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Genetic and Functional Differences of Escherichia coli Strains from Colorectal Cancer Mucosal Tissues

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Engineering 2022年第9期16卷 210-219页

作者： Yuxiao Chang Xiang Li Lei Ding Chao Yang Zhiyuan Pan Ni Han Yujun Cui Fachao Zhi Ruifu Yang Hong Gao yujing bi State Key Laboratory of Pathogen and biosecurity Beijing Institute of Microbiology and EpidemiologyBeijing 100071China Beijing Shijitan Hospital Capital Medical UniversityBeijing 100038China Guangdong Provincial Key Laboratory of Gastroenterology Institute of Gastroenterology of Guangdong Province&Department of GastroenterologyNanfang HospitalSouthern Medical UniversityGuangzhou 510515China Shenzhen Center for Disease Control and Prevention Shenzhen 518055China

Colorectal cancer(CRC)is the third leading cancer *** has been widely used to analyze the association between the gut microbiota and CRC based on bacterial genus-or species-level comparisons,providing evidence of dysbiosis in CRC ***,this kind of analysis is unable to provide strain-level information for understanding the individual role of a species in ***,we used culturomics to isolate CRC mucosal samples and selected 158 Escherichia coli strains to reveal their differences in both genomics and functions by means of phylogenetic analysis and inflammatory induction based on cell and animal *** genomic comparison,these strains were divided into five *** representative strains of each phylogroup significantly induced different levels of cytokine secretion by human leukemic monocyte(THP-1 cell)-based Transwell and animal *** bioinformatic analysis revealed different profiles of single-nucleotide polymorphisms,genes,and metabolic pathways in the different phylogroups,which can improve the current understanding of the phenotypic differences between these *** strain differences revealed in both genomics and functions indicate that the microbiota’s function at the strain level should be investigated in order to understand the interacting mechanisms between hosts and gut bacteria.

关键词： Colorectal cancer Gut microbiota Culturomics Escherichia coli Strain level

Arabidopsis SYP121 acts as an ROP2 effector in the regulation of root hair tip growth

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Molecular Plant 2022年第6期15卷 1008-1023页

作者： Xiankui Cui Shuwei Wang Yaohui Huang Xuening Ding Zirong Wang Lidan Zheng yujing bi Fanghui Ge Lei Zhu Ming Yuan Shaul Yalovsky Ying Fu State Key Laboratory of Plant Physiology and biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China Joint Laboratory for International Cooperation in Crop Molecular Breeding Ministry of EducationChina Agricultural UniversityBeijing 100193China Department of Plant Sciences Tel Aviv UniversityTel Aviv 69978Israel

Tip growth is an extreme form of polarized cell expansion that occurs in all eukaryotic kingdoms to generate highly elongated tubular cells with specialized functions, including fungal hyphae, animal neurons, plant pollen tubes, and root hairs (RHs). RHs are tubular structures that protrude from the root epidermis to facilitate water and nutrient uptake, microbial interactions, and plant anchorage. RH tip growth requires polarized vesicle targeting and active exocytosis at apical growth sites. However, how apical exocytosis is spatially and temporally controlled during tip growth remains elusive. Here, we report that the Qa-Soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) SYP121 acts as an effector of Rho of Plants 2 (ROP2), mediating the regulation of RH tip growth. We show that active ROP2 promotes SYP121 targeting to the apical plasma membrane. Moreover, ROP2 directly interacts with SYP121 and promotes the interaction between SYP121 and the R-SNARE VAMP722 to form a SNARE complex, probably by facilitating the release of the Sec1/Munc18 protein SEC11, which suppresses the function of SYP121. Thus, the ROP2-SYP121 pathway facilitates exocytic trafficking during RH tip growth. Our study uncovers a direct link between an ROP GTPase and vesicular trafficking and a new mechanism for the control of apical exocytosis, whereby ROP GTPase signaling spatially regulates SNARE complex assembly and the polar distribution of a Q-SNARE.

