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Washed microbiota transplantation *** fecal microbiota transplantation:clinical findings,animal studies and in vitro screening

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Protein & Cell 2020年第4期11卷 251-266页

作者： Ting Zhang Gaochen Lu Zhe Zhao Yafei Liu Quan Shen Pan Li Yaoyao Chen Haoran Yin Huiquan Wang Cicilia Marcella Bota Cui Lei Cheng Guozhong Ji Faming Zhang Medical Center for Digestive Diseases The Second Affiliated Hospital of Nanjing Medical UniversityNanjing 210011China key lab of Holistic Integrative Enterology Nanjing Medical UniversityNanjing 210011China tianjin key laboratory of Optoelectronic Detection Technology and Systems Tianjin 300387China Department of microbiology School of MedicineJiangsu UniversityZhenjiang 212013China Biogas Institute of Ministry of Agriculture and Rural Affairs Chengdu 610041China Center for Anaerobic Microbial Resources of Sichuan Province Chengdu 610041China Division of Microbiotherapy Sir Run Run Shaw HospitalNanjing Medical UniversityNanjing 211166China

Fecal microbiota transplantation(FMT)by manual preparation has been applied to treat diseases for thousands of ***,this method still endures safety risks and challenges the psychological endurance and acceptance of doctors,patients and *** evidence showed the washed microbiota preparation with microfiltration based on an automatic purification system followed by repeated centrifugation plus suspension for three times significantly reduced FMT-related adverse *** washing preparation makes delivering a precise dose of the enriched microbiota feasible,instead of using the weight of *** injection in mice with the fecal microbiota supernatant obtained after repeated centrifugation plus suspension for three times induced less toxic reaction than that by the first centrifugation following the *** toxic reactions that include death,the change in the level of peripheral white blood cells,and the proliferation of germinal center in secondary lymphoid follicles in spleen were *** metagenomic next-generation sequencing(NGS)indicated the increasing types and amount of viruses could be washed out during the washing *** analysis indicated metabolites with pro-inflammatory effects in the fecal microbiota supernatant such as leukotriene B4,corticosterone,and prostaglandin G2 could be removed by repeated ***-infrared absorption spectroscopy could be served as a rapid detection method to control the quality of the *** conclusion,this study for the first time provides evidence linking clinical findings and animal experiments to support that washed microbiota transplantation(WMT)is safer,more precise and more quality-controllable than the crude FMT by manual.

关键词： fecal microbiota transplantation washed microbiota transplantation adverse event safety infection virus metabolomics spectroscopy transplant

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Metabolic responses of indigenous bacteria in chicken faeces and maggots to multiple antibiotics via heavy water labeled single-cell Raman spectroscopy

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Journal of Environmental Sciences 2022年第3期34卷 394-402页

作者： Oladipo Oladiti Olaniyi Hongzhe Li Yongguan Zhu Li Cui key lab of Urban Environment and Health Institute of Urban EnvironmentChinese Academy of SciencesXiamen 361021China Department of microbiology Federal University of TechnologyPMB 704 AkureNigeria University of Chinese Academy of Sciences Beijing 100049China

The use of maggots derived from chicken faeces as fish diets might serve as a vehicle for the widespread of multiple antibiotic resistant bacteria(ARB) in the environment. Heavy water labeled single-cell Raman spectroscopy(D_(2)O-Raman) was applied to detect the metabolic responses of indigenous bacteria in chicken faeces and maggots to different concentrations of combined colistin, kanamycin, and vancomycin. By incubating the samples with D_(2)O and antibiotics, metabolically active bacterial cells to antibiotics were distinguished from those inactive by the exhibition of C-D Raman band. Using the C-D band as a universal metabolic biomarker, 96% and 100% of cells in chicken faeces and maggots were revealed to be metabolically active to 1 × minimum inhibition concentration(MIC) of the aforementioned antibiotics. A noticeable decrease in the percentage of active cells from 96% to 76% in faeces and 100% to 93% in maggots was observed at 5 × MIC of antibiotics. However, these ratios were still far above that obtained from the same faeces(1.84%) and maggots(0.51%) samples using a cultivation method, indicating the wide presence of nongrowing but metabolically active bacterial cells under antibiotic treatment. Conclusively, the cultureindependent D_(2)O-Raman approach detected and quantified a large portion of metabolically active indigenous bacteria to multiple antibiotics in their native environments, illustrating the great potential risks of these active cells to spread antibiotic resistance via food chain.

