mLife最新文献

{"title":"Protective efficacy of a universal influenza mRNA vaccine against the challenge of H1 and H5 influenza A viruses in mice","authors":"Yulei Li, Xi Wang, Xi Zeng, Wenbo Ren, Pu Liao, Baoli Zhu","doi":"10.1002/mlf2.12085","DOIUrl":"https://doi.org/10.1002/mlf2.12085","url":null,"abstract":"Abstract Current influenza vaccines need to be updated annually owing to constant antigenic drift in the globular head of the viral surface hemagglutinin (HA) glycoprotein. The immunogenic subdominant stem domain of HA is highly conserved and can be recognized by antibodies capable of binding multiple HA subtypes. Therefore, the HA stem antigen is a promising target for the design of universal influenza vaccines. On the basis of an established lipid nanoparticle‐encapsulated mRNA vaccine platform, we designed and developed a novel universal influenza mRNA vaccine (mHAs) encoding the HA stem antigen of the influenza A (H1N1) virus. We tested the efficacy of the mHAs vaccine using a mouse model. The vaccine induced robust humoral and specific cellular immune responses against the stem region of HA. Importantly, two doses of the mHAs vaccine fully protected mice from lethal challenges of the heterologous H1N1 and heterosubtypic H5N8 influenza viruses. Vaccinated mice had less pathological lung damage and lower viral titers than control mice. These results suggest that an mRNA vaccine using the conserved stem region of HA may provide effective protection against seasonal and other possible influenza variants.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing mechanisms for microbial taxa and community dynamics using process models","authors":"Linwei Wu, Yunfeng Yang, Daliang Ning, Qun Gao, Huaqun Yin, Naija Xiao, Benjamin Y. Zhou, Si Chen, Qiang He, Jizhong Zhou","doi":"10.1002/mlf2.12076","DOIUrl":"https://doi.org/10.1002/mlf2.12076","url":null,"abstract":"Abstract 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, quantitative 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 competitions 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.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135298314","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A modified isooctane‐based DNA extraction method from crude oil","authors":"Armando Alibrandi, Rolando di Primio, Alexander Bartholomäus, Jens Kallmeyer","doi":"10.1002/mlf2.12081","DOIUrl":"https://doi.org/10.1002/mlf2.12081","url":null,"abstract":"Abstract Microbes from oil reservoirs shape petroleum composition through processes such as biodegradation or souring. Such processes are considered economically detrimental and might pose health and safety hazards. It is therefore crucial to understand the composition of a reservoir's microbial community and its metabolic capabilities. However, such analyses are hindered by difficulties in extracting DNA from such complex fluids as crude oil. Here, we present a novel DNA extraction method from oils with a wide American Petroleum Institute (API) gravity (density) range. We investigated the ability to extract cells from oils with different solvents and surfactants, the latter both nonionic and ionic. Furthermore, we evaluated three DNA extraction methods. Overall, the best DNA yields and the highest number of 16S rRNA reads were achieved with isooctane as a solvent, followed by an ionic surfactant treatment using sodium dodecyl sulfate and DNA extraction using the PowerSoil Pro Kit (Qiagen). The final method was then applied to various oils from oil reservoirs collected in aseptic conditions. Despite the expected low cell density of 10 1 –10 3 cells/ml, the new method yielded reliable results, with average 16S rRNA sequencing reads in the order of 41431 (±8860) per sample. Thermophilic, halophilic, and anaerobic taxa, which are most likely to be indigenous to the oil reservoir, were found in all samples. API gravity and DNA yield, despite the sufficient DNA obtained, did not show a correlation.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135588201","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Acquisition of a novel conjugative multidrug‐resistant hypervirulent plasmid leads to hypervirulence in clinical carbapenem‐resistant <i>Klebsiella pneumoniae</i> strains","authors":"Gong Li, Ling Jia, Lei Wan, Lijuan Xia, Ang Gao, Runshi Yang, Ruanyang Sun, Minge Wang, Juan Du, Xinlei Lian, Rongmin Zhang, Liangxing Fang, Xiaoping Liao, Yahong Liu, Bao‐Tao Liu, Jian Sun","doi":"10.1002/mlf2.12086","DOIUrl":"https://doi.org/10.1002/mlf2.12086","url":null,"abstract":"Abstract The co‐occurrence of plasmid‐mediated multidrug resistance and hypervirulence in epidemic carbapenem‐resistant Klebsiella pneumoniae has emerged as a global public health issue. In this