Archives of Microbiology最新文献

{"title":"Machine learning models for predicting cerebrospinal fluid bacterial culture outcomes in post-neurosurgical meningitis-development and temporal three-year validation","authors":"Guanghui Zheng,&nbsp;Shanbo Zhao,&nbsp;Donghua Mi,&nbsp;Haotian Hou,&nbsp;Yijun Shi,&nbsp;Jialu Sun,&nbsp;Cheng Peng,&nbsp;Zixuan Zhang,&nbsp;Chuyang Ye,&nbsp;Meihui Zhang,&nbsp;Guojun Zhang","doi":"10.1007/s00203-026-05196-8","DOIUrl":"10.1007/s00203-026-05196-8","url":null,"abstract":"<div><p>Post-neurosurgical bacterial meningitis (PNBM) is a serious complication associated with substantial morbidity and mortality. Bacterial culture presently serves as the gold standard for diagnosis, however, clinical reliance on third-tier reports to address empirical antibiotic concerns, with a turnaround time of 3–5 days, can lead to imprecise antibiotic administration in patients. Therefore, we develop and validate a branch of machine learning method to predict the result of cerebrospinal fluid (CSF) culture, which can shorten the time for precise diagnosis to within 2 h. A cohort study was conducted in nonmaternity inpatient units at Beijing Tiantan Hospital &amp; Capital Medical University during Jan 2016 to Dec 2020. Six machine learning models including 4 decision tree models(Random Forest, Catboost, LightGBM, and XGboost), Support Vector Classification(SVC) and Multi-Layer Perceptron(MLP) were applied for two models construction by utilizing tenfold cross-validation.The performances of these models were assessed in terms of discrimination, calibration, and clinical application in another 3 years cohort. In this study, the derivation cohort included 4014 patients, of whom 995 had positive CSF cultures, including 431 Gram-negative and 564 Gram-positive cultures, and 3019 had negative cultures. The temporal validation cohort included 1059 patients. LightGBM achieved the highest the area under the receiver operating characteristic curve (AUC) for Model 1 and Model 2, at 0.898 and 0.875, respectively. SHapley Additive exPlanations (SHAP) analysis identified CSF leukocyte(C-Leu) count as the leading predictor of culture positivity and Gram-negative cultures, whereas platelet count was the principal contributor to Gram-positive culture classification. Machine learning, specifically leveraging LightGBM modeling showed good discrimination in predicting CSF bacterial culture outcomes after neurosurgery. The model may support early risk stratification while culture results are pending.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035346","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Identification of a novel linear B-cell epitope in the N-terminus of varicella-zoster virus glycoprotein B","authors":"Yumei Chen,&nbsp;Mengru Yang,&nbsp;Hongliang Liu,&nbsp;Enping Liu,&nbsp;Jingming Zhou,&nbsp;Xifang Zhu,&nbsp;Sixuan Wu,&nbsp;Yanhua Qi,&nbsp;Aiping Wang","doi":"10.1007/s00203-026-05013-2","DOIUrl":"10.1007/s00203-026-05013-2","url":null,"abstract":"<div><p>Varicella-zoster virus (VZV), a highly contagious human alphaherpesvirus, imposes a substantial economic burden on global healthcare systems. Glycoprotein B (gB), a central fusogen mediating viral entry and cell-cell fusion, represents a promising target for developing VZV vaccines and diagnostic reagents. This study aimed to systematically characterize the antigenicity of VZV gB and map novel linear epitopes to facilitate the development of targeted diagnostics. Methodologically, recombinant glycoprotein B was successfully expressed in a eukaryotic expression system and subsequently purified using nickel-affinity chromatography, and its antigenicity was confirmed with VZV-positive convalescent human serum. Six monoclonal antibodies (mAbs 3B9, 4D2, 5E2, 6G7, 8C9 and 10F11) specifically targeting gB were generated via hybridoma technology. Subsequently, three rounds of progressive truncation using a peptide-overlapping approach and alanine scanning mutagenesis, were employed to precisely identify the antibody binding sites. The results demonstrated that several generated mAbs, particularly the primary detection candidate mAb 6G7, exhibited high titers (up to 1:1024,000) and strong binding affinity (Ka ≈ 7.89 × 10⁸). Crucially, we identified a novel linear B-cell epitope, ⁹⁷LGDGDEIR¹⁰⁴, located within the flexible N-terminal region of gB, which was critical for antibody binding. This epitope lies proximal to previously reported functional motifs involved in membrane fusion. In conclusion, our findings reveal a new antigenic site on VZV gB, providing a robust experimental foundation for the development of epitope-specific serological assays and vaccine strategies.