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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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Direct ammonium oxidation to nitrogen gas (Dirammox) in Alcaligenes strain HO-1: The electrode role

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Environmental Science and Ecotechnology 2023年第3期15卷 121-127页

作者： Narcís Pous Lluis Baneras Philippe F-XCorvini shuang-jiang liu Sebastia Puig Laboratory of Chemical and Environmental Engineering(LEQUiA) Institute of the EnvironmentUniversity of GironaCarrer Maria Aurelia Capmany69E-17003GironaSpain Group of Environmental Microbial Ecology Institute of Aquatic EcologyUniversity of GironaC/Maria Aurelia Capmany40E-17003GironaSpain School of Life Sciences University of Applied Sciences and Arts Northwestern SwitzerlandMuttenz4132Switzerland State Key Laboratory of Microbial Resource at Institute of Microbiology Chinese Academy of SciencesBeijing100101China

It has been recently suggested that Alcaligenes use a previously unknown pathway to convert ammonium into dinitrogen gas(Dirammox)via hydroxylamine(NH2OH).This fact alone already implies a significant decrease in the aeration requirements for the process,but the process would still be dependent on external *** work studied the potential use of a polarised electrode as an electron acceptor for ammonium oxidation using the recently described Alcaligenes strain HO-1 as a model heterotrophic *** indicated that Alcaligenes strain HO-1 requires aeration for metabolism,a requirement that cannot be replaced for a polarised electrode ***,concomitant elimination of succinate and ammonium was observed when operating a previously grown Alcaligenes strain HO-1 culture in the presence of a polarised electrode and without *** usage of a polarised electrode together with aeration did not increase the succinate nor the nitrogen removal rates observed with aeration ***,current density generation was observed along a feeding batch test representing an electron share of 3%of the ammonium removed in the presence of aeration and 16%without *** tests suggested that hydroxylamine oxidation to dinitrogen gas could have a relevant role in the electron discharge onto the ***,the presence of a polarised electrode supported the metabolic functions of Alcaligenes strain HO-1 on the simultaneous oxidation of succinate and ammonium.

关键词： Bioelectrochemical systems Electroactive bacteria Microbial electrochemical technologies Nitrification Nitrogen removal

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Unraveling the Acidithiobacillus caldus complete genome and its central metabolisms for carbon assimilation

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Journal of Genetics and Genomics 2011年第6期38卷 243-252页

作者： Xiao-Yan You Xu Guo Hua-Jun Zheng Ming-jiang Zhang Li-Jun liu Yong-Qiang Zhu Baoli Zhu Sheng-YueWang Guo-Ping Zhao Ansgar Poetsch Cheng-Ying jiang shuang-jiang liu State Key Laboratory of Microbial Resource Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Shanghai MOST Key Laboratory of Health and Disease Genomics Chinese National Human Genome Center Shanghai 201203 China Microbial Genome Research Center Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China Institute of Plant Physiology and Ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200032 China Institute for Plant Biochemistry Faculty of Biology and Biotechnology Ruhr University Bochum Bochum D44780 Germany Environmental Microbiology Research Center Institute of Microbiology Chinese Academy of Sciences Beijing 100101 China

Acidithiobacillus caldus is one of the dominant sulfur-oxidizing bacteria in bioleaching reactors. It plays the essential role in maintaining the high acidity and oxidation of reduced inorganic sulfur compounds during bioleaching process. In this report, the complete genome sequence of A. caldus SM-1 is presented. The genome is composed of one chromosome （2,932,225 bp） and four plasmids （pLAtcl, pLAtc2, pLAtc3, pLAtcm） and it is rich in repetitive sequences （accounting for 11% of the total genome）, which are often associated with transposable genetic elements. In particular, twelve copies of ISAtfe and thirty-seven copies of ISAtcl have been identified, suggesting that they are active transposons in the genome. A. caldus SM-1 encodes all enzymes for the central metabolism and the assimilation of carbon compounds, among which 29 proteins/enzymes were identifiable with proteomic tools. The SM-1 fixes CO2 via the classical Calvin-Bassham--Benson （CBB） cycle, and can operate complete Embden-Meyerhof pathway （EMP）, pentose phosphate pathway （PPP）, and gluconeogenesis. It has an incomplete tricarboxylic acid cycle （TCA）. Four putative transporters involved in carbohydrate uptake were identified. Taken together, the results suggested that SM-1 was able to assimilate carbohydrates and this was subsequently confirmed experimentally because addition of 1% glucose or sucrose in basic salt medium significantly increased the growth of SM-1. It was concluded that the complete genome of SM-1 provided fundamental data for further investigation of its physiology and genetics, in addition to the carbon metabolism revealed in this study.