study, an ST23 carbapenem‐resistant hypervirulent K. pneumoniae (CR‐HvKP) strain VH1‐2 was identified from cucumber in China and harbored a novel hybrid plasmid pVH1‐2‐VIR. The plasmid pVH1‐2‐VIR carrying both virulence and multidrug‐resistance (MDR) genes was likely generated through the recombination of a virulence plasmid and an IncFIIK conjugative MDR plasmid in clinical ST23 18622 isolated from a sputum sample. The plasmid pVH1‐2‐VIR exhibited the capacity for transfer to the clinical ST11 carbapenem‐resistant K. pneumoniae (CRKP) strain via conjugation assay. Acquisition of pVH1‐2‐VIR plasmid directly converted a CRKP into CR‐HvKP strain characterized by hypermucoviscosity, heightened virulence for Galleria mellonella larvae, and increased colonization ability in the mouse intestine. The emergence of such a hybrid plasmid may expedite the spread of CR‐HvKP strains, posing a significant risk to human health.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135587902","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cultivating the unseen: Lessons from James Tiedje","authors":"Yoichi Kamagata","doi":"10.1002/mlf2.12083","DOIUrl":"https://doi.org/10.1002/mlf2.12083","url":null,"abstract":"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. Dr. Tiedje embarked on his career in soil microbiology at Cornell University in 1964 under the guidance of Martin Alexander. Motivated by Rachel Carson's Silent Spring published in 1962, he developed a keen interest in studying the degradation of 2,4-dichlorophenoxy acetic acid (2,4-D), widely used as a broad-leaf herbicide. Dr. Tiedje found that an Arthrobacter species converts 2,4-D into chlorocatechols, facilitated by a soluble ether linkage-cleaving enzyme1, 2. Subsequently, extensive investigations into the 2,4-D degradation by aerobic microorganisms were conducted, leading to the identification of α-ketoglutarate-dependent dioxygenase, the enzyme involved in the first step of 2,4-D metabolism3 (Figure 1). The story starts with my involvement in the “2,4-D project.” The project took place at the Center for Microbial Ecology, Michigan State University (MSU), where we focused on microbial evolution. 2,4-D, being an anthropogenic chemical with no analogous compounds found in nature, provided an excellent opportunity to explore how enzymes with different original functions were recruited and evolved to adapt to 2,4-D degradation. The project was initiated by Profs. James M. Tiedje and Keiji Yano (followed by Prof. Koki Horikoshi) in 1991 and received funding from Japan Science and Technology Agency (JST, formerly JRDC) and National Science Foundation USA. It involved numerous scientists and over 10 postdocs from various parts of the world. It was the mid-1990s, a time before high-throughput genome sequencing became available, and molecular biological studies were conducted using classical methods such as DNA sequencing using big gel plates. During this period, I had been working on methanogenic Archaea till I joined the project. To begin, we initiated genetic analysis of known 2,4-D-degraders, as well as search for previously unknown 2,4-D-degrading microbes4, 5. Meanwhile, Dr. Tiedje, who was supposed to lead the project, was on sabbatical, enjoying the warmer climate of Hawaii (quite different from Michigan) and collaborating with Hawaiian researchers. He learned that there were soils in Hawaii that had not been exposed to 2,4-D, and he brought those untouched soils back to Michigan. The underlying idea was to investigate whether the microorganisms capable of breaking down this widely used chemical, which was artificially synthesized and sprayed in large quantities, were absent in the Hawaiian soils, or there were microbes possessing th","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual functions: A coumarin–chalcone conjugate inhibits cyclic‐di‐GMP and quorum‐sensing signaling to reduce biofilm formation and virulence of pathogens","authors":"Yu Zhang, Pramod Bhasme, Dinesh S. Reddy, Dejian Liu, Zhaoxiao Yu, Tianhu Zhao, Yaqian Zheng, Amit Kumar, Haiying Yu, Luyan Z. Ma","doi":"10.1002/mlf2.12087","DOIUrl":"https://doi.org/10.1002/mlf2.12087","url":null,"abstract":"Abstract 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 , Staphylococcus 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.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915613","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Widespread <i>Bathyarchaeia</i> encode a novel methyltransferase utilizing lignin‐derived aromatics","authors":"Tiantian Yu, Haining Hu, Xianhong Zeng, Yinzhao Wang, Donald Pan, Longhui Deng, Lewen Liang, Jialin Hou, Fengping Wang","doi":"10.1002/mlf2.12082","DOIUrl":"https://doi.org/10.1002/mlf2.12082","url":null,"abstract":"Abstract 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 Bathyarchaeia , 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.