关键词： Chicken faeces and maggot Antibiotic resistance Heavy water-Raman spectroscopy Single-cell Metabolically active cells

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Mixed surfactant washing of petroleum contaminants from the soils and sediments in the unsaturated zone

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Journal of Environmental Sciences 2000年第1期12卷 110-116页

作者： Xia, Xing-Hui Lin, Li Xu, Jia-Lin Institute of Environmental Sciences Beijing Normal University State Key Jt. Lab. Environ. S. Beijing 100875 China Institute of microbiology Chinese Academy of Sciences Beijing 100080 China

A laboratory study was conducted to evaluate the suitability of a mixed surfactant for washing oil from soils in the unsaturated zone. The commercial surfactant used for making mixed surfactant were alcohol polyethoxylate (AEO\|9, nonionic) and sodium alcohol polyethoxylated ethers sulfate (AES, anionic). Based on the properties (critical micelle concentration, hydrophilic/ lipophilic balance and surface tension) of individual surfactants and the mixed surfactant, the preferred composition of an aqueous mixed surfactant solution was determined which consisted of 0 5% AEO\|9 and 0 1% AES. The batch washing experiments have shown that the removal efficiency of oil from soils with mixed surfactant was higher than that with individual surfactants. Soil column washing results have shown that the sequence of oil removal efficiency was mixed surfactant (0.5% AEO\|9 and 0.1% AES)>AEO\|9 (0.1%)>AES (0.2%)>water, and the ratio was 1∶0 84∶0 66∶0 06. Biodegradation experiments by growth cells and resting cells were carried out to evaluate the environmental acceptability of the test surfactants. The results have shown that the surfactants were able to serve as sole carbon source for strains Pseudomonos sp. 52 and Weeksella sp. 6 which were isolated from petroleum contaminated soil. More than 90% of the parent mixed surfactants disappeared in two weeks under growth cell conditions.

关键词： surfactant petroleum contaminants the unsaturated zone remediation CLC number: X53 Document code: A

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LSQP‑DB:a species‑specific quantitative PCR primer database for 307 Lactobacillaceae species

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Systems microbiology and Biomanufacturing 2023年第4期3卷 593-601页

作者： Rubing Du Shilei Wang Qun Wu Yan Xu lab of Brewing microbiology and Applied Enzymology State Key Laboratory of Food Science and TechnologySynergetic Innovation Center of Food Safety and NutritionSchool of BiotechnologyJiangnan UniversityWuxi 214122JiangsuChina

Quantitative real-time PCR is widely used to determine absolute abundance of microbes in food ***,it remains challenges in the application for quantification at the species level due to the difficulty in designing species-specific primer *** work,using Lactobacillaceae,a dominant family within the lactic acid bacteria that involved in diversity food fermentations,as a case,presents an extendable strategy to design species-specific primer sets for microbial quantita-tive analysis.136,257 species-specific genes were obtained from all 307 species within Lactobacillaceae family through comparative genomics analysis.A total of 130,521 primer sets were designed using species-specific *** them,81,710 primer sets had 100%interspecific specificity and 100%intraspecific coverage,and were reserved to quantify all 307 individual Lactobacillaceae *** primer sets had uniform melting temperature(57–63℃)and product size(100–300 bp),that allowed simultaneously quantify different Lactobacillaceae species with the same qPCR *** then established a Lactobacillaceae species quantitation primer database(LSQP-DB,http://***)containing all 81,710 species-specific primer *** database would facilitate a fast and easy absolute quantitation analysis of all indi-vidual Lactobacillaceae *** work represented the first ever large-scale integration of species-specific primer sets for microorganism,it can be extended to other bacterial and fungal genera to advance development of microbial absolute quantification.

关键词： Lactobacillaceae Primer database Species-specific primer qPCR

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Overview of yeast environmental stress response pathways and the development of tolerant yeasts

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Systems microbiology and Biomanufacturing 2022年第2期2卷 232-245页

作者： Nai-Xin Lin Yan Xu Xiao-Wei Yu lab of Brewing microbiology and Applied Enzymology School of BiotechnologyJiangnan UniversityWuxi 214122China key laboratory of Industrial Biotechnology Ministry of EducationSchool of BiotechnologyJiangnan UniversityWuxi 214122China

Yeast is widely used for industrial production of various types of products,such as ethanol and ***,its fermentation efficiency is strongly reduced by harmful environmental ***,harmful environmental stresses damage important cellular components,such as cell wall,cell membrane,proteins,***,these damages cause cellular metabolic disorders or even *** the past decades,there has been a portfolio of studies on the environmental stress tolerance of yeasts,which mainly aimed at cell damages caused by different environmental stresses,different ways to improve yeast environmental stress tolerance or a tolerance mechanism for certain environmental ***,a comprehensive overview of how yeasts respond to environmental stresses is lacking,and the correlation of tolerance mechanism between different environmental stresses is *** this review,we summarized the general damages induced by most of environmental stresses,the existing major mechanisms of environmental stress tolerance from the perspective of key signalling pathways,and the common ways to improve the resistance to environmental stresses in yeast *** tolerance mechanisms of yeast cells to different environmental stresses are diverse,but sometimes they share the same signalling *** use sensors on the cell surface to recognize environmental stresses and transmit signals to the nucleus to cause changes in gene *** summarizing the main signalling pathways,including MAPK pathway,cAMP/PKA pathway,YAP1/SKN7 pathway,it will provide a powerful reference for future efforts to promote yeast environmental stress tolerance and study yeast tolerance mechanisms.

