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Gut microbial interactions based on network construction and bacterial pairwise cultivation

Science China(Life Sciences) 2024年第8期67卷 1751-1762页

作者： Min-Zhi Jiang Chang Liu Chang Xu He Jiang Yulin Wang Shuang-Jiang Liu State Key laboratory of Microbial Technology Shandong UniversityQingdao 266000China State Key laboratory of Microbial Resources and Environmental Microbiology Research Center(EMRC)Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

Association networks are widely applied for the prediction of bacterial interactions in studies of human gut ***,the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated *** this study,we addressed this challenge by integrating in vitro time series network(TSN)associations and cocultivation of TSN taxon *** samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 *** cells were harvested for DNA extraction and metagenomic sequencing.A total of 198 metagenome-assembled genomes(MAGs)were *** dynamics of bacteria growing on the YCFA agar were used to infer microbial association *** experimentally validate the interactions of taxon pairs in networks,we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank,respectively,for pairwise *** co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism(51.67%),followed by commensalism(21.67%),amensalism(18.33%),competition(5%)and exploitation(3.33%).Genome-centric analysis further revealed that the commensal gut bacteria(helpers and beneficiaries)might interact with each other via the exchanges of amino acids with high biosynthetic costs,short-chain fatty acids,and/or *** also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7%of these strains was significantly *** approach provides new insights into the gut microbiome complexity and microbial interactions in association *** work highlights that the positive relationships in gut microbial communities tend to be overestimated,and that amino acids,short-chain fatty acids,and vitamins are contributed to the positive relationships.

关键词： human gut microbiome gut microbial pairwise interaction co-culture association network microbial community

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Sodium Sulfite as a Novel Hypoxia Revulsant Involved in Hypoxic Regulation in Escherichia coli

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Biomedical and Environmental Sciences 2024年第2期37卷 228-232页

作者： YE Qiao HUO Jia Nan LUO Yuan MEI Zhu Song FANG Long Mei GUO Bing Qian WANG Guang Yun laboratory of clinical medicine Air Force Medical CenterAir Force Medical UniversityBeijing 100142China

As a reducing salt,sodium sulfite could deprive oxygen in solution,which could mimic hypoxic stress in Caenorhabditis *** this study,the wildtype Escherichia coli strain MG1655 was used to examine the inhibition of so... 详细信息

关键词： hypoxic Sodium observing

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Heavy metals potentially drive co-selection of antibiotic resistance genes by shifting soil bacterial communities in paddy soils along the middle and lower Yangtze River

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Pedosphere 2024年第3期34卷 606-619页

作者： Ya ZHANG Hao WANG Minghui HU Rui CAI Yuqing MIAO Xiancan ZHU Anhui Provincial Key laboratory of Molecular Enzymology and Mechanism of Major Metabolic Diseases Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological ResourcesCollege of Life SciencesAnhui Normal UniversityWuhu 241000(China) School of Geography and Tourism Anhui Normal UniversityWuhu 241003(China)

Heavy metals(HMs)and antibiotic resistance have become serious environmental problems affecting soil and human *** microorganisms play key roles in pollutant degradation and biogeochemical cycling processes;however,the interactions among HMs,soil microbial communities,and antibiotic resistance genes(ARGs)in agricultural soils remain *** quantitative real-time polymerase chain reaction and NovaSeq sequencing,we evaluated heavy metal contents,abundances of ARGs,soil bacterial community structure and functions,and their correlations in paddy soils at 43 sampling sites along the middle and lower reaches of the Yangtze River,central and eastern *** results showed the co-occurrence of HMs,ARGs,and HM resistance genes across all paddy ***,significant positive associations were detected between HMs and resistance ***,czcA,and int1 were positively correlated with bacterial community *** Mantel test showed that bacterial community composition and functions were significantly associated with HMs and resistance genes,such as Cd,Cr,Zn,copA,czcA,int1,and ***,HMs and ARGs were the major factors shaping soil bacterial communities;thus,HMs triggered proliferation of HM and antibiotic resistances by influencing the mobile genetic element(int1)and soil microbial *** study revealed that HMs potentially drive the co-selection of ARGs by shifting soil bacterial community structure and functions,thereby increasing the potential risks to human health as well as ecological environment in the paddy soils along the middle and lower reaches of the Yangtze River.

关键词： agricultural ecosystem ecological risk heavy metal resistance microbial community soil contamination soil pollution

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Run-and-Tumble Dynamics and Mechanotaxis Discovered in Microglial Migration

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Research 2024年第2期2023卷 95-103页

作者： Yiyu Zhang Da Wei Xiaochen Wang Boyi Wang Ming Li Haiping Fang Yi Peng Qihui Fan Fangfu Ye Beijing National laboratory for Condensed Matter Physics Institute of PhysicsChinese Academy of SciencesBeijing 100190China School of Physical Sciences University of Chinese Academy of SciencesBeijing 100049China Wenzhou Institute University of Chinese Academy of SciencesWenzhouZhejang 325000China Songshan Lake Materials laboratory DongguanGuangdong 523808China School of Science East China University of Science and TechnologyShanghai 200237China Oujang laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)WenzhouZhejiang 325000China

Microglia are resident macrophage cells in the central nervous system that search for pathogens or abnormal neural activities and migrate to resolve the *** effective search and targeted motion of macrophages mean dearly to maintaining a healthy brain,yet little is known about their migration *** this work,we study microglial motion with and without the presence of external *** discover that the cells are promptly attracted by the applied forces(i.e.,mechanotaxis),which is a tactic behavior as yet unconfirmed in ***,in both the explorative and the targeted migration,microglia display dynamics that is strikingly analogous to bacterial run-and-tumble motion.A closer examination reveals that microglial run-and-tumble is more sophisticated,e.g.,they display a short-term memory when tumbling and rely on active steering during runs to achieve mechanotaxis,probably via the responses of mechanosensitive ion *** differences reflect the sharp contrast between microglia and bacteria cells(eukaryotes ***)and their environments(compact tissue ***).Further analyses suggest that the reported migration dynamics has an optimal search efficiency and is shared among a subset of immune cells(human monocyte and macrophage).This work reveals a fruitful analogy between the locomotion of 2 remote systems and provides a framework for studying immune cells exploring complex environments.

关键词： analogy closer prompt

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Global characterization of modifications to the charge isomers of IgG antibody

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Journal of Pharmaceutical Analysis 2022年第1期12卷 156-163页

作者： Xinling Cui Wei Mi Zhishang Hu Xiaoyu Li Bo Meng Xinyuan Zhao Xiaohong Qian Tao Zhu Wantao Ying State Key laboratory of Proteomics Beijing Proteome Research CenterNational Center for Protein Sciences(Beijing)Beijing Institute of LifeomicsBeijingChina National Institute of Metrology Center for Advanced Measurement ScienceBeijingChina National Institute of Metrology Chemical Metrology&Analytical Science DivisionBeijingChina CanSino Bio Corporation Tianjin Key laboratory of Recombinant bacterial Recombination and bacterial vaccines TianjinChina

Posttranslational modifications of antibody products affect their stability,charge distribution,and drug activity and are thus a critical quality *** comprehensive mapping of antibody modifications and different charge isomers(CIs)is of utmost importance,but is *** intended to quantitatively characterize the posttranslational modification status of CIs of antibody drugs and explore the impact of posttranslational modifications on charge *** CIs of antibodies were fractionated by strong cation exchange chromatography and verified by capillary isoelectric focusing-whole column imaging detection,followed by stepwise structural characterization at three ***,the differences between CIs were explored at the intact protein level using a top-down mass spectrometry approach;this showed differences in glycoforms and deamidation ***,at the peptide level,common modifications of oxidation,deamidation,and glycosylation were *** mapping showed nonuniform deamidation and glycoform distribution among *** total,10 N-glycoforms were detected by peptide ***,an in-depth analysis of glycan variants of CIs was performed through the detection of enriched *** and quantitative analyses demonstrated the dynamics of 24 *** results revealed that sialic acid modification is a critical factor accounting for charge heterogeneity,which is otherwise missed in peptide mapping and intact molecular weight *** study demonstrated the importance of the comprehensive analyses of antibody CIs and provides a reference method for the quality control of biopharmaceutical analysis.

关键词： Antibody Charge isomers Mass spectrometry Posttranslational modification Glycopeptide

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Bioinspired polysaccharide-based nanocomposite membranes with robust wet mechanical properties for guided bone regeneration

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National Science Review 2024年第3期11卷 215-226页

