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A comprehensive review of advanced strategies to combat antimicrobial resistance 全面审查抗微生物药物耐药性的先进战略。
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-26 DOI: 10.1007/s00203-025-04464-3
Bikramaditya Behera, Rajrattan Singh, Komal Sharma, Ansh Rai, Shreya Singh, Biji Balan
{"title":"A comprehensive review of advanced strategies to combat antimicrobial resistance","authors":"Bikramaditya Behera,&nbsp;Rajrattan Singh,&nbsp;Komal Sharma,&nbsp;Ansh Rai,&nbsp;Shreya Singh,&nbsp;Biji Balan","doi":"10.1007/s00203-025-04464-3","DOIUrl":"10.1007/s00203-025-04464-3","url":null,"abstract":"<div><p>Antimicrobial Resistance (AMR) is a growing global issue, as many first-line antibiotics are becoming less effective due to their overuse and misuse. Recent advances in novel antibiotic derivatives reveal mechanisms designed to counteract AMR. Even though conventional antimicrobial therapy has failed, no new antibiotic class has been developed in the past decade. Consequently, various innovative alternative tactics have been discovered to counteract drug-resistant pathogens. The article reviews novel approaches in combating AMR, which include antimicrobial peptides, phage therapy, CRISPR-Cas gene editing, nanomaterial-based antimicrobials, immunomodulatory agents, innovative physicochemical strategies, and combination therapy. Collectively, these approaches utilize cutting edge technologies that mark a shift from the traditional paradigm of antibiotics to integrated next-generation therapeutics. AMR remains a serious issue despite all of the noted advancements, and hence, a collaborative and multidisciplinary action involving researchers, healthcare professionals, policymakers, and pharmaceutical sector is urgently required. The emergence and burden of AMR can be better tackled by inventiveness, cooperation, and proactive approaches.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147445","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}
引用次数: 0
Progress and perspectives on microbial dye remediation: enzymatic pathways, microbial diversity, and hybrid microbial-based technologies 微生物染料修复的进展与展望:酶途径、微生物多样性和混合微生物技术。
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-26 DOI: 10.1007/s00203-025-04477-y
Sreedeep Dey, Barnali Mandal
{"title":"Progress and perspectives on microbial dye remediation: enzymatic pathways, microbial diversity, and hybrid microbial-based technologies","authors":"Sreedeep Dey,&nbsp;Barnali Mandal","doi":"10.1007/s00203-025-04477-y","DOIUrl":"10.1007/s00203-025-04477-y","url":null,"abstract":"<div>\u0000 \u0000 <p>Synthetic dyes are extensively used in the textile industry and related industries. These structurally stable dyes persist in aquatic systems and cause severe ecotoxicological and human health risks. Widely applied conventional physicochemical treatments are constrained by high costs, sludge production, and incomplete mineralization. This review emphasizes the microbial diversity (i.e., fungi, bacteria, yeast, algae, and consortia) and enzymatic (azoreductase, laccases, peroxidase, etc.) machinery responsible for the reductive and oxidative transformation of recalcitrant dyes. Accessible plate and spectrophotometric assays are some enzymatic identification methods that have been discussed alongside some scalable production strategies (i.e., immobilization, fed-batch, and continuous systems). Upstream resource demand has been highlighted in sustainability assessments, but reduced sludge, less chemical input, and energy recovery revealed downstream gains. Furthermore, compared with conventional adsorbents, hybrid microbial technologies have demonstrated a broader substrate range and technoeconomic competitiveness. While, under optimized laboratory conditions, 80–100% decolorization could be achieved, scaling up to real wastewater matrices, maintaining the stability of microbial consortia, and ensuring the biosafety of nanomaterials are some persistent challenge. Future studies should include long-term pilot trials, omics-assisted microbial design, multispecies microcosm studies, and biomass valorization.</p>\u0000 </div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145147456","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}
引用次数: 0
Physiological and genomic insights into Bacillus sp. BRTN from Baratang mud volcano with emphasis on SUF system proteins Baratang泥火山芽孢杆菌sp. BRTN的生理和基因组分析,重点研究SUF系统蛋白。
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-25 DOI: 10.1007/s00203-025-04480-3
Karuna Soren, Dibyendu Khan, Ashutosh Kabiraj, Urmi Halder, Moitri Let, Annapurna Chitikineni, Rajeev K. Varshney, Aparna Banerjee, Rajib Bandopadhyay
{"title":"Physiological and genomic insights into Bacillus sp. BRTN from Baratang mud volcano with emphasis on SUF system proteins","authors":"Karuna Soren,&nbsp;Dibyendu Khan,&nbsp;Ashutosh Kabiraj,&nbsp;Urmi Halder,&nbsp;Moitri Let,&nbsp;Annapurna Chitikineni,&nbsp;Rajeev K. Varshney,&nbsp;Aparna Banerjee,&nbsp;Rajib Bandopadhyay","doi":"10.1007/s00203-025-04480-3","DOIUrl":"10.1007/s00203-025-04480-3","url":null,"abstract":"<div><p>Bacterial genome analysis provides valuable insights into the identification of potential biomolecules for diverse biotechnological and therapeutic applications. Particularly, bacteria isolated from extreme environments such as mud volcanoes possess unique physiological and genetic traits that may offer novel opportunities for both in vitro studies and in silico drug target discovery. In this study, a total of 10 bacteria were isolated from Baratang mud volcano, located in Andaman and Nicobar Islands of India; of which strain BRTN was selected for further study based on its best ferrous sulfate (FeSO<sub>4</sub> MTC value 600 mg L<sup>−1</sup>) tolerance capability and antibiotic sensitivity profile (resistant to Gentamycin, Streptomycin, Ceftriaxone, and Sulphatriad). Optimum growth of BRTN was found at pH 8.0 and it could tolerate up to 16% NaCl. The whole genome sequencing, assembly, and annotation identified that BRTN had the most proximity with <i>Bacillus</i> genera. The bacterium was associated with 3.35 Mb genome with 35.9% of GC content and harbored 3514 genes. Genome analysis revealed that Sulfur Utilization Factor (SUF) proteins was present in the accessory genome. Genome analyses confirmed the presence of <i>SufB</i>, <i>SufC</i>, <i>SufD</i>, <i>SufE2</i>, etc. SUF genes (non-homologous to human genome) that could be considered as potent targets to develop antimicrobial compounds. Furthermore, in silico analysis including homology modeling and receptor-ligand docking were carried out to characterize the selected SUF proteins and to assess their potentiality for functional inhibition by candidