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Potential antiviral effects of the marine probiotic Paraliobacillus zengyii on the respiratory syncytial virus. 海洋益生菌增益副杆菌对呼吸道合胞病毒的潜在抗病毒作用。
IF 6.7
mLife Pub Date : 2025-06-18 eCollection Date: 2025-06-01 DOI: 10.1002/mlf2.70015
Qianjin Fan, Beijie Li, Lan Chen, Mengqi Jiao, Zhijie Cao, Kun Yue, Haoyue Huangfu, Hui Sun, Xiaoxia Wang, Xuelian Luo, Jianguo Xu
{"title":"Potential antiviral effects of the marine probiotic <i>Paraliobacillus zengyii</i> on the respiratory syncytial virus.","authors":"Qianjin Fan, Beijie Li, Lan Chen, Mengqi Jiao, Zhijie Cao, Kun Yue, Haoyue Huangfu, Hui Sun, Xiaoxia Wang, Xuelian Luo, Jianguo Xu","doi":"10.1002/mlf2.70015","DOIUrl":"10.1002/mlf2.70015","url":null,"abstract":"<p><p>Probiotics can reduce the incidence of respiratory syncytial virus (RSV) disease in premature infants; this approach is resource-intensive and less expensive than other strategies and easier to implement than most current methods worldwide. Traditional lactic acid-producing bacteria are the main probiotics that have been studied for RSV treatment. Marine probiotics promote the survival, immunity, and disease resistance of aquatic plants and animals. However, relatively little research has been conducted on viral infections in humans. Here, we report a slightly halophilic and extremely halotolerant marine bacterium, <i>Paraliobacillus zengyii</i>, which has antiviral activity and grows at a relatively low temperature (28°C). We found that <i>P. zengyii</i> inhibited RSV infection by regulating the interferon (IFN) response both in vitro and in vivo. <i>P. zengyii</i> significantly increased the RSV-induced phosphorylation of TBK1 and IRF3 and the expression of antiviral factors interferon-induced transmembrane protein 1 (IFITM1) and interferon-induced transmembrane protein 3 (IFITM3). Furthermore, <i>P. zengyii</i> upregulated Sendai virus (SeV)- and poly(I:C)-induced IFN-β expression. These results indicate that the marine bacterium <i>P. zengyii</i> inhibits RSV infection and increases IFN-β production in response to RSV, SeV infection, or poly(I:C) stimulation. Consequently, <i>P. zengyii</i> has potential as a broad-spectrum anti-RNA virus probiotic.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 3","pages":"249-258"},"PeriodicalIF":6.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546687","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}
引用次数: 0
Legionella pneumophila modulates the host cytoskeleton by an effector of transglutaminase activity. 嗜肺军团菌通过谷氨酰胺转氨酶活性的效应调节宿主细胞骨架。
IF 6.7
mLife Pub Date : 2025-06-18 eCollection Date: 2025-06-01 DOI: 10.1002/mlf2.70013
Yan Liu, Yao Liu, Zhao-Qing Luo
{"title":"<i>Legionella pneumophila</i> modulates the host cytoskeleton by an effector of transglutaminase activity.","authors":"Yan Liu, Yao Liu, Zhao-Qing Luo","doi":"10.1002/mlf2.70013","DOIUrl":"10.1002/mlf2.70013","url":null,"abstract":"<p><p>The bacterial pathogen <i>Legionella pneumophila</i> delivers more than 330 effector proteins into host cells through its Dot/Icm type IV secretion system (T4SS) to facilitate its intracellular replication. A number of these effectors modulate organelle trafficking pathways to create a membrane-bound niche called the <i>Legionella</i>-containing vacuole (LCV). In this study, we found that <i>L. pneumophila</i> induces F-actin accumulation in the host cell cortex by its Dot/Icm substrate RavJ (Lpg0944). RavJ harbors a C<sub>101</sub>H<sub>138</sub>D<sub>170</sub> motif associated with human tissue transglutaminases (TGs). We show that RavJ catalyzes a covalent linkage between actin and members of the Motin family of proteins, including Angiomotin (AMOT) and Angiomotin-like 1 (AMOTL1), which are known to regulate cell migration and contribute to the formation of cellular structures such as endothelial cell junctions and tubes. Further study reveals that RavJ-induced crosslink between actin and AMOT occurs on its Gln<sub>354</sub> residue. Crosslink between actin and AMOT significantly reduces the binding between actin and its binding partner cofilin, suggesting that RavJ inhibits actin depolymerization. We also demonstrate that the metaeffector LegL1 directly interacts with RavJ to antagonize its TG activity, leading to reduced crosslinks between actin and Motin proteins. Our results reveal a novel mechanism of modulating the host actin cytoskeleton by <i>L. pneumophila</i>.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 3","pages":"232-248"},"PeriodicalIF":6.7,"publicationDate":"2025-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207909/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546682","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}