关键词： Acidithiobacillus caldus SM-1 Biomining CO2 fixation Central metabolism CBB/EMP/PPP/TCA cycle

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Mechanical behavior of 2G NPR bolt anchored rock samples under static disturbance loading

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Journal of Mountain Science 2024年第7期21卷 2494-2516页

作者： WANG Jiong jiang Jian WANG Siyu CHANG Yiwen liu Peng HE Manchao CHENG shuang State Key Laboratory for Tunnel Engineering China University of Mining and Technology(Beijing)Beijing 100083China School of Mechanics and Civil Engineering China University of Mining and Technology(Beijing)Beijing 100083China

The deep mining of coal resources is accompanied by severe environmental challenges and various potential engineering *** implementation of NPR(negative Poisson's ratio)bolts are capable of controlling large deformations in the surrounding rock *** paper focuses on studying the mechanical properties of the NPR bolt under static disturbance *** deep nonlinear mechanical experimental system was used to study the mechanical behavior of rock samples with different anchored types(unanchored/PR anchored/2G NPR anchored)under static disturbance *** whole process of rock samples was taken by high-speed camera to obtain the real-time failure characteristics under static disturbance *** the same time,the acoustic emission signal was collected to obtain the key characteristic parameters of acoustic emission such as acoustic emission count,energy,and *** deformation at the failure of the samples was calculated and analyzed by digital speckle *** findings indicate that the failure mode of rock is influenced by different types of *** peak failure strength of 2G NPR bolt anchored rock samples exhibits an increase of 6.5%when compared to the unanchored rock *** cumulative count and cumulative energy of acoustic emission exhibit a decrease of 62.16%and 62.90%,*** maximum deformation of bearing capacity exhibits an increase of 59.27%,while the failure time demonstrates a delay of 42.86%.The peak failure strength of the 2G NPR bolt anchored ones under static disturbance load exhibits an increase of 5.94%when compared to the rock anchored by PR(Poisson's ratio)*** cumulative count and cumulative energy of acoustic emission exhibit a decrease of 47.16%and 43.86%,*** maximum deformation of the bearing capacity exhibits an increase of 50.43%,and the failure time demonstrates a delay of 32%.After anchoring by 2G NPR bolt,anchoring support effectively reduces the risk of damage caused by s

关键词： Anchored rock samples Static disturbance load Acoustic emission characteristics Digital speckle Negative Poisson's ratio

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Unidirectional movement behavior of underwater bubbles on the wettability gradient mesh via asymmetrical bounce

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Science China Chemistry 2024年第8期67卷 2606-2613页

作者： Yuzhen Ning Zhihong Zhao shuang Ben Qiang Li Cunming Yu Xudong Zhang Huawei Chen Kesong liu Lei jiang School of Mechanical Engineering and Automation Beihang UniversityBeijing 100191China Key Laboratory of Bio-Inspired Smart Interfacial Science and Technology School of ChemistryBeihang UniversityBeijing 100191China Research Institute of Aero-Engine Beihang UniversityBeijing 100191China School of Materials Science and Engineering Shenyang Ligong UniversityShenyang 110159China Tianmushan Laboratory Hangzhou 310023China The Analysis Testing CenterBeihang UniversityBeijing 100191China