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Alkaliphilic microbial cellulases: sources, structural insights, and bioengineering approaches for industrial applications","authors":"Ayushi Srivastav,&nbsp;Shiv Shankar,&nbsp;Pardeep Kaur,&nbsp;Soham Dutta,&nbsp;Abdulhadi Yakubu,&nbsp;Gurkanwal Kaur,&nbsp;Ashish Vyas,&nbsp;Nisha Gaur","doi":"10.1007/s00203-026-05227-4","DOIUrl":"10.1007/s00203-026-05227-4","url":null,"abstract":"<div><p>As the biofuel/biorefinery/green economy advances quickly, the need for durable cellulases to operate under varying conditions in the industrial sector has increased. A specific type of cellulase that has emerged from this demand is alkaliphilic cellulase (ALKC). Due to their stability and high catalytic activity at elevated pH ranges (e.g., pH 8–11), ALKCs are being developed as biocatalysts for alkaline pretreatment and other harsh, high-pH industrial processes.The purpose of this review is to provide an updated overview of ALKCs focusing on their microbial origins, structural characteristics, and modes of action; it will summarize how ALKCs can be used in numerous applications including: the conversion of lignocellulosic biomass into biofuels; pulp and paper production; formulation of laundry detergents; textile bioprocessing; and waste management. Integrating ALKCs into modern biorefineries will be beneficial to society by decreasing the overall amount of chemicals needed in a bioprocess (and their associated costs), reducing water usage, and increasing the efficiency of the process. Significant advances in enzyme engineering, synthetic biology, and designer cellulosomes have all contributed to the enhanced catalytic performance, stability, and substrate specificity of ALKCs. Despite the benefits that would result from their use, there remain significant impediments to the large-scale application of ALKCs; their long-term stability, incompatibility with conventional fermentation systems, and lack of standardised methods for measuring activity are among these barriers. In order for ALKCs to be employed at industrial levels and used to their full potential in sustainable bioprocessing, these identified constraints will require resolution.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Editorial Expression of Concern: Impact of polystyrene microplastics on major marine primary (phytoplankton) and secondary producers (copepod)","authors":"P. Raju,&nbsp;P. Santhanam,&nbsp;S. Sonai Pandian,&nbsp;M. Divya,&nbsp;A. Arunkrishnan,&nbsp;K. Nanthini Devi,&nbsp;S. Ananth,&nbsp;J. Roopavathy,&nbsp;P. Perumal","doi":"10.1007/s00203-026-05201-0","DOIUrl":"10.1007/s00203-026-05201-0","url":null,"abstract":"","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149035107","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteriophage-bacteria coevolution: from molecular arms races to ecological and applied perspectives","authors":"Junjie Shang,&nbsp;Linghui Li,&nbsp;Chengqian Dong,&nbsp;Yunlin Wei","doi":"10.1007/s00203-026-05221-w","DOIUrl":"10.1007/s00203-026-05221-w","url":null,"abstract":"<div><p>Bacteriophages are the most abundant biological entities, driving bacterial evolution through long-term coevolution. Bacteria have evolved diverse defense strategies against phage, including receptor modification, restriction-modification systems, CRISPR-Cas, abortive infection systems, and newly discovered systems such as BREX, DISARM, CBASS, Thoeris, and Zorya. In response, phages deploy countermeasures such as receptor-binding diversification, anti-CRISPR proteins, DNA modification, and inhibitors targeting host immunity. These interactions generate distinct evolutionary dynamics–arms race and fluctuating selection–shaping microbial population structure and ecological stability. Phage-host coevolution promotes microbial diversity, horizontal gene transfer, and regulates community composition across ecosystems. Understanding these processes is critical for applications like phage therapy, microbiome engineering, and biotechnology. This review summarizes molecular mechanisms of bacterial defense and phage counter-defense, discusses coevolutionary models, highlights ecological and applied implications, and outlines future research directions.