引用次数: 0
"Misuse" of RNA-seq data in microbiome studies: A cautionary tale of poly(A). 微生物组研究中RNA-seq数据的“误用”:聚(A)的警世故事。
IF 6.7
mLife Pub Date : 2025-06-02 eCollection Date: 2025-06-01 DOI: 10.1002/mlf2.70012
John Maringa Githaka
{"title":"\"Misuse\" of RNA-seq data in microbiome studies: A cautionary tale of poly(A).","authors":"John Maringa Githaka","doi":"10.1002/mlf2.70012","DOIUrl":"10.1002/mlf2.70012","url":null,"abstract":"","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 3","pages":"227-231"},"PeriodicalIF":6.7,"publicationDate":"2025-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207903/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546680","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}
引用次数: 0
Archaea show different geographical distribution patterns compared to bacteria and fungi in Arctic marine sediments. 与细菌和真菌相比,古细菌在北极海洋沉积物中具有不同的地理分布模式。
IF 6.7
mLife Pub Date : 2025-04-24 eCollection Date: 2025-04-01 DOI: 10.1002/mlf2.70006
Jianxing Sun, Hongbo Zhou, Haina Cheng, Zhu Chen, Yuguang Wang
{"title":"Archaea show different geographical distribution patterns compared to bacteria and fungi in Arctic marine sediments.","authors":"Jianxing Sun, Hongbo Zhou, Haina Cheng, Zhu Chen, Yuguang Wang","doi":"10.1002/mlf2.70006","DOIUrl":"10.1002/mlf2.70006","url":null,"abstract":"<p><p>Microorganisms dominate marine environments in the polar oceans and are known to harbor greater diversity and abundance than was once thought, and yet, little is known about their biogeographic distribution patterns in marine sediments at a broad spatial scale. In this study, we conducted extensive sampling of marine sediments along a latitudinal transect spanning 2500 km from the Bering Sea to the Arctic Ocean to investigate the geographical distribution patterns of bacteria, archaea, and fungi. Our findings revealed that the community similarities of bacteria and fungi decay at similar rates with increasing geographical distance (slope: -0.005 and -0.002), which are much lower than the decay rate of archaeal communities (slope: -0.012). Notably, microbial richness and community composition showed significant differences in the region of 75-80°N compared to other regions in 60-75°N. Salinity, temperature, pH, ammonium nitrogen, and total organic carbon are key factors that significantly affect microbial community variations. Furthermore, bacterial co-occurrence networks showed more complex interactions but lower modularity than fungal counterparts. This study provides crucial insights into the spatial distribution patterns of bacteria, archaea, and fungi in the Arctic marine sediments and will be critical for a better understanding of microbial global distribution and ecological functions.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 2","pages":"205-218"},"PeriodicalIF":6.7,"publicationDate":"2025-04-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042116/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061369","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}
引用次数: 0
Cpx-mediated amino acid sensing diversifies gastrointestinal colonization of Klebsiella pneumoniae. cpx介导的氨基酸感知使肺炎克雷伯菌胃肠道定植多样化。
IF 6.7
mLife Pub Date : 2025-04-23 eCollection Date: 2025-04-01 DOI: 10.1002/mlf2.70005
Danyang Li, Qiucheng Shi, Liuqing He, Jianhua Luo, Huajie Zhu, Xiaoting Hua, Yunsong Yu, Yan Jiang, Liang Tao