关键词： ROP GTPase SYP121 SNARE protein exocytosis root hair tip growth

Crucial role of histone deacetylase SIRT1 in myeloid-derived suppressor cell-mediated reprogramming of CD4^(+) T-cell differentiation

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Cellular & Molecular Immunology 2020年第7期17卷 785-787页

作者： Lin Dong yujing bi Anna Jia Qing Yu Yuexin Wang Yufei Wang Qiuli Yang Yejin Cao Ying He Ruichen Liu Yan Li Guangwei Liu Key Laboratory of Cell Proliferation and Regulation biology Ministry of EducationInstitute of Cell BiologyCollege of Life SciencesBeijing Normal University100875 BeijingChina State Key Laboratory of Pathogen and biosecurity Beijing Institute of Microbiology and Epidemiology100071 BeijingChina

Myeloid-derived suppressor cells(MDSCs)are heterogeneous,immature myeloid cells that inhibit the immune responses of T cells.1–5 MDSCs play a crucial role in infection,6,7 transplantation,8,9 autoimmune diseases10,11,and tumors12,13 by driving the differentiation of specific T-cell subsets,but the precise regulatory mechanism is still ***,our results showed that SIRT1,a histone deacetylase,suppresses the functions of proinflammatory MDSCs and promotes tumor growth.14 However,it remains unclear whether SIRT1 regulates the MDSC-induced differentiation of T ***,we identified the regulatory effects of SIRT1 in CD11b+Gr1+MDSCs on T-cell differentiation.

关键词： SIRT1 CD11b myeloid

Alterations in gut microbiota and metabolites associated with altitude-induced cardiac hypertrophy in rats during hypobaric hypoxia challenge

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Science China(Life Sciences) 2022年第10期65卷 2093-2113页

作者： Zhiyuan Pan Yichen Hu Zongyu Huang Ni Han Yan Li Xiaomei Zhuang Jiye Yin Hui Peng Quansheng Gao Wenpeng Zhang Yong Huang Yujun Cui yujing bi Zhenjiang Zech Xu Ruifu Yang State Key Laboratory of Pathogen and biosecurity Beijing Institute of Microbiology and EpidemiologyBejing 10o071China State Key Laboratory of Food Science and Technology Nanchang UniversityNanchang 330047China State Key Laboratory of Toxicology and Medical Countermeasures Beijing Institute of Pharmacology and ToxicologyBejing 100850China Tianjin Institute of Environmental&Operational Medicine Tianjin 300050China Microbiome Medicine Center Department of Laboratory MedicineZhujiang HospitalSouthern Medical UniversityGuangzhou510280China

The gut microbiota is involved in host responses to high ***,the dynamics of intestinal microecology and their association with altitude-related illness are poorly ***,we used a rat model of hypobaric hypoxia challenge to mimic plateau exposure and monitored the gut microbiome,short-chain fatty acids(SCFAs),and bile acids(BAs)over 28 *** identified weight loss,polycythemia,and pathological cardiac hypertrophy in hypoxic rats,accompanied by a large compositional shift in the gut microbiota,which is mainly driven by the bacterial families of Prevotellaceae,Porphyromonadaceae,and *** aberrant gut microbiota was characterized by increased abundance of the Parabacteroides,Alistipes,and Lactococcus genera and a larger Bacteroides to Prevotella ***-omics analyses showed that the gut microbiome was significantly correlated with the metabolic abnormalities of SCFAs and BAs in feces,suggesting an interaction network remodeling of the microbiome-metabolome after the hypobaric hypoxia ***,the transplantation of fecal microbiota significantly increased the diversity of the gut microbiota,partially inhibited the increased abundance of the Bacteroides and Alistipes genera,restored the decrease of plasma propionate,and moderately ameliorated cardiac hypertrophy in hypoxic *** results provide an insight into the longitudinal changes in intestinal microecology during the hypobaric hypoxia *** in the gut microbiota and microbial metabolites contribute to the development of high-altitude heart disease in rats.

关键词： high altitude gut microbiota short-chain fatty acids bile acids hypobaric hypoxia cardiac hypertrophy

Glucocorticoid receptor promotes the function of myeloid-derived suppressor cells by suppressing HIF1α-dependent glycolysis

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Cellular & Molecular Immunology 2018年第6期15卷 618-629页