关键词： Yeast Environmental stress Signalling pathway Protein aggregation

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Innate immunity in tuberculosis: host defense vs pathogen evasion

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Cellular & Molecular Immunology 2017年第12期14卷 963-975页

作者： Cui Hua Liu Haiying Liu Baoxue Ge CAS key laboratory of Pathogenic microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China Savaid Medical School University of Chinese Academy of SciencesBeijing 101408China MOH key laboratory of Systems Biology of Pathogens Institute of Pathogen Biologyand Center for Tuberculosis ResearchChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100176China Shanghai key lab of Tuberculosis Shanghai Pulmonary HospitalTongji University School of MedicineShanghai 200433China

The major innate immune cell types involved in tuberculosis(TB)infection are macrophages,dendritic cells(DCs),neutrophils and natural killer(NK)*** immune cells recognize the TB-causing pathogen Mycobacterium tuberculosis(Mtb)through various pattern recognition receptors(PRRs),including but not limited to Toll-like receptors(TLRs),Nod-like receptors(NLRs)and C-type lectin receptors(CLRs).Upon infection by Mtb,the host orchestrates multiple signaling cascades via the PRRs to launch a variety of innate immune defense functions such as phagocytosis,autophagy,apoptosis and inflammasome *** contrast,Mtb utilizes numerous exquisite strategies to evade or circumvent host innate *** we discuss recent research on major host innate immune cells,PRR signaling,and the cellular functions involved in Mtb infection,with a specific focus on the host’s innate immune defense and Mtb immune evasion.A better understanding of the molecular mechanisms underlying host–pathogen interactions could provide a rational basis for the development of effective anti-TB therapeutics.

关键词： host–pathogen interactions immune evasion innate immune defense Mycobacterium tuberculosis tuberculosis

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Active DNA demethylation regulates MAMP-triggered immune priming in Arabidopsis

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Journal of Genetics and Genomics 2022年第8期49卷 796-809页

作者： Mengling Huang Ying Zhang Ying Wang Jiatao Xie Jiasen Cheng Yanping Fu Daohong Jiang Xiao Yu Bo Li State key laboratory of Agricultural microbiology Huazhong Agricultural UniversityWuhanHubei 430070China The Provincial key lab of Plant Pathology of Hubei Province College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei 430070China Hubei Hongshan laboratory WuhanHubei 430070China

Plants recognize microbe-associated molecular patterns(MAMPs)to activate immune responses and defense priming to defend against pathogen *** regulation of gene expression is crucial for plant immunity and is mediated by multiple factors,including DNA ***,it remains unknown whether and how DNA demethylation contributes to immune responses in MAMPtriggered ***,we report that active DNA demethylation is required for MAMP-triggered immunity to bacterial *** rdd-2 triple mutant carrying mutations in ROS1,DML2,and DML3 that encode DNA glycosylases,which are key DNA demethylation enzymes,exhibits compromised immune responses triggered by the MAMPs fig22 and ***-wide methylome analysis reveals that fig22 induces rapid and specific DNA demethylation in an RDD-dependent *** expression levels of salicylic acid signaling-related and phytoalexin biosynthesis-related genes are tightly associated with the fig22-induced promoter *** compromised accumulation of priming compounds and antimicrobial metabolites ultimately leads to a defense priming defect in the rdd-2 *** results reveal the critical role of active DNA demethylation in the MAMP-triggered immune response and provide unique insight into the molecular mechanism of fig22-modulated DNA demethylation.

