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| 1 | Rapid, automated, and reliable antimicrobial susceptibility test from positive blood culture by CAST‐R显示文摘Antimicrobial susceptibility tests(ASTs)are pivotal in combating multidrug resistant pathogens,yet they can be time‐consuming,labor‐intensive,and unstable.Using the AST of tigecycline for sepsis as the main model,here we establish an automated system of Clinical Antimicrobials Susceptibility Test Ramanometry(CAST‐R),based on D2O‐probed Raman microspectroscopy.Featuring a liquid robot for sample pretreatment and a machine learning‐based control scheme for data acquisition and quality control,the 3‐h,automated CAST‐R process accelerates AST by>10‐fold,processes 96 paralleled antibiotic‐exposure reactions,and produces high‐quality Raman spectra.The Expedited Minimal Inhibitory Concentration via Metabolic Activity is proposed as a quantitative and broadly applicable parameter for metabolism‐based AST,which shows 99%essential agreement and 93%categorical agreement with the broth microdilution method(BMD)when tested on 100 Acinetobacter baumannii isolates.Further tests on 26 clinically positive blood samples for eight antimicrobials,including tigecycline,meropenem,ceftazidime,ampicillin/sulbactam,oxacillin,clindamycin,vancomycin,and levofloxacin reveal 93%categorical agreement with BMD‐based results.The automation,speed,reliability,and general applicability of CAST‐R suggest its potential utility for guiding the clinical administration of antimicrobials. | Pengfei Zhu Lihui Ren Ying Zhu Jing Dai Huijie Liu Yuli Mao Yuandong Li Yuehui He Xiaoshan Zheng Rongze Chen Xiaoting Fu Lili Zhang Lijun Sun Yuanqi Zhu Yuetong Ji Bo Ma Yingchun Xu Jian Xu Qiwen Yang | 2022 | mLife2022，1，3： | 3 |
| 2 | Artificial intelligence-assisted automatic and index-based microbial single-cell sorting system for One-Cell-One-Tube显示文摘Identification,sorting,and sequencing of individual cells directly from in situ samples have great potential for in-depth analysis of the structure and function of microbiomes.In this work,based on an artificial intelligence(AI)-assisted object detection model for cell phenotype screening and a cross-interface contact method for single-cell exporting,we developed an automatic and index-based system called EasySort AUTO,where individual microbial cells are sorted and then packaged in a microdroplet and automatically exported in a precisely indexed,“One-Cell-One-Tube”manner.The target cell is automatically identified based on an AI-assisted object detection model and then mobilized via an optical tweezer for sorting.Then,a crossinterface contact microfluidic printing method that we developed enables the automated transfer of cells from the chip to the tube,which leads to coupling with subsequent single-cell culture or sequencing.The efficiency of the system for single-cell printing is>93%.The throughput of the system for single-cell printing is~120 cells/h.Moreover,>80%of single cells of both yeast and Escherichia coli are culturable,suggesting the superior preservation of cell viability during sorting.Finally,AI-assisted object detection supports automated sorting of target cells with high accuracy from mixed yeast samples,which was validated by downstream single-cell proliferation assays.The automation,index maintenance,and vitality preservation of EasySort AUTO suggest its excellent application potential for single-cell sorting. | Zhidian Diao Lingyan Kan Yilong Zhao Jingyun Song Chen Wang Yang Liu Fengli Zhang Teng Xu Rongze Chen Xixian Wang Xiaoyan Jing Jian Xu Yuandong Li Bo Ma | 2022 | mLife2022，1，4： | 2 |
| 3 | “Life is short,and art is long”:RNA degradation in cyanobacteria and model bacteria显示文摘RNA turnover plays critical roles in the regulation of gene expression and allows cells to respond rapidly to environmental changes.In bacteria,the mechanisms of RNA turnover have been extensively studied in the models Escherichia coli and Bacillus subtilis,but not much is known in other bacteria.Cyanobacteria are a diverse group of photosynthetic organisms that have great potential for the sustainable production of valuable products using CO_(2)and solar energy.A better understanding of the regulation of RNA decay is important for both basic and applied studies of cyanobacteria.Genomic analysis shows that cyanobacteria have more than 10 ribonucleases and related proteins in common with E.coli and B.subtilis,and only a limited number of them have been experimentally investigated.In this review,we summarize the current knowledge about these RNAturnover-related proteins in cyanobacteria.Although many of them are biochemically similar to their counterparts in E.coli and B.subtilis,they appear to have distinct cellular functions,suggesting a different mechanism of RNA turnover regulation in cyanobacteria.The identification of new players involved in the regulation of RNA turnover and the elucidation of their biological functions are among the future challenges in this field. | Ju-Yuan Zhang Wolfgang R.Hess Cheng-Cai Zhang | 2022 | mLife2022，1，1： | 1 |