{"title":"Cpx-mediated amino acid sensing diversifies gastrointestinal colonization of <i>Klebsiella pneumoniae</i>.","authors":"Danyang Li, Qiucheng Shi, Liuqing He, Jianhua Luo, Huajie Zhu, Xiaoting Hua, Yunsong Yu, Yan Jiang, Liang Tao","doi":"10.1002/mlf2.70005","DOIUrl":"10.1002/mlf2.70005","url":null,"abstract":"<p><p><i>Klebsiella pneumoniae</i> is a Gram-negative opportunistic pathogenic bacterium that occasionally inhabits the human gastrointestinal tracts. Gut-colonized <i>K. pneumoniae</i> may then metastasize to other organs and tissues, thus causing severe infections. In this study, we identified three <i>cpxA</i> mutations in <i>K. pneumoniae</i> that experimentally evolved to show reduced adhesive ability. CpxA is a sensor histidine kinase that rendered reduced surface adhesion and gut colonization ability in <i>K. pneumoniae</i>. Interestingly, one experimentally gained CpxA mutant (L168del) also commonly occurs in nature. <i>K. pneumoniae</i> containing CpxA variants showed different colonization potentials through altered type 3 fimbriae expression. Lastly, we demonstrated that CpxA contributes to amino acid sensing, thus regulating the colonization of <i>K. pneumoniae</i> both on solid surfaces and in mouse intestines. The polymorphism of CpxA may help to broaden the environmental adaptation of the bacterium. These findings together reveal a Cpx-mediated regulation to diversify intestinal colonization in <i>K. pneumoniae</i>.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 2","pages":"181-192"},"PeriodicalIF":6.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042121/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061804","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}
引用次数: 0
A CRISPR-nonhomologous end-joining-based strategy for rapid and efficient gene disruption in Mycobacterium abscessus. 基于crispr -非同源末端连接的策略快速有效地破坏脓肿分枝杆菌的基因。
IF 6.7
mLife Pub Date : 2025-04-23 eCollection Date: 2025-04-01 DOI: 10.1002/mlf2.70007
Sanshan Zeng, Yanan Ju, Md Shah Alam, Ziwen Lu, H M Adnan Hameed, Lijie Li, Xirong Tian, Cuiting Fang, Xiange Fang, Jie Ding, Xinyue Wang, Jinxing Hu, Shuai Wang, Tianyu Zhang
{"title":"A CRISPR-nonhomologous end-joining-based strategy for rapid and efficient gene disruption in <i>Mycobacterium abscessus</i>.","authors":"Sanshan Zeng, Yanan Ju, Md Shah Alam, Ziwen Lu, H M Adnan Hameed, Lijie Li, Xirong Tian, Cuiting Fang, Xiange Fang, Jie Ding, Xinyue Wang, Jinxing Hu, Shuai Wang, Tianyu Zhang","doi":"10.1002/mlf2.70007","DOIUrl":"10.1002/mlf2.70007","url":null,"abstract":"<p><p><i>Mycobacterium abscessus</i>, a fast-growing, non-tuberculous mycobacterium resistant to most antimicrobial drugs, causes a wide range of serious infections in humans, posing a significant public health challenge. The development of effective genetic manipulation tools for <i>M. abscessus</i> is still in progress, limiting both research and therapeutic advancements. However, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) systems have emerged as promising tools for generating highly specific double-strand breaks (DSBs) in its genome. One of the mechanisms that repair these DSBs is the error-prone nonhomologous end-joining (NHEJ) pathway, which facilitates targeted gene editing. In this study, we introduced a novel application of the CRISPR-NHEJ approach in <i>M. abscessus</i>. We demonstrated that NrgA from <i>M. marinum</i> plays a crucial role in repairing DSBs induced by the CRISPR-Cas system in <i>M. abscessus</i>. Contrary to previous findings, our study also revealed that inhibiting or overexpressing components of homologous recombination/single-strand annealing significantly reduces the efficiency of NHEJ repair in <i>M. abscessus</i>. This discovery challenges current perspectives and suggests that NHEJ repair in <i>M. abscessus</i> may involve components from both homologous recombination and single-strand annealing pathways, highlighting the complex interactions among the three DSB repair mechanisms in <i>M. abscessus</i>.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 2","pages":"169-180"},"PeriodicalIF":6.7,"publicationDate":"2025-04-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144039856","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}
引用次数: 0
The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates n-alkane degradation in Pseudomonas aeruginosa SJTD-1. GntR/VanR转录调控因子AlkR抑制铜绿假单胞菌SJTD-1中AlkB2单加氧酶的表达并调控正烷烃降解。
IF 6.7
mLife Pub Date : 2025-04-21 eCollection Date: 2025-04-01 DOI: 10.1002/mlf2.70004
Wanli Peng, Xiuli Wang, Qinchen Liu, Zhihong Xiao, Fulin Li, Nannan Ji, Zhuo Chen, Jiaying He, Junhao Wang, Zixin Deng, Shuangjun Lin, Rubing Liang