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Unlocking the hidden potential of the genus Salvia through a systematic review of endophytic bacterial and fungal diversity and biotechnological prospects","authors":"Mouliraj Palanisamy,&nbsp;Laxman Thalavaipandian,&nbsp;Divya Selvaraj,&nbsp;Kiruba Rajamani,&nbsp;Olubukola Oluranti Babalola,&nbsp;Sathishkumar Ramalingam","doi":"10.1007/s00203-026-05222-9","DOIUrl":"10.1007/s00203-026-05222-9","url":null,"abstract":"<div><p>The genus <i>Salvia</i> is one of the largest and the most pharmacologically important genera within the family Lamiaceae, which is known for its rich diversity of bioactive compounds, including phenolics and terpenoids. Recent studies have shown that endophytic fungi and bacteria associated with <i>Salvia</i> play important roles in plant growth, development, and chemical composition, which in turn contribute to species adaptability. This review presents a comprehensive, PRISMA-guided systematic review that emphasises the diversity and biotechnological potential of these endophytes. Available evidence indicates that although <i>Salvia</i>-associated endophytes have been widely studied, most research has focused on a single species, namely <i>Salvia miltiorrhiza</i>, with comparatively limited attention to other species and their associated endophytic communities. This review compiles comprehensive, current knowledge on endophyte diversity, tissue-specific distribution, and ecological roles, along with their biotechnological applications related to plant growth promotion, stress tolerance, biocontrol activity, and the production of bioactive compounds. It also highlights the role of endophytes in enhancing host secondary metabolite accumulation, with appropriate citations. Despite significant advances, gaps remain in understanding endophyte diversity across different <i>Salvia</i> species and in linking microbial functions to host-associated metabolic outcomes. This review identifies key knowledge gaps and outlines future directions to advance our understanding of plant-endophyte interactions and to support their effective application in sustainable agriculture and biotechnology.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Advances in erythritol production through synthetic biology and systems metabolic engineering","authors":"Yan Zhang,&nbsp;Shuo Xia,&nbsp;Yuefan Zhang,&nbsp;Jung-Kul Lee,&nbsp;Vipin Chandra Kalia,&nbsp;Hongtao Bi,&nbsp;Chunjie Gong","doi":"10.1007/s00203-026-05219-4","DOIUrl":"10.1007/s00203-026-05219-4","url":null,"abstract":"<div><p>Synthetic biology has delivered a toolkit for erythritol production, yet a metabolic trade-off persists: strict dependence on pentose phosphate flux and NADPH regeneration pits product synthesis against cell growth and stress adaptation, rendering most engineering interventions unable to break the yield–productivity trade-off. This Review frames erythritol biomanufacturing within a hierarchical constraint cascade, tracing the progression from native strain optimization through synthetic biology-driven pathway rewiring, cofactor balancing, modular design, to AI-integrated design-build-test-learn (DBTL) cycles. Carbon precursor supply sets the flux ceiling, cofactor availability modulates conversion, and scale-dependent heterogeneities in mixing and feedstocks widen the gap between laboratory design and industrial operation. Comparison with other rare sugars (allulose, tagatose) reveals erythritol’s unique challenges: deep pathway embedding and high reducing-power demand. While accelerating enzyme engineering, metabolic modelling and process control, current AI applications are most likely to succeed when coupled with mechanism-based, cross-scale models, rather than merely statistical fits. The next breakthrough lies in closing the loop between real-time sensing and adaptive flux regulation. This vision could be realized through integrated biomanufacturing platforms that combine mechanistic modeling, automated DBTL cycles, and cell-free systems where cellular constraints prove limiting. This Review offers a unified, scale-spanning framework for diagnosing systemic bottlenecks in erythritol biosynthesis and outlines principles for intelligent biomanufacturing of sugar alcohols.</p><h3>Graphical abstract</h3><div><figure><div><div><picture><source><img></source></picture></div></div></figure></div></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015375","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Contrasting regulation of the ecp common pilus operon in Citrobacter rodentium: essential roles of a distal element and IHF even in the absence of H-NS","authors":"María I. Isidro-Coxca,&nbsp;Verónica I. Martínez-Santos,&nbsp;Andrés Escalera-Maurer,&nbsp;José L. Puente","doi":"10.1007/s00203-026-05216-7","DOIUrl":"10.1007/s00203-026-05216-7","url":null,"abstract":"<div><p>The <i>Escherichia coli</i> common pilus (ECP) is a chaperone–usher pilus widely distributed in <i>E. coli</i> and other enterobacteria, where it mediates adhesion, biofilm formation, and colonization. <i>Citrobacter rodentium</i>, a surrogate model for the human attaching-and-effacing pathogens enteropathogenic and enterohemorrhagic <i>E. coli</i>, contains a conserved <i>ecp</i> operon (<i>Cr</i>-<i>ecp</i>) whose regulation has substantially diverged from <i>E. coli</i>. <i>Cr-ecp</i> expression is induced under static DMEM growth at temperatures below 37 °C, driven by a σ⁷⁰-dependent promoter embedded in a regulatory region of approximately 410 bp. We identified an essential distal regulatory element (DRE) between positions − 378 and − 359 relative to the transcription start site, with a 10-bp core required for promoter activity. In contrast to the EcpR-dependent model in <i>E. coli</i>, the <i>ecpR</i> ortholog is dispensable under the conditions tested. The nucleoid-associated proteins IHF and H-NS bind the regulatory region; IHF is strictly required for activation even when H-NS is absent. These findings define a regulatory architecture distinct from <i>E. coli ecp</i>.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13593695/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015463","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Deep learning-driven de novo discovery of binders targeting the transmembrane domain of BamA","authors":"Minghui Du,&nbsp;Yuqiao Xin,&nbsp;Benao Xu,&nbsp;Yang Zhang,&nbsp;Linjie Han,&nbsp;Bingjie Ji,&nbsp;Jian Zhao,&nbsp;Yongshan Zhao","doi":"10.1007/s00203-026-05218-5","DOIUrl":"10.1007/s00203-026-05218-5","url":null,"abstract":"<div><p>Antimicrobial resistance (AMR) is an escalating global health threat, with multidrug-resistant Gram-negative bacteria presenting a particularly serious clinical challenge. The unique outer membrane (OM) structure serves as a natural barrier against conventional therapeutics, so that treatment strategies become more complicated. Notably, drug development aimed at the transmembrane (TM) domains of membrane proteins remains highly limited. To overcome this bottleneck, we established an artificial intelligence (AI)-driven framework for the design and screening of BamA transmembrane (TM) domain-targeting binders. This framework employs a multi-channel convolutional neural network (DeepTM-Bind), which integrates heterogeneous protein features to achieve high predictive accuracy. Building upon this foundation, we further developed a multidimensional evaluation system to guide <i>de novo</i> design strategies. Using this integrated approach, binders targeting the lateral gate of BamA were successfully generated. All-atom molecular dynamics (MD) simulations within a membrane environment, combined with multiscale mechanistic analyses, confirmed the structural stability and strong binding potential of the candidate molecules, and revealed a previously unrecognized binding mode. Collectively, this study introduces an advanced computational paradigm for therapeutic design targeting TM domains and provides a promising strategy to combat multidrug-resistant Gram-negative pathogens.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015472","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Biodegradation characteristics and mechanism of citrinin by Rhodotorula mucilaginosa LWJJ06 from metabolomic and transcriptomic perspectives","authors":"Jiayin Sun,&nbsp;Yuji Ruan,&nbsp;Yuqing Liang,&nbsp;Kexin Gao,&nbsp;Chun Yang,&nbsp;Shaobo Tan,&nbsp;Yuexin Luo,&nbsp;Lingyun Zhang,&nbsp;Zhusheng Liu,&nbsp;Haiyun Li","doi":"10.1007/s00203-026-05208-7","DOIUrl":"10.1007/s00203-026-05208-7","url":null,"abstract":"<div><p>Liupao tea, a type of dark tea produced through pile fermentation, is susceptible to contamination by mycotoxin citrinin (CIT), posing significant health risks due to its nephrotoxic and hepatotoxic properties. In this study, <i>Rhodotorula mucilaginosa</i> LWJJ06, isolated from Liupao tea fermentation samples, completely degraded 10~ 100 µg/mL of CIT within 48 h under optimized conditions (28 °C, pH: 4.0, inoculum size: 1 × 10⁷ CFU/mL). Metabolomic and transcriptomic analyses suggested that extensive metabolic adjustments accompanied CIT degradation, including apparent reallocation of energy resources, responses indicative of oxidative stress, and changes in membrane lipid profiles potentially linked to toxin transport. Two key degradation products, dihydrocitrinin and dihydrocitrinone, were tentatively identified, and the degradation pathway was preliminarily elucidated with reduced cytotoxicity confirmed. The cell counting kit-8 cytotoxicity assay demonstrated that the degradation products were significantly less toxic to alpha mouse liver 12 cells than CIT. These findings highlighted the potential of <i>Rhodotorula mucilaginosa</i> LWJJ06 as a probiotic agent for mycotoxin mitigation in food systems, offering a sustainable strategy and theoretical basis for controlling mycotoxin in Liupao tea.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"208 12","pages":""},"PeriodicalIF":3.4,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149015487","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}