| 4 | Legionella pneumophila temporally regulates the activity of ADP/ATP translocases by reversible ADP-ribosylation显示文摘The mitochondrion is an important signaling hub that governs diverse cellular functions,including metabolism,energy production,and immunity.Among the hundreds of effectors translocated into host cells by the Dot/Icm system of Legionella pneumophila,several are targeted to mitochondria but the function of most of them remains elusive.Our recent study found that the effector Ceg3 inhibits the activity of ADP/ATP translocases(ANTs)by ADP-ribosylation(ADPR).Here,we show that the effect of Ceg3 is antagonized by Larg1,an effector encoded by lpg0081,a gene that is situated next to ceg3.Larg1 functions to reverse Ceg3-mediated ADPR of ANTs by cleaving the N-glycosidic bond between the ADPR moiety and the modified arginine residues in ANTs,leading to restoration of their activity in ADP/ATP exchange.Structural analysis of Larg1 and its complex with ADPR reveals that this ADPR glycohydrolase harbors a unique macrodomain that catalyzes the removal of ADPR modification on ANTs.Our results also demonstrate that together with Ceg3,Larg1 imposes temporal regulation of the activity of ANTs by reversible ADPR during L.pneumophila infection. | Jiaqi Fu Pengwei Li Hongxin Guan Dan Huang Lei Song Songying Ouyang Zhao-Qing Luo | 2022 | mLife2022，1，1： | 1 |
| 5 | Delivery of an Rhs-family nuclease effector reveals direct penetration of the gram-positive cell envelope by a type VI secretion system in Acidovorax citrulli显示文摘The type VI secretion system(T6SS)is a double-tubular nanomachine widely found in gram-negative bacteria.Its spear-like Hcp tube is capable of penetrating a neighboring cell for cytosol-to-cytosol protein delivery.However,gram-positive bacteria have been considered impenetrable to such T6SS action.Here we report that the T6SS of a plant pathogen,Acidovorax citrulli(AC),could deliver an Rhsfamily nuclease effector RhsB to kill not only gram-negative but also gram-positive bacteria.Using bioinformatic,biochemical,and genetic assays,we systematically identified T6SS-secreted effectors and determined that RhsB is a crucial antibacterial effector.RhsB contains an N-terminal PAAR domain,a middle Rhs domain,and an unknown C-terminal domain.RhsB is subject to self-cleavage at both its N-and C-terminal domains and its secretion requires the upstream-encoded chaperone EagT2 and VgrG3.The toxic Cterminus of RhsB exhibits DNase activities and such toxicity is neutralized by either of the two downstream immunity proteins,RimB1 and RimB2.Deletion of rhsB significantly impairs the ability of killing Bacillus subtilis while ectopic expression of immunity proteins RimB1 or RimB2 confers protection.We demonstrate that the AC T6SS not only can effectively outcompete Escherichia coli and B.subtilis in planta but also is highly potent in killing other bacterial and fungal species.Collectively,these findings highlight the greatly expanded capabilities of T6SS in modulating microbiome compositions in complex environments. | Tong-Tong Pei Yumin Kan Zeng-Hang Wang Ming-Xuan Tang Hao Li Shuangquan Yan Yang Cui Hao-Yu Zheng Han Luo Xiaoye Liang Tao Dong | 2022 | mLife2022，1，1： | 1 |
| 6 | Climate warming restructures seasonal dynamics of grassland soil microbial communities显示文摘Soil microbial community's responses to climate warming alter the global carbon cycle.In temperate ecosystems,soil microbial communities function along seasonal cycles.However,little is known about how the responses of soil microbial communities to warming vary when the season changes.In this study,we investigated the seasonal dynamics of soil bacterial community under experimental warming in a temperate tall‐grass prairie ecosystem.Our results showed that warming significantly(p=0.001)shifted community structure,such that the differences of microbial communities between warming and control plots increased nonlinearly(R^(2)=0.578,p=0.021)from spring to winter.Also,warming significantly(p<0.050)increased microbial network complexity and robustness,especially during the colder seasons,despite large variations in network size and complexity in different seasons.In addition,the relative importance of stochastic processes in shaping the microbial community decreased by warming in fall and winter but not in spring and summer.Our study indicates that climate warming restructures the seasonal dynamics of soil microbial community in a temperate ecosystem.Such seasonality of microbial responses to warming may enlarge over time and could have significant impacts on the terrestrial carbon cycle. | Xue Guo Mengting Yuan Jiesi Lei Zhou Shi Xishu Zhou Jiabao Li Ye Deng Yunfeng Yang Liyou Wu Yiqi Luo James MTiedje Jizhong Zhou | 2022 | mLife2022，1，3： | 1 |
| 7 | The late Archaean to early Proterozoic origin and evolution of anaerobic methane-oxidizing archaea显示文摘Impact statement Microorganisms,called anaerobic methane-oxidizing archaea(ANME),can reduce a large amount of greenhouse gas methane and therefore have the potential to cool the Earth.We collected nearly all ANMEs genomes in public databases and performed a comprehensive comparative genomic analysis and molecular dating.Our results show that ANMEs originated in the late Archaean to early Proterozoic eon.During this period of time,our planet Earth was experiencing the Great Oxygenation Event and Huronian Glaciation,a dramatic drop in the Earth's surface temperature.This suggests that the emergence of ANMEs may contribute to the reduction of methane at that time,which is an unappreciated potential cause that led to the Huronian Glaciation. | Yinzhao Wang Ruize Xie Jialin Hou Zhenbo Lv Liuyang Li Yaoxun Hu Hungchia Huang Fengping Wang | 2022 | mLife2022，1，1： | 1 |
| 8 | Different outer membrane c‐type cytochromes are involved in direct interspecies electron transfer to Geobacter or Methanosarcina species显示文摘Direct interspecies electron transfer(DIET)may be most important in methanogenic environments,but mechanistic studies of DIET to date have primarily focused on cocultures in which fumarate was the terminal electron acceptor.To better understand DIET with methanogens,the transcriptome of Geobacter metallireducens during DIET‐based growth with G.sulfurreducens reducing fumarate was compared with G.metallireducens grown in coculture with diverse Methanosarcina.The transcriptome of G.metallireducens cocultured with G.sulfurreducens was significantly different from those with Methanosarcina.Furthermore,the transcriptome of G.metallireducens grown with Methanosarcina barkeri,which lacks outer‐surface c‐type cytochromes,differed from those of G.metallireducens cocultured with M.acetivorans or M.subterranea,which have an outer‐surface c‐type cytochrome that serves as an electrical connect for DIET.Differences in G.metallireducens expression patterns for genes involved in extracellular electron transfer were particularly notable.Cocultures with c‐type cytochrome deletion mutant strains,ΔGmet_0930,ΔGmet_0557 andΔGmet_2896,never became established with G.sulfurreducens but adapted to grow with all three Methanosarcina.Two porin–cytochrome complexes,PccF and PccG,were important for DIET;however,PccG was more important for growth with Methanosarcina.Unlike cocultures with G.sulfurreducens and M.acetivorans,electrically conductive pili were not needed for growth with M.barkeri.Shewanella oneidensis,another electroactive microbe with abundant outer‐surface c‐type cytochromes,did not grow via DIET.The results demonstrate that the presence of outer‐surface c‐type cytochromes does not necessarily confer the capacity for DIET and emphasize the impact of the electron‐accepting partner on the physiology of the electron‐donating DIET partner. | Dawn E.Holmes Jinjie Zhou Jessica A.Smith Caiqin Wang Xinying Liu Derek R.Lovley | 2022 | mLife2022，1，3： | 1 |