{"title":"The GntR/VanR transcription regulator AlkR represses AlkB2 monooxygenase expression and regulates <i>n</i>-alkane degradation in <i>Pseudomonas aeruginosa</i> SJTD-1.","authors":"Wanli Peng, Xiuli Wang, Qinchen Liu, Zhihong Xiao, Fulin Li, Nannan Ji, Zhuo Chen, Jiaying He, Junhao Wang, Zixin Deng, Shuangjun Lin, Rubing Liang","doi":"10.1002/mlf2.70004","DOIUrl":"10.1002/mlf2.70004","url":null,"abstract":"<p><p>Transmembrane alkane monooxygenase (AlkB)-type monooxygenases, especially AlkB2 monooxygenases, are crucial for aerobic degradation of the medium-to-long-chain <i>n</i>-alkanes in hydrocarbon-utilizing microorganisms. In this study, we identified a GntR/VanR transcription regulator AlkR of <i>Pseudomonas aeruginosa</i> SJTD-1 involved in the negative regulation of AlkB2 and deciphered its nature of DNA binding and ligand release. The deletion of <i>alkR</i> enhanced the transcription levels of the <i>alkB2</i> gene and the utilization efficiency of the medium-to-long-chain <i>n</i>-alkanes by strain SJTD-1. The dimer of AlkR recognizes and binds to a conserved palindromic motif in the promoter of the <i>alkB</i>2 gene, and structural symmetry is vital for DNA binding and transcription repression. The long-chain fatty acyl coenzyme A compounds can release AlkR and stimulate transcription of <i>alkB</i>2, reflecting the effect of alkane catabolic metabolites. Structural insights unveiled that the arginine residues and scaffold residues of AlkR are critical for DNA binding. Further bioinformatics analysis of AlkR revealed the widespread VanR-AlkB couples distributed in <i>Pseudomonadaceae</i> with high conservation in the sequences of functional genes and intergenic regions, highlighting a conserved regulatory pattern for <i>n</i>-alkane utilization across this family. These findings demonstrate the regulatory mechanism and structural basis of GntR/VanR transcription regulators in modulating <i>n</i>-alkane biodegradation and provide valuable insights in improving the bioremediation efficiency of hydrocarbon pollution.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 2","pages":"126-142"},"PeriodicalIF":6.7,"publicationDate":"2025-04-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042122/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144061003","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}
引用次数: 0
Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria. 一种苯酯共价酪蛋白水解蛋白酶抑制剂的鉴定及分枝杆菌对ClpP1P2的抑制作用分析。
IF 6.7
mLife Pub Date : 2025-04-15 eCollection Date: 2025-04-01 DOI: 10.1002/mlf2.12169
Genhui Xiao, Yumeng Cui, Liangliang Zhou, Chuya Niu, Bing Wang, Jinglan Wang, Shaoyang Zhou, Miaomiao Pan, Chi Kin Chan, Yan Xia, Lan Xu, Yu Lu, Shawn Chen
{"title":"Identification of a phenyl ester covalent inhibitor of caseinolytic protease and analysis of the ClpP1P2 inhibition in mycobacteria.","authors":"Genhui Xiao, Yumeng Cui, Liangliang Zhou, Chuya Niu, Bing Wang, Jinglan Wang, Shaoyang Zhou, Miaomiao Pan, Chi Kin Chan, Yan Xia, Lan Xu, Yu Lu, Shawn Chen","doi":"10.1002/mlf2.12169","DOIUrl":"10.1002/mlf2.12169","url":null,"abstract":"<p><p>The caseinolytic protease complex ClpP1P2 is crucial for protein homeostasis in mycobacteria and stress response and virulence of the pathogens. Its role as a potential drug target for combating tuberculosis (TB) has just begun to be substantiated in drug discovery research. We conducted a biochemical screening targeting the ClpP1P2 using a library of compounds phenotypically active against <i>Mycobacterium tuberculosis</i> (Mtb). The screening identified a phenyl ester compound GDI-5755, inhibiting the growth of Mtb and <i>M. bovis</i> BCG, the model organism of mycobacteria. GDI-5755 covalently modified the active-site serine residue of ClpP1, rendering the peptidase inactive, which was delineated through protein mass spectrometry and kinetic analyses. GDI-5755 exerted antibacterial activity by inhibiting ClpP1P2 in the bacteria, which could be demonstrated through a minimum inhibitory concentration (MIC) shift assay with a <i>clpP1</i> CRISPRi knockdown (<i>clpP1</i>-KD) mutant GH189. The knockdown also remarkably heightened the mutant's sensitivity to ethionamide and meropenem, but not to many other TB drugs. On the other hand, a comparative proteomic analysis of wild-type cells exposed to GDI-5755 revealed the dysregulated proteome, specifically showing changes in the expression levels of multiple TB drug targets, including EthA, Ldt<sub>Mt2</sub>, and PanD. Subsequent evaluation confirmed the synergistic activity of GDI-5755 when combined with the TB drugs to inhibit mycobacterial growth. Our findings indicate that small-molecule inhibitors targeting ClpP1P2, when used alongside existing TB medications, could represent novel therapeutic strategies.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 2","pages":"155-168"},"PeriodicalIF":6.7,"publicationDate":"2025-04-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12042115/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144048477","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}
引用次数: 0
iDOM: Statistical analysis of dissolved organic matter characterized by high-resolution mass spectrometry. 用高分辨率质谱法对溶解有机物进行统计分析。
IF 6.7
mLife Pub Date : 2025-04-14 eCollection Date: 2025-06-01 DOI: 10.1002/mlf2.70002
Fanfan Meng, Ang Hu, Kyoung-Soon Jang, Jianjun Wang
{"title":"<i>iDOM</i>: Statistical analysis of dissolved organic matter characterized by high-resolution mass spectrometry.","authors":"Fanfan Meng, Ang Hu, Kyoung-Soon Jang, Jianjun Wang","doi":"10.1002/mlf2.70002","DOIUrl":"10.1002/mlf2.70002","url":null,"abstract":"<p><p>Dissolved organic matter (DOM) contains thousands of molecules and is key for biogeochemical cycles in aquatic and terrestrial ecosystems by interacting with microbes. Over the last decade, the study of DOM has been advanced and accelerated with the developments of instrumental and statistical approaches. However, it is still challenging in statistical analyses, data visualization, and theoretical interpretations largely due to the complexity of molecular composition and underlying ecological mechanisms. In this study, we developed an R package <i>iDOM</i> with functions for the basic and advanced statistical analyses and the visualization of DOM derived from Fourier transform ion cyclotron resonance mass spectrometer (FT-ICR MS). The package could handle various data types of DOM, including molecular compositional data, molecular traits, and uncharacterized molecules (i.e., dark matter). It could integrate explanatory data, such as environmental and microbial data, to explore the relationships between DOM and abiotic or biotic drivers. To illustrate its use, we presented case studies with an example dataset of DOM and microbial communities under experimental warming. We included case studies of basic functions for the calculation of molecular traits, the assignment of molecular classes, and the compositional analyses of chemical diversity and dissimilarity. We further showed the case studies with advanced functions to quantify DOM assembly processes, assess the effects of dark matter on molecular interactions, analyze the ecological networks between DOM and microbes, and explore their response to warming. The source code and example dataset of <i>iDOM</i> are publicly available on https://github.com/jianjunwang/iDOM. We expect that <i>iDOM</i> will serve as a comprehensive pipeline for DOM statistical analyses and bridge the gap between chemical characterization and ecological interpretation in a theoretical framework.</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 3","pages":"319-331"},"PeriodicalIF":6.7,"publicationDate":"2025-04-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12207904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546681","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}
引用次数: 0
Correction to "High-efficiency genome editing of an extreme thermophile Thermus thermophilus using endogenous type I and type III CRISPR-Cas systems". 更正“使用内源性I型和III型CRISPR-Cas系统高效编辑极端嗜热嗜热菌的基因组”。
IF 4.5
mLife Pub Date : 2025-04-04 eCollection Date: 2025-08-01 DOI: 10.1002/mlf2.70010
{"title":"Correction to \"High-efficiency genome editing of an extreme thermophile <i>Thermus thermophilus</i> using endogenous type I and type III CRISPR-Cas systems\".","authors":"","doi":"10.1002/mlf2.70010","DOIUrl":"10.1002/mlf2.70010","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1002/mlf2.12045.].</p>","PeriodicalId":94145,"journal":{"name":"mLife","volume":"4 4","pages":"470"},"PeriodicalIF":4.5,"publicationDate":"2025-04-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12396201/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144984329","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}
引用次数: 0
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