriptomic analysis
        4.3.7.KEGG pathway enrichment
        4.3.8.Validation of DEGs using quantitative real time PCR
        4.3.9.Statistical analysis
        4.3.10.Data availability
    4.4.Results
        4.4.1.Nitrogen Metabolism of S.dextrinosolvens Z6 in different nitrogen sources
        4.4.2.Different nitrogen sources utilization and Ammonia concentration
        4.4.3.Ammonia assimilation of S.dextrinosolvens Z6 in different nitrogen sources
        4.4.4.RNA sequencing and read mapping
        4.4.5.Quantitative Real Time PCR validation
        4.4.6.Transcriptomic analysis of genes in response to different nitrogen sources
        4.4.7.KEGG pathway enrichment analysis of differentially expressed gene
    4.5.Discussion
    4.6.Conclusion
Chapter5.General conclusion
References
Appendix
Acknowledgements
Author Resume



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