The impact of underwater bubbles on solid surfaces with a gradient wettability is important for fundamental science and technological applications. Despite progress in the translational motion of underwater bubbles on asymmetric surface, a fundamental dynamic understanding of asymmetrical bounce behavior of the underwater bubble needs to be further ***, we investigate asymmetrical bounce of underwater bubbles after impacting the wettability gradient copper mesh *** bounce of the underwater bubble on the wettability gradient mesh(WGM) surface is composed by asymmetrical spread in the spread process and asymmetrical recoil in the recoil process, which induce the unidirectional movement ***, effective bubble-size manipulation can be easily implemented due to different volumes of bubbles remaining at different locations of WGM surface. We envision that this work will provide a new understanding of asymmetrical bounce behavior of the underwater bubble on the wettability gradient surface, and propose a novel and feasible strategy for constructing the underwater bubble manipulation system.

关键词： asymmetrical bounce unidirectional movement behavior gradient wettability

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Mitigation of N_(2)O emissions in water-saving paddy fields:Evaluating organic fertilizer substitution and microbial mechanisms

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Journal of Integrative Agriculture 2024年第9期23卷 3159-3173页

作者： Delei Kong Xianduo Zhang Qidong Yu Yaguo Jin Peikun jiang shuang Wu Shuwei liu Jianwen Zou College of Environment and Resources/College of Carbon Neutrality Zhejiang A&F UniversityHangzhou 311300China jiangsu Key Laboratory of Low Carbon Agriculture and GHGs Mitigation College of Resources and Environmental SciencesNanjing Agricultural UniversityNanjing 210095China Department of Biochemistry and Molecular Biology College of Life SciencesNanjing Agricultural UniversityNanjing 210095China jiangsu Key Lab and Engineering Center for Solid Organic Waste Utilization Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNanjing Agricultural UniversityNanjing 210095China

Water-saving irrigation strategies can successfully alleviate methane emissions from rice fields,but significantly stimulate nitrous oxide(N_(2)O)emissions because of variations in soil oxygen level and redox ***,the relationship linking soil N_(2)O emissions to nitrogen functional genes during various fertilization treatments in water-saving paddy fields has rarely been ***,the mitigation potential of organic fertilizer substitution on N_(2)O emissions and the microbial mechanism in rice fields must be further *** study examined how soil N_(2)O emissions were affected by related functional microorganisms(ammonia-oxidizing archaea(AOA),ammonia-oxidizing bacteria(AOB),nirS,nirK and nosZ)to various fertilization treatments in a rice field in southeast China over two *** this study,three fertilization regimes were applied to rice cultivation:a no nitrogen(N)(Control),an inorganic N(Ni),and an inorganic N with partial N substitution with organic manure(N_(i)+N_(o)).Over two rice-growing seasons,cumulative N_(2)O emissions averaged 0.47,4.62 and 4.08 kg ha^(−1)for the Control,Ni and N_(i)+N_(o)treatments,*** comparison to the Ni treatment,the N_(i)+N_(o)fertilization regime considerably reduced soil N_(2)O emissions by 11.6%while maintaining rice yield,with a lower N_(2)O emission factor(EF)from fertilizer N of 0.95%.Nitrogen fertilization considerably raised the AOB,nirS,nirK and nosZ gene abundances,in comparison to the Control ***,the substitution of organic manure for inorganic N fertilizer significantly decreased AOB and nirS gene abundances and increased nosZ gene *** AOB responded to N fertilization more sensitively than the *** N_(2)O emissions significantly correlated positively with AOB and nirS gene abundances while having a negative correlation with nosZ gene abundance and the nosZ/nirS ratio across N-fertilized *** summary,we conclude that organic manure substi

关键词： organic manure substitution inorganic fertilizer N_(2)O functional microbe rice paddy

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The monkey microbial biobank brings previously uncultivated bioresources for nonhuman primate and human gut microbiomes