| 9 | A novel Methylomirabilota methanotroph potentially couples methane oxidation to iodate reduction显示文摘Impact statement Methane oxidizing microbes play a key role in reducing the emission of this potent greenhouse gas to the atmosphere.The known versatility of the recently discovered anaerobic Methylomirabilota methanotrophs is limited.Here,we report a novel uncultured Methylomirabilis species,Candidatus Methylomirabilis iodofontis,with the genetic potential of iodate respiration from biofilm in iodine‐rich cavern spring water.Star‐like cells resembling Methylomirabilis oxyfera were directly observed from the biofilm and a high‐quality metagenome‐assembled genome(MAG)of Ca.M.iodofontis was assembled.In addition to oxygenic denitrification and aerobic methane oxidation pathways,the M.iodofontis MAG also indicated its iodate‐reducing potential,a capability that would enable the bacterium to use iodate other than nitrite as an electron acceptor,a hitherto unrecognized metabolic potential of Methylomirabilota methanotrophs.The results advance the current understanding of the ecophysiology of anaerobic Methylomirabilota methanotrophs and may suggest an additional methane sink,especially in iodate‐rich ecosystems. | Baoli Zhu Clemens Karwautz Stefan Andrei Andreas Klingl Jakob Pernthaler Tillmann Lueders | 2022 | mLife2022，1，3： | 1 |
| 10 | DANMEL:A manually curated reference database for analyzing mobile genetic elements associated with bacterial drug resistance显示文摘Impact statement We have developed a manually curated online reference database,DANMEL(http://gffzzc938d18ffd334cb4h5q5ub56o5xqc6fnw.ffgz.tsg.suse.edu.cn/danmel/),that addresses the lack of accurate dissection and annotation of the genetic structures of mobile genetic elements(MGEs)with genes for drug resistance.DANMEL contains accurately annotated and genetically dissected reference MGEs covering 5 categories and 135 subcategories/subfamilies of MGEs.Further,DANMEL provides a detailed guide on how to precisely annotate MGEs.DANMEL also provides SEARCH/BLAST functions to facilitate finding reference MGEs.Overall,DANMEL will aid researchers to conduct in-depth genetic analysis of sequenced bacterial MGEs with drug-resistance genes and further facilitate a better understanding of bacterial MGEs associated with drug resistance at a genomic level. | Peng Wang Xiaoyuan Jiang Kai Mu Ying Jing Zhe Yin Yujun Cui Cuidan Li Xinhua Luo Fangzhou Chen Ting Yu Zhichen Zhu Yansong Sun Fei Chen Dongsheng Zhou | 2022 | mLife2022，1，4： | 1 |
| 11 | Fatty acid feedstocks enable a highly efficient glyoxylate-TCA cycle for high-yield production of β-alanine显示文摘Metabolic engineering to produce tricarboxylic acid(TCA)cycle-derived chemicals is usually associated with problems of low production yield and impaired cellular metabolism.In this work,we found that fatty acid(FA)feedstocks could enable high-yield production of TCA cycle-derived chemicals,while maintaining an efficient and balanced metabolic flux of the glyoxylate-TCA cycle,which is favorable for both product synthesis and cell growth.Here,we designed a novel synthetic pathway for production of β-alanine,an important TCA cycle-derived product,from FAs with a high theortecial yield of 1.391 g/g.By introducing panD,improving aspA,and knocking out iclR,glyoxylate shunt was highly activated in FAs and the yield of β-alanine reached 0.71 g/g from FAs,much higher than from glucose.Blocking the TCA cycle at icd/sucA/fumAC nodes could increase β-alanine yield in a flask cultivation,but severely reduced cell growth and FA utilization during fed-batch processes.Replenishing oxaloacetate by knocking out aspC and recovering fumAC could restore the growth and lead to a titer of 35.57 g/l.After relieving the oxidative stress caused by FA metabolism,β-alanine production could reach 72.05 g/l with a maximum yield of 1.24 g/g,about 86% of the theoretical yield.Our study thus provides a promising strategy for the production of TCA cycle-derived chemicals. | Yingchun Miao Jiao Liu Xuanlin Wang Bo Liu Weifeng Liu Yong Tao | 2022 | mLife2022，1，2： | 1 |
| 12 | Comparative genomic analysis of Thermus provides insights into the evolutionary history of an incomplete denitrification pathway显示文摘Biological denitrification is a crucial process in the nitrogen biogeochemical cycle,and Thermus has been reported to be a significant heterotrophic denitrifier in terrestrial geothermal environments.However,neither the denitrification potential nor the evolutionary history of denitrification genes in the genus Thermus or phylum Deinococcota is well understood.Here,we performed a comparative analysis of 23 Thermus genomes and identified denitrification genes in 15 Thermus strains.We confirmed that Thermus harbors an incomplete denitrification pathway as none of the strains contain the nosZ gene.Ancestral character state reconstructions and phylogenetic analyses showed that narG,nirS,and norB genes were acquired by the last common ancestor of Thermales and were inherited vertically.In contrast,nirK of Thermales was acquired via two distinct horizontal gene transfers from Proteobacteria to the genus Caldithermus and from an unknown donor to the common ancestor of all known Thermus species except Thermus filiformis.This study expands our understanding of the genomic potential for incomplete denitrification in Thermus,revealing a largely vertical evolutionary history of the denitrification pathway in the Thermaceae,and supporting the important role for Thermus as an important heterotrophic denitrifier in geothermal environments. | Jian-Yu Jiao Zheng-Han Lian Meng-Meng Li Nimaichand Salam En-Min Zhou Lan Liu Hong Ming Guoxing Nie Wensheng Shu Guoping Zhao Brian P.Hedlund Wen-Jun Li | 2022 | mLife2022，1，2： | 1 |
| 13 | Cultivating the unseen:Lessons from James Tiedje显示文摘In recounting Dr.James M.Tiedje's outstanding research achievements spanning the past 55 years,it is easy to overlook his early and mid-career endeavors.Specifically,his contribution to the aerobic degradation of pesticides and other chemicals,as well as methanogenic degradation of those compounds retains their brilliance.Many researchers in environmental microbiology have gained invaluable knowledge from these studies,which have been applied to the elucidation of previously uncultivated microorganisms. | Yoichi Kamagata | 2023 | mLife2023，2，3： | 0 |
| 14 | Roadmap to tackle antibiotic resistance in the environment under the One Health framework显示文摘Antibiotic resistance has been recognized as a major challenge worldwide for humans.“One Health”has been recognized as a key concept for containment of antibiotic resistance.Under the framework,the role of the environment in the development of antibiotic resistance genes(ARGs)has become increasingly obvious.Despite numerous efforts,response to antibiotic re-sistance is considered to be inadequate,which is probably due to the lack of a clear roadmap.Here,we propose a“One Health”roadmap to combat antibiotic resistance in the environment through(1)understanding environmental resistome.The environmental gene pool has long been recognized as the single largest reservoir of both known and novel ARGs.(2)Standardizing ARG quantification.Systematic joint efforts based on standardized quantification are urgently needed to un-derstand the true tempospatial profiles of the environmental resistome.(3)Identifying mechanisms of resistome development.Horizontal gene transfer and co-selection have been recognized as the two main mechanisms contributing to the environmental resistome.(4)Establishing a risk-assessment framework.The first critical step for large-scale cost-effective targeted ARG management in the environment is the risk assessment to identify the priority ARGs for control.(5)Formulating regulatory standards.By correlating the environmental ARG profile with public health,we may identify the indicator ARGs that can be integrated into current environmental quality standards.(6)Developing control strategies.Systematic analysis of available control technologies is required to identify the most feasible ones to curtail the spread of ARGs in the environment.The proposed roadmap under the“One Health”framework provides a guide to tackle antibiotic resistance in the environment. | Liguan Li Tong Zhang | 2023 | mLife2023，2，3： | 0 |
| 15 | Denitrification and the challenge of scaling microsite knowledge to the globe显示文摘Our knowledge of microbial processes—who is responsible for what,the rates at which they occur,and the substrates consumed and products produced—is imperfect for many if not most taxa,but even less is known about how microsite processes scale to the ecosystem and thence the globe.In both natural and managed environments,scaling links fundamental knowledge to application and also allows for global assessments of the importance of microbial processes.But rarely is scaling straightforward:More often than not,process rates in situ are distributed in a highly skewed fashion,under the influence of multiple interacting controls,and thus often difficult to sample,quantify,and predict.To date,quantitative models of many important processes fail to capture daily,seasonal,and annual fluxes with the precision needed to effect meaningful management outcomes.Nitrogen cycle