作者： Jian-Hong Xiao Zhen-Bang Zhang JiaHao Li Si-Ming Chen Huai-Ling Gao YinXiu Liao Lu Chen ZiShuo Wang YiFan Lu YuanZhen Hou HengAn Wu DuoHong Zou Shu-Hong Yu Department of Chemistry New Cornerstone Science Laboratory Institute of Biomimetic Materials&Chemistry Anhui Engineering Laboratory of Biomimetic MaterialsDivision of Nanomaterials&Chemistry Hefei National Research Center for Physical Sciences at the Microscale University of Science and Technology of China Department of Dental Implant Center Stomatologic Hospital and College Key Laboratory of Oral Diseases Research of Anhui Province Anhui Medical University CAS Key laboratory of Mechanical Behavior and Design of Materials Department of Modern Mechanics CAS Center for Excellence in Complex System Mechanics University of Science and Technology of China Department of Oral Surgery College of Stomatology National Clinical Research Center for Oral DiseasesShanghai Key Laboratory of Stomatology Shanghai Research Institute of Stomatology Shanghai Ninth People's Hospital Affiliated to Shanghai Jiao Tong University School of Medicine Institute of Innovative Materials(I2M) Department of Chemistry Department of Materials Science and Engineering Southern University of Science and Technology

Polysaccharide-based membranes with excellent mechanical properties are highly desired. However, severe mechanical deterioration under wet conditions limits their biomedical applications. Here, inspired by the structural heterogeneity of strong yet hydrated biological materials, we propose a strategy based on heterogeneous crosslink-and-hydration（HCH） of a molecule/nano dual-scale network to fabricate polysaccharide-based nanocomposites with robust wet mechanical properties. The heterogeneity lies in that the crosslink-and-hydration occurs in the molecule-network while the stress-bearing nanofiber-network remains unaffected. As one demonstration, a membrane assembled by bacterial cellulose nanofiber-network and Ca2+-crosslinked and hydrated sodium alginate molecule-network is designed. Studies show that the crosslinked-and-hydrated molecule-network restricts water invasion and boosts stress transfer of the nanofiber-network by serving as interfibrous bridge. Overall, the molecule-network makes the membrane hydrated and flexible; the nanofiber-network as stress-bearing component provides strength and *** HCH dual-scale network featuring a cooperative effect stimulates the design of advanced biomaterials applied under wet conditions such as guided bone regeneration membranes.

关键词： bioinspiration heterogeneous crosslink-and-hydration dual-scale network nanocomposite membrane wet mechanical properties guided bone regeneration

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Pathogen-induced methylglyoxal negatively regulates rice bacterial blight resistance by inhibiting OsCDR1 protease activity

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Molecular Plant 2024年第2期17卷 325-341页

作者： Zheng-Wei Fu Jian-Hui Li Xiang Gao Shi-Jia Wang Ting-Ting Yuan Ying-Tang Lu State Key laboratory of Hybrid Rice College of Life SciencesRenmin Hospital of Wuhan UniversityWuhan UniversityWuhan 430072China Key laboratory of Biology and Genetic Improvement of OilCrops Ministry of Agriculture and Rural AffairsOilCrops Research Institute of the Chinese Academy of Agricultural SciencesWuhan 430062China

Xanthomonas oryzae ***(Xoo)causes bacterial blight(BB),a globally devastating disease of rice(Oryza sativa)that is responsible for significant crop *** and sugar metabolites are important for pathogen infection,providing energy and regulating events associated with defense responses;howev-er,the mechanisms by which they regulate such events in BB are *** an inevitable sugar metabolite,methylglyoxal(MG)is involved in plant growth and responses to various abiotic stresses,but the underlying mechanisms remain *** and how MG functions in plant biotic stress responses is almost completely ***,we report that the Xoo strain PXO99 induces OsWRKY62.1 to repress transcrip-tion of OsGLY Il genes by directly binding to their promoters,resulting in overaccumulation of *** negatively regulates rice resistance against Pxo99:osglyll2 mutants with higher MG levels are more sus-ceptible to the pathogen,whereas OsGLYIl2-overexpressing plants with lower MG content show greater resistance than the wild *** of OsGLYll2 to prevent excessive MG accumulation confers broad-spectrum resistance against the biotrophic bacterial pathogens Xoo and Xanthomonas oryzae *** and the necrotrophic fungal pathogen Rhizoctonia solani,which causes rice sheath *** evidence shows that MG reduces rice resistance against PXO99 through CONSTITUTIVE DISEASE RESISTANCE 1(OsCDR1).MGmodifies the Arg97 residue of OsCDR1to inhibit its aspartic protease activ-ity,which is essential for OsCDR1-enhanced *** together,these findings illustrate how Xoo promotes infection by hijacking a sugar metabolite in the host plant.