作者： Yun Lu Huanrong Liu yujing bi Hui Yang Yan Li Jian Wang Zhengguo Zhang Yu Wang Chunxiao Li Anna Jia Linian Han Ying Hu Yong Zhao Ruoning Wang Guangwei Liu Department of Immunology School of Basic Medical SciencesFudan UniversityShanghai 200032China Key Laboratory of Cell Proliferation and Regulation biology of Ministry of Education Institute of Cell BiologyCollege of Life SciencesBeijing Normal UniversityBeijing 100875China State Key laboratory of Pathogen and biosecurity Beijing Institute of Microbiology and EpidemiologyBeijing 100071China State Key Laboratory of Membrane biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Center for Childhood Cancer and Blood Diseases Hematology/Oncology and BMTThe Research Institute at Nationwide Children's HospitalOhio State UniversityColumbusOhio 43205USA

Immunomodulatory signaling imposes tight regulations on metabolic programs within immune cells and consequentially determines immune response *** the glucocorticoid receptor(GR)has been recently implicated in regulating the function of myeloid-derived suppressor cells(MDSCs),whether the dysregulation of GR in MDSCs is involved in immune-mediated hepatic diseases and how GR regulates the function of MDSCs in such a context remains ***,we revealed the dysregulation of GR expression in MDSCs during innate immunological hepatic injury(IMH)and found that GR regulates the function of MDSCs through modulating HIF1α-dependent *** modulation of GR by its agonist(dexamethasone,Dex)protects IMH mice against inflammatory ***,GR signaling suppresses HIF1αand HIF1α-dependent glycolysis in MDSCs and thus promotes the immune suppressive activity of *** studies reveal a role of GR-HIF1αin regulating the metabolism and function of MDSCs and further implicate MDSC GR signaling as a potential therapeutic target in hepatic diseases that are driven by innate immune cell-mediated systemic inflammation.

关键词： glucocorticoid-receptor glycolysis innate immunity liver injuries metabolism myeloid-derived suppressive cells tolerance

The kinase AKT1 potentiates the suppressive functions of myeloid-derived suppressor cells in inflammation and cancer

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Cellular & Molecular Immunology 2021年第4期18卷 1074-1076页

作者： Anna Jia Yuexin Wang Yufei Wang Yan Li Qiuli Yang Yejin Cao Ying He Lin Dong Yingjie Dong Yueru Hou Ruoning Wang yujing bi Guangwei Liu Key Laboratory of Cell Proliferation and Regulation biology Ministry of EducationInstitute of Cell BiologyCollege of Life SciencesBeijing Normal UniversityBeijing 100875China Center for Childhood Cancer&Blood Diseases The Research Institute at Nationwide Children'sHospitalOhio State UniversityColumbusOH 43205USA State Key Laboratory of Pathogen and biosecurity Beijing Institute of Microbiology and EpidemiologyBeijing 100071China

Myeloid-derived suppressor cells(MDSCs)are a group of heterogeneous cells1 that play crucial negative regulatory roles in immune-associated diseases,including infections,2 cancer,3 transplantation4,and autoimmunity.5 We and others have shown that mTOR signaling and its downstream metabolic pathways regulate MDSC recruitment and function in inflammation and autoimmunity.

关键词： inflammation suppressor cancer

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人体肠道微生物群、营养与健康

科学通报 2019年第3期64卷 260-271页

作者：毕玉晶杨瑞馥军事科学院军事医学研究院微生物流行病研究所北京100071

人体肠道微生物群是人体消化道系统中栖息的微生物总称.这些微生物与人体长期共进化,形成了一个平衡的微生态系统.人体微生物群与健康和疾病密切相关,被视为人体最大的内分泌"器官".该器官具有调节功能,通过改变微生物群的构成、种类与... 详细信息

人体肠道微生物群是人体消化道系统中栖息的微生物总称.这些微生物与人体长期共进化,形成了一个平衡的微生态系统.人体微生物群与健康和疾病密切相关,被视为人体最大的内分泌"器官".该器官具有调节功能,通过改变微生物群的构成、种类与比例实现维护和恢复人体健康的目的.因此,人体微生物群及其与机体互作平衡网络研究,将为精准医学的诊断、治疗和预后评估带来革命性变化.肠道微生物群与摄入食物营养密切互作,不仅有助于降解食物营养素,还能够合成多种营养素供人体利用.研究者逐步认识到人体、微生物群、营养和免疫存在密切互作关系,因此,解析这一互作网络将为精准营养学的发展带来前所未有的新机遇.本文在总结目前人体肠道微生物群、营养与健康关系研究成果的基础上,从多个视角综述了此交叉领域日新月异的进展.