processes are a case in point,and denitrification is a prime example.Statistical models based on machine learning can improve predictability and identify the best environmental predictors but are—by themselves—insufficient for revealing process-level knowledge gaps or predicting outcomes under novel environmental conditions.Hybrid models that incorporate well-calibrated process models as predictors for machine learning algorithms can provide both improved understanding and more reliable forecasts under environmental conditions not yet experienced.Incorporating trait-based models into such efforts promises to improve predictions and understanding still further,but much more development is needed. | G.Philip Robertson | 2023 | mLife2023，2，3： | 0 |
| 16 | Assessing mechanisms for microbial taxa and community dynamics using process models显示文摘Disentangling the assembly mechanisms controlling community composition,structure,distribution,functions,and dynamics is a central issue in ecology.Although various approaches have been proposed to examine community assembly mechanisms,quanti-tative characterization is challenging,particularly in microbial ecology.Here,we present a novel approach for quantitatively delineating community assembly mechanisms by combining the consumer–resource model with a neutral model in stochastic differential equations.Using time-series data from anaerobic bioreactors that target microbial 16S rRNA genes,we tested the applicability of three ecological models:the consumer–resource model,the neutral model,and the combined model.Our results revealed that model performances varied substantially as a function of population abundance and/or process conditions.The combined model performed best for abundant taxa in the treatment bioreactors where process conditions were manipulated.In contrast,the neutral model showed the best performance for rare taxa.Our analysis further indicated that immigration rates decreased with taxa abundance and com-petitions between taxa were strongly correlated with phylogeny,but within a certain phylogenetic distance only.The determinism underlying taxa and community dynamics were quantitatively assessed,showing greater determinism in the treatment bioreactors that aligned with the subsequent abnormal system functioning.Given its mechanistic basis,the framework developed here is expected to be potentially applicable beyond microbial ecology. | Linwei Wu Yunfeng Yang Daliang Ning Qun Gao Huaqun Yin Naija Xiao Benjamin YZhou Si Chen Qiang He Jizhong Zhou | 2023 | mLife2023，2，3： | 0 |
| 17 | Environmental selection and evolutionary process jointly shape genomic and functional profiles of mangrove rhizosphere microbiomes显示文摘Mangrove reforestation with introduced species has been an important strategy to restore mangrove ecosystem functioning.However,how such activities affect microbially driven methane(CH4),nitrogen(N),and sulfur(S)cycling of rhizosphere microbiomes remains unclear.To understand the effect of environmental selection and the evolutionary process on microbially driven biogeochemical cycles in native and introduced mangrove rhizospheres,we analyzed key genomic and functional profiles of rhizosphere microbiomes from native and introduced mangrove species by metagenome sequencing technologies.Compared with the native mangrove(Kandelia obovata,KO),the introduced mangrove(Sonneratia apetala,SA)rhizosphere microbiome had significantly(p<0.05)higher average genome size(AGS)(5.8 vs.5.5 Mb),average 16S ribosomal RNA gene copy number(3.5 vs.3.1),relative abundances of mobile genetic elements,and functional diversity in terms of the Shannon index(7.88 vs.7.84)but lower functional potentials involved in CH4 cycling(e.g.,mcrABCDG and pmoABC),N2 fixation(nifHDK),and inorganic S cycling(dsrAB,dsrC,dsrMKJOP,soxB,sqr,and fccAB).Similar results were also observed from the recovered Proteobacterial metagenome-assembled genomes with a higher AGS and distinct functions in the introduced mangrove rhizosphere.Additionally,salinity and ammonium were identified as the main environmental drivers of functional profiles of mangrove rhizosphere microbiomes through deterministic processes.This study advances our understanding of microbially mediated biogeochemical cycling of CH_(4),N,and S in the mangrove rhizosphere and provides novel insights into the influence of environmental selection and evolutionary processes on ecosystem functions,which has important implications for future mangrove reforestation. | Xiaoli Yu Qichao Tu Jihua Liu Yisheng Peng Cheng Wang Fanshu Xiao Yingli Lian Xueqin Yang Ruiwen Hu Huang Yu Lu Qian Daoming Wu Ziying He Longfei Shu Qiang He Yun Tian Faming Wang Shanquan Wang Bo Wu Zhijian Huang Jianguo He Qingyun Yan Zhili He | 2023 | mLife2023，2，3： | 0 |