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mLife 2022年第2期1卷 210-217页

作者： Danhua Li Chang liu Rexiding Abuduaini Mengxuan Du Yujing Wang Haizhen Zhu Honghe Chen Nan Zhou Yuhua Xin Linhuan Wu Juncai Ma Yuguang Zhou Yong Lu Chengying jiang Qiang Sun shuang-jiang liu State Key Laboratory of Microbial Resources and Environmental Microbiology Research Center at Institute of Microbiology Chinese Academy of SciencesBeijingChina College of Life Science University of Chinese Academy of SciencesBeijingChina State Key Laboratory of Microbial Biotechnology Shandong UniversityQingdaoChina China General Microorganism Culture Collection Institute of MicrobiologyChinese Academy of SciencesBeijingChina Microbial Resources and Big Data Center Institute of MicrobiologyChinese Academy of SciencesBeijingChina State Key Laboratory of Neuroscience CAS Key Laboratory of Primate NeurobiologyCAS Center for Excellence in Brain Science and Intelligence TechnologyChinese Academy of SciencesInstitute of NeuroscienceShanghaiChina

Impact statement Nonhuman primates(NHPs)such as monkeys are the closest living relatives to humans and are the best available models for causative studies of human health and *** microbiomes are intensively involved in host *** this study,by large-scale cultivation of microbes from fecal samples of monkeys,we obtained previously uncultured bacterial species and constructed a Macaca fascicularis Gut Microbial Biobank(MfGMB).The MfGMB consisted of 250 strains that represent 97 species of 63 genera,25 families,and 4 *** information of the 250 strains and the genomes of 97 cultured species are publicly *** MfGMB represented nearly 50% of core gut microbial compositions at the genus level and covered over 80% of the KO-based known gut microbiome functions of *** mining showed that the bacterial species in the MfGMB were prevalent not only in NHPs gut microbiomes but also in human gut *** study will help the understanding and future investigations on how gut microbiomes interact with their mammalian hosts.

关键词： statement monkey gut

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RNA modifications in cellular metabolism:implications for metabolism-targeted therapy and immunotherapy

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Signal Transduction and Targeted Therapy 2024年第4期9卷 1565-1594页

作者： Wei-Wei liu Si-Qing Zheng Tian Li Yun-Fei Fei Chen Wang shuang Zhang Fei Wang Guan-Min jiang Hao Wang Department of Laboratory Medicine The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina School of Clinical Medicine Shandong UniversityJinanChina Core Unit of National Clinical Research Center for Laboratory Medicine HefeiChina Neurosurgical Department The First Affiliated Hospital of USTCDivision of Life Sciences and MedicineUniversity of Science and Technology of ChinaHefeiChina Department of Clinical Laboratory The Fifth Affiliated HospitalSun Yat-sen UniversityZhuhaiChina

Cellular metabolism is an intricate network satisfying bioenergetic and biosynthesis requirements of *** studies have been constantly making inroads in our understanding of pathophysiology,and inspiring development of *** a crucial component of epigenetics at post-transcription level,RNA modification significantly determines RNA fates,further affecting various biological processes and cellular *** be noted,immunometabolism defines the metabolic alterations occur on immune cells in different stages and immunological *** this review,we characterize the distribution features,modifying mechanisms and biological functions of 8 RNA modifications,including N6-methyladenosine(m6A),N6,2'-O-dimethyladenosine(m6Am),N1-methyladenosine(m1A),5-methylcytosine(m5C),N4-acetylcytosine(ac4C),N7-methylguanosine(m7G),Pseudouridine(V),adenosine-to-inosine(A-to-l)editing,which are relatively the most studied *** regulatory roles of these RNA modification on metabolism in diverse health and disease contexts are comprehensively described,categorized as glucose,lipid,amino acid,and mitochondrial *** we highlight the regulation of RNA modifications on immunometabolism,further influencing immune *** all,we provide a thorough discussion about clinical implications of RNA modification in metabolism-targeted therapy and immunotherapy,progression of RNA modification-targeted agents,and its potential in RNAtargeted ***,we give legitimate perspectives for future researches in this field from methodological requirements,mechanistic insights,to therapeutic applications.