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135349559","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A small, polyphyletic group of <i>Firmicutes</i> synthesizes trimethylamine from <scp>l</scp>‐carnitine","authors":"Marius Vital, Ylenia Heinrich‐Sanchez","doi":"10.1002/mlf2.12079","DOIUrl":"https://doi.org/10.1002/mlf2.12079","url":null,"abstract":"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 biochemical 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 involving γ‐butyrobetaine as an intermediate product. By comprehensive (meta) genomic screening of publicly available data, namely, genomes of the UHGG catalog ( n &gt; 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.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135304857","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of atypical T4SS effector proteins mediating bacterial defense","authors":"Xi Shen, Zixiang Yang, Zihan Li, Dan Xiong, Jinxing Liao, Weimei He, Danyu Shen, Xiaolong Shao, Ben Niu, Yongxing He, Yong‐Gui Gao, Guoliang Qian","doi":"10.1002/mlf2.12084","DOIUrl":"https://doi.org/10.1002/mlf2.12084","url":null,"abstract":"Abstract To remain competitive, proteobacteria use various contact‐dependent weapon systems to defend against microbial competitors. The bacterial‐killing type IV secretion system (T4SS) is one such powerful weapon. It commonly controls the killing/competition between species by secreting the lethal T4 SS e ffector (T4E) proteins carrying conserved XVIPCD domains into competing cells. In this study, we sought knowledge to understand whether the bacterial‐killing T4SS‐producing bacteria encode T4E‐like proteins and further explore their biological functions. To achieve this, we designed a T4E‐guided approach to discover T4E‐like proteins that are designated as atypical T4Es. Initially, this approach required scientists to perform simple BlastP search to identify T4E homologs that lack the XVIPCD domain in the genomes of T4SS‐producing bacteria. These homologous genes were then screened in Escherichia coli to identify antibacterial candidates (atypical T4Es) and their neighboring detoxification proteins, followed by testing their gene cotranscription and validating their physical interactions. Using this approach, we did discover two atypical T4E proteins from the plant‐beneficial Lysobacter enzymogenes and the phytopathogen Xanthomonas citri . We also provided substantial evidence to show that the atypical T4E protein Le1637‐mediated bacterial defense in interspecies interactions between L. enzymogenes and its competitors. Therefore, the newly designed T4E‐guided approach holds promise for detecting functional atypical T4E proteins in bacterial cells.","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134915609","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genome-wide identification of endogenous retrovirus elements and their active transcription in mink genome.","authors":"Zheng Li, Qing Wang, Na Lv, Guojin Xu, Xuemei Yang, Baoli Zhu","doi":"10.1002/mlf2.12074","DOIUrl":"10.1002/mlf2.12074","url":null,"abstract":"<p><p>Mammalian endogenous retroviruses (ERVs) are ancient retroviruses that have been integrated into genomes. ERVs were believed to be inactive until the discovery of ERV transcription in the mouse genome. However, the transcription level and function of ERV elements in mammalian genomes are not well understood. In this study, we performed the first genome-wide scanning of ERV loci in the American mink (<i>Neogale vison</i>) genome (NeoERV) followed by transcriptomic analysis to detect actively transcribed NeoERV elements. A total of 365,791 NeoERV loci were identified, and161,205 (44%) of these loci were found to be actively transcribed based on transcriptomic data from three types of tissues (amygdala, trachea and lung). More than one third of the actively transcribed NeoERV loci were tissue-specific. Furthermore, some of the active loci were associated with host gene transcription, and the level of NeoERV transcription was positively correlated with that of host genes, specifically when active loci were located in overlapped gene regions. An in-depth analysis of the envelope protein coding <i>env</i> gene showed that, in general, its transcription level was higher than that of NeoERVs, which is believed to be associated with host immunity.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2023-06-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10989824/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76378368","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}