关键词： Pattern-triggered immunity Immune priming Defense gene expression DNA demethylation Immune signal transduction

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Solvent effects and mass transfer on aroma extraction during solid-state distillation

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Food Bioscience 2023年第3期53卷 1692-1702页

作者： Yuchen Gao Shuang Chen Guangyuan Jin Shuyu Song Xuliang Wang Rongzhen Zhang Yan Xu lab of Brewing microbiology and Applied Enzymology Key Laboratory of Industrial Biotechnology of Ministry of EducationState Key Laboratory of Food Science&Technology&School of BiotechnologyJiangnan UniversityWuxi214122JiangsuChina China Alcoholic Drinks Association Beijing100831China

Steam distillation is an important unit operation to extract valuable compounds from natural solid-state ***-state distillation with steam can extract aroma from fermented solid substrate such as fermented grains of Chinese liquor ***,this procedure is still operated based on generations of empirical skills rather than a technique under process control based on scientific *** resulting drawback is poor mass and heat transfer with undesired consequences concerning productivity,quality and *** modelling can be a powerful tool to get insight into such an empirical process for potential rational design,optimization and ***,we established a mathematical model to describe the mass transfer based on kinetic *** simulation results show that the distillation had a natural column plate structure that more effectively concentrated ***,this structure resulted in a high ethanol concentration in the *** evaluate subsequent effect of high ethanol concentration,we analysed aroma compounds in the distillates under simulated conditions with or without *** hydrophobic compounds were fitted well under conditions with ethanol,whereas hydrophilic compounds had similar outcomes under both *** results show that ethanol could accelerate the release of hydrophobic compounds in Chinese liquor ***,solvent could be one of the important factors to optimize the distillation *** findings provide a reference for improving the extraction during solid-state distillation.

关键词： Solid-state distillation Solvent effect Mathematical model Aroma compounds Chinese liquor

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Augmentation of tribenuron methyl removal from polluted soil with Bacillus *** BS2 and indigenous earthworms

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Journal of Environmental Sciences 2012年第8期24卷 1492-1497页

作者： Qiang Tang Zhiping Zhao Yajun Liu Nanxi Wang Baojun Wang Yanan Wang Ningyi Zhou Shuangjiang Liu State key laboratory of Microbial Resources Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China College of Life Science University of Science and TechnologyHefei 230026China key laboratory of Microbial Engineering at the Institute of Biology Henan Academy of SciencesZhengzhou 450008China key laboratory of Agricultural and Environmental microbiology Wuhan Institute of VirologyChinese Academy of Sciences44 Xiao-Hong-ShanWuhan 430071China

Tribenuron methyl （TBM） is a member of the sulfonylurea herbicide family and is widely used worldwide. In this study, TBM- degrading bacteria were enriched with TBM as potential carbon, nitrogen or sulfur source, and 44 bacterial isolates were obtained. These isolates were phylogenetically diverse, and were grouped into 25 operational taxonomic units and 14 currently known genera. Three representatives, Bacillus sp. strain BS2, Microbacterium sp. strain BS3, and Cellulosimicrobium sp. strain BSI 1, were selected, and their growth and TBM removal from culture broth were investigated. In addition, indigenous earthworms were collected and applied to augment TBM degradation in lab-scale soil column experiments. Results demonstrated that Bacillus sp. strain BS2 and earthworms significantly increased TBM removal during soil column experiments.

关键词： biodegradation of tribenuron methyl Bacillus Microbacterium Cellulosimicrobium earthworm

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Suppression of ETI by PTI priming to balance plant growth and defense through an MPK3/MPK6-WRKYs-PP2Cs module

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Molecular Plant 2023年第5期16卷 903-918页

作者： Dacheng Wang Lirong Wei Ting Liu Jinbiao Ma keyi Huang Huimin Guo Yufen Huang Lei Zhang Jing Zhao Kenichi Tsuda Yiming Wang key laboratory of Biological Interactions and Crop Health Department of Plant PathologyNanjing Agricultural UniversityNanjing 210095China key laboratory of Integrated Management of Crop Disease and Pests Ministry of EducationNanjing Agricultural UniversityNanjingChina State key laboratory of Agricultural microbiology Hubei Hongshan LaboratoryHubei Key Lab of Plant PathologyCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanChina

Pattern-triggered immunity(PTI)and effector-triggered immunity(ETI)are required for host defense against *** PTI and ETI are intimately connected,the underlying molecular mechanisms remain *** this study,we demonstrate that flg22 priming attenuates Pseudomonas syringae *** DC3000(Pst)AvrRpt2-induced hypersensitive cell death,resistance,and biomass reduction in ***-activated protein kinases(MAPKs)are key signaling regulators of PTI and *** absence of MPK3 and MPK6 significantly reduces pre-PTI-mediated ETI suppression(PES).We found that MPK3/MPK6 interact with and phosphorylate the downstream transcription factor WRKY18,which regulates the expression of AP2C1 and PP2C5,two genes encoding protein ***,we observed that the PTI-suppressed ETI-triggered cell death,MAPK activation,and growth retardation are significantly attenuated in wrky18/40/60 and ap2c1 pp2c5 *** together,our results suggest that the MPK3/MPK6-WRKYs-PP2Cs module underlies PES and is essential for the maintenance of plant fitness during ETI.

关键词： PAMP-triggered immunity effector-triggered immunity MAPK,WRKY18 protein phosphatase

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