关键词： metabolism targeted alterations

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Bright dual-color electrochemiluminescence of a structurally determined Pt1Ag18 nanocluster

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Aggregate 2024年第1期5卷 345-352页

作者： Bing Yin Lirong jiang Xiaojian Wang Ying liu Kaiyang Kuang Mengmeng Jing Chunmin Fang Chuanjun Zhou shuang Chen Manzhou Zhu Institutes of Physical Science and Information Technology and Centre for Atomic Engineering of Advanced Materials Key Laboratory of Structure and Functional Regulation of Hybrid Materials of Ministry of EducationDepartment of Chemistry and Anhui Province Key Laboratory of Chemistry for Inorganic/Organic Hybrid Functionalized MaterialsAnhui UniversityHefeiChina

Metal nanoclusters possess excellent electrochemical,optical,and catalytic properties,but correlating these properties remains challenging,which is the foundation to generate electrochemiluminescence(ECL).Herein,we report for the first time that a structurally determined Pt1Ag18 nanocluster generates intense ECL and simultaneously enhances the ECL of carbon dots(CDs)via an electrocatalytic ***^(1)Ag_(18)nanocluster show aggregation-induced emission enhancement and aggregation-induced ECL enhancement under light and electrochemical stimulation,*** the presence of tripropylamine(TPrA)as a coreactant,solid Pt1Ag18 shows unprecedented ECL efficiency,which is more than nine times higher than that of 1 mM Ru(bpy)32+with the same TPrA ***-resolved ECL spectra reveal two ECL emission bands in the presence of *** ECL emission centered at 650 nm is assigned to the solid Pt_(1)Ag_(18)nanocluster,consistent with the peak wavelength in self-annihilation ECL and photoluminescence of the solid *** ECL emission centered at 820 nm is assigned to the CDs on the glassy carbon *** electrocatalytic effect of the nanoclusters enhanced the ECL of the CDs by a factor of more than 180 in comparison to that without *** on the combined optical and electrochemical results,the ECL generation pathways and mechanisms of Pt1Ag18 and CDs are *** findings are extremely promising for designing multifunctional nanocluster luminophores with strong emissions and developing ratiometric sensing devices.

关键词： AIECLE AIEE electrochemiluminescence nanocluster photoluminescence structure

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Impact of Carbon Chain Structures in the Backbone on the Flexibility of Modified Polyarylene Sulfide Resins: Molecular Dynamics Simulations and Mesoscopic Analysis

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Chinese Journal of Polymer Science 2024年第4期42卷 544-557页

作者： Chi Zhang Rong liu Jing-Yuan liu Wen-Wei jiang Key Laboratory of Fine Chemical Engineering and Functional Materials School of Chemical EngineeringSichuan UniversityChengdu610065China

In the domain of high-performance engineering polymers, the enhancement of mechanical flexibility in poly(phenylene sulfide) (PPS) resins has long posed a significant challenge. A novel molecular structure, designated as PP-He-IS, wherein imide rings and an aliphatic hexylene chain are covalently incorporated into the PPS backbone to enhance its flexibility, is introduced in this study. Molecular dynamics (MD) simulations are employed to systematically explore the effects of diversifying the backbone chain structures by substituting phenyl units with alkyl chains of varying lengths, referred to as PP-A-IS where “A” signifies the distinct intermediary alkyl chain configurations. Computational analyses reveal a discernable decrement in the glass transition temperature (Tg) and elastic modulus, counterbalanced by an increment in yield strength as the alkyl chain length is extended. Notably, the PP-He-IS variant is shown to exhibit superior yield strength while simultaneously maintaining reduced elastic modulus and Tg values, positioning it as an advantageous candidate for flexible PPS applications. Mesoscopic analyses further indicate that structures such as PP-He-IS, PP-Pe-IS, and PP-Bu-IS manifest remarkable flexibility, attributable to the presence of freely rotatable carbon-carbon single bonds. Experimental validation confirms that a melting temperature of 504 K which is lower than that of conventional PPS, and lower crystallinity are exhibited by PP-He-IS, thereby affording enhanced processability without compromising inherent thermal stability. Novel insights into the strategic modification of PPS for mechanical flexibility are thus furnished by this study, which also accentuates the pivotal role played by molecular dynamics simulations in spearheading high-throughput investigations in polymer material modifications.

关键词： Molecular dynamics simulations Polyarylene Sulfide Main-chain modifications Flexibility Aliphatic hexylene chain

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