关键词：肠道微生物群营养健康疾病

IL-17A-dependent gut microbiota is essential for regulating diet-induced disorders in mice

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Science Bulletin 2017年第15期62卷 1052-1063页

作者： yujing bi Chunxiao Li Lin Liu Jiyuan Zhou Zhengchao Li Huimin Deng Chunyan Wu Yanping Han Yajun Song Yafang Tan Xiaoyi Wang Zongmin Du Yujun Cui Yanfeng Yan Fachao Zhi Guangwei Liu Nan Qin Heping Zhang Ruifu Yang State Key laboratory of Pathogen and biosecurity. Beijing Institute of MicrobiologY and Epidemiology Beijing 100071 China Key Laboratory of Cell Proliferation and Regulation biology Ministry of Education Institute of Cell Biology College of Life Science Beijing Normal University Beijing 100875 China State Key Laboratory for Diagnosis and Treatment of Infectious Disease The First Affiliated Hospital College of Medicine Zhejiang University Hangzhou 310003 China Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases Zhejiang University Hangzhou 310003 China Guangdong Provincial Key Laboratory of Gastroenterology Institute of Gastroenterology of Guangdong Province Department of Gastroenterology Nan fang Hospital Southern Medical University Guangzhou 510515 China Realbio Genomics Institute Shanghai 200050 China Key Laboratory of Dairy biotechnology and Engineering Education Ministry of China Inner Mongolia Agricultural University Hohhot 010018 China

The gut microbiota plays a key role in obesity and related metabolic disorders, and multiple factors including diet, host genotype, and age regulate it. Many studies have examined the contribution of extrinsic factors to the regulation of the gut microbiota, but the importance of the host genetic constitution cannot be ignored, lnterleukin 17A （lL-17A）, a pro-inflammatory cytokine, is important in the defense against infection and diseases. Here, we investigated the association among IL-17, a high-fat diet （HFD）, and the gut microbiota. Mice deficient in 1L-17A were resistant to diet-induced obesity and related diseases. Compared with the I1-17a^-/1 mice, wild-type （WT） mice challenged with HFD showed obvious weight fluctuations, such as those seen in type 2 diabetes, and hematological changes similar to those associated with metabolic syndrome. However, housing WT mice and Il-17a^-/- mice together signifi- cantly alleviated these symptoms in the WT mice. A metagenomic analysis of the mouse feces indicated that the microbial community compositions of these two groups differed before HFD feeding. The HFD mediated shifts in the gut microbial compositions, which were associated with the mouse phenotypes. We also identified potentially beneficial and harmful species present during this period, and drew net- works of the most abundant species. A functional analysis indicated pathway changes in the WT and I1-17a^- /- mice when fed the HFD. Collectively, these data underscore the importance of the host factor IL-17A in shaping and regulating the gut microbiota, which conversely, influences the host health.

关键词： Gut microbiota Obesity IL-17A Metagenomics

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肠道微生物群研究的测序与培养组学方法

中华炎性肠病杂志（中英文） 2019年第3期3卷 189-193页

作者：毕玉晶杨瑞馥军事科学院军事医学研究院微生物流行病研究所北京100071

肠道微生物群是定居在宿主消化道内的肠道微生物的总称.研究表明,许多疾病都与肠道菌群的改变密切相关.在复杂生态系统中使用高通量测序技术,即16S rRNA测序及元基因组测序,极大地丰富了肠道微生物组数据库,也鉴定出了很多细菌新种,促... 详细信息

肠道微生物群是定居在宿主消化道内的肠道微生物的总称.研究表明,许多疾病都与肠道菌群的改变密切相关.在复杂生态系统中使用高通量测序技术,即16S rRNA测序及元基因组测序,极大地丰富了肠道微生物组数据库,也鉴定出了很多细菌新种,促进了肠道微生物组与健康和疾病关系的研究.但测序技术也存在明显的不足,如DNA提取差异、引物偏差、测序深度偏差及分析偏性等.而早期被忽略的培养组学研究,由于方法的改进,能培养出更多的肠道细菌,发现了很多测序中无法鉴定到的新物种.这对促进肠道微生物群株水平的研究具有重要的意义.本文主要讨论目前常用的肠道菌群研究的方法及其应用.

关键词：肠道菌群 16S rRNA 测序元基因组培养组学