关键词： Oryza sativa bacterial blight OsWRKY62.1 methylglyoxal OsCDR1

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Advances in immunotherapy for biliary tract cancers

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Chinese Medical Journal 2024年第5期137卷 524-532页

作者： Yuhao Zhao Mao Yang Jiayi Feng Xu’an Wang Yingbin Liu Department of Biliary–Pancreatic Surgery Renji Hospital Affiliated to Shanghai Jiao Tong University School of MedicineShanghai 200127China Shanghai Cancer Institute State Key Laboratory of Oncogenes and Related GenesShanghai 200127China Shanghai Key laboratory of Biliary Tract Disease Shanghai 200082China

Biliary tract cancers(BTC),a heterogeneous disease with poor prognosis,including gallbladder cancer(GBC),intrahepatic cholangiocarcinoma(ICC),and extrahepatic cholangiocarcinoma(ECC).Although surgery is currently the primary regimen to treat BTC,most BTC patients are diagnosed at an advanced stage and miss the opportunity of surgical *** a result,non-surgical therapy serves as the main intervention for advanced *** recent years,immunotherapy has emerged as one of the most promising therapies in a number of solid cancers,and it includes immune checkpoint inhibitors(ICIs)monotherapy or combined therapy,tumor vaccines,oncolytic virus immunotherapy,adoptive cell therapy(ACT),and cytokine ***,these therapies have been practiced in limited clinical settings in patients with *** this review,we focus on the discussion of latest advances of immunotherapy in BTC and update the progress of multiple current clinical trials with different immunotherapies.

关键词： Immunotherapy Biliary tract cancers Immune checkpoint inhibitors Cholangiocarcinoma Gallbladder cancer

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Spontaneous mutations and mutational responses to penicillin treatment in the bacterial pathogen Streptococcus pneumoniae D39

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Marine Life Science & Technology 2024年第2期6卷 198-211页

作者： Wanyue Jiang Tongtong Lin Jiao Pan Caitlyn ERivera Clayton Tincher Yaohai Wang Yu Zhang Xiang Gao Yan Wang Ho‑Ching T.Tsui Malcolm E.Winkler Michael Lynch Hongan Long Institute of Evolution and Marine Biodiversity KLMMEOcean University of ChinaQingdao 266003China laboratory for Marine Biology and Biotechnology Laoshan LaboratoryQingdao 266237China Department of Biology Indiana UniversityBloomingtonIN 47405USA School of Mathematics Science Ocean University of ChinaQingdao 266000China State Key laboratory of Microbial Technology Microbial Technology InstituteSchool of Life ScienceShandong UniversityQingdao 266237China Biodesign Center for Mechanisms of Evolution Arizona State UniversityTempeAZ 85281USA

Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic ***,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)*** rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T *** high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in *** line with this,*** D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among *** with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and *** lacks a stress response *** findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.

关键词： Neutral evolution Mutation spectrum Antibiotics DNA mismatch repair Oxidative damage repair

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Triclosan-conjugated,Lipase-responsive Polymeric Micelles for Eradication of Staphylococcal Biofilms

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Chinese Journal of Polymer Science 2024年第6期42卷 718-728页

作者： Yan-Qiang Huang Yuan-Feng Li Yong Liu Lin-Qi Shi Guangxi Technology Innovation Cooperation Base of Prevention and Control Pathogenic Microbes with Drug Resistance Youjiang Medical University for NationalitiesBaise533000China Translational Medicine laboratory the First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325035China Wenzhou Institute University of Chinese Academy of SciencesWenzhou325001China State Key laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Educationand Institute of Polymer ChemistryCollege of ChemistryNankai UniversityTianjin300071China

bacterial biofilms present a significant challenge in treating drug-resistant infections,necessitating the development of innovative *** this study,we introduce triclosan-conjugated,lipase-responsive polymeric micelles designed to exploit biofilm properties and serve as a responsive drug delivery *** micelles were created using an amphiphilic block polymer synthesized via ring-opening polymerization ofε-caprolactone(CL)and triclosan-containing cyclic trimethylene carbonate(MTC-Tri).Poly(ethylene glycol)(PEG-OH)acted as the macro-initiator,resulting in micelles with a PEG shell that facilitated their penetration into bacterial *** important advantage of our micelles lies in their interaction with local bacterial lipases within *** lipases triggered rapid micelle degradation,releasing triclosan in a controlled *** liberated triclosan effectively eliminated bacteria embedded in the ***,the triclosan-conjugated micelles displayed minimal toxicity to murine fibroblasts,indicating their biocompatibility and *** finding emphasizes the potential application of these micelles in combatting drug resistance observed in bacterial *** triclosan-conjugated,lipase-responsive polymeric micelles exhibit promising characteristics for addressing drug resistance in bacterial *** harnessing biofilm properties and implementing a responsive drug delivery system,we seek to provide an effective solution in the fight against drug-resistant bacteria.

关键词： Self-assembly Polymer prodrug Ring-opening polymerization Biofilm eradication Cytotoxicity

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