| 18 | A small,polyphyletic group of Firmicutes synthesizes trimethylamine from L-carnitine显示文摘Impact statement Gut microbiota-derived trimethylamine(TMA)is associated with cardiometabolic disorders and exemplifies a microbial involvement in the etiology of emerging,noncommunicable diseases,the leading causes of death worldwide.Three bio-chemical pathways taking dietary compounds as intake have been described with distinct taxa involved that are all present at low relative abundances.A recently discovered pathway is now considered to be the main route for TMA synthesis from L-carnitine involvingγ-butyrobetaine as an intermediate product.By comprehensive(meta)genomic screening of publicly available data,namely,genomes of the UHGG catalog(n>200,000)and 10 metagenomic(transcriptomic)data sets,we revealed bacteria synthesizing TMA via this pathway and specified their ecophysiology.Results will contribute to stratification of individuals based on their gut microbiota's potential to synthesize TMA and might aid in the development of strategies restricting TMA formation. | Marius Vital Ylenia Heinrich-Sanchez | 2023 | mLife2023，2，3： | 0 |
| 19 | Widespread Bathyarchaeia encode a novel methyltransferase utilizing lignin-derived aromatics显示文摘Lignin degradation is a major process in the global carbon cycle across both terrestrial and marine ecosystems.Bathyarchaeia,which are among the most abundant microorganisms in marine sediment,have been proposed to mediate anaerobic lignin degradation.However,the mechanism of bathyarchaeial lignin degradation remains unclear.Here,we report an enrichment culture of Bathy-archaeia,named Candidatus Baizosediminiarchaeum ligniniphilus DL1YTT001(Ca.B.ligniniphilus),from coastal sediments that can grow with lignin as the sole organic carbon source under mesophilic anoxic conditions.Ca.B.ligniniphilus possesses and highly expresses novel methyltransferase 1(MT1,mtgB)for transferring methoxyl groups from lignin monomers to cob(I)alamin.MtgBs have no homology with known microbial methyltransferases and are present only in bathyarchaeial lineages.Heterologous expression of the mtgB gene confirmed O-demethylation activity.The mtgB genes were identified in metagenomic data sets from a wide range of coastal sediments,and they were highly expressed in coastal sediments from the East China Sea.These findings suggest that Bathyarchaeia,capable of O-demethylation via their novel and specific methyltransferases,are ubiquitous in coastal sediments. | Tiantian Yu Haining Hu Xianhong Zeng Yinzhao Wang Donald Pan Longhui Deng Lewen Liang Jialin Hou Fengping Wang | 2023 | mLife2023，2，3： | 0 |
| 20 | Dual functions:A coumarin–chalcone conjugate inhibits cyclic-di-GMP and quorum-sensing signaling to reduce biofilm formation and virulence of pathogens显示文摘Antibiotic resistance or tolerance of pathogens is one of the most serious global public health threats.Bacteria in biofilms show extreme tolerance to almost all antibiotic classes.Thus,use of antibiofilm drugs without bacterial-killing effects is one of the strategies to combat antibiotic tolerance.In this study,we discovered a coumarin–chalcone conjugate C9,which can inhibit the biofilm formation of three common pathogens that cause nosocomial infections,namely,Pseudomonas aeruginosa,Staph-ylococcus aureus,and Escherichia coli,with the best antibiofilm activity against P.aeruginosa.Further investigations indicate that C9 decreases the synthesis of the key biofilm matrix exopolysaccharide Psl and bacterial second messenger cyclic-di-GMP.Meanwhile,C9 can interfere with the regulation of the quorum sensing(QS)system to reduce the virulence of P.aeruginosa.C9 treatment enhances the sensitivity of biofilm to several antibiotics and reduces the survival rate of P.aeruginosa under starvation or oxidative stress conditions,indicating its excellent potential for use as an antibiofilm-forming and anti-QS drug. | Yu Zhang Pramod Bhasme Dinesh S.Reddy Dejian Liu Zhaoxiao Yu Tianhu Zhao Yaqian Zheng Amit Kumar Haiying Yu Luyan Z.Ma | 2023 | mLife2023，2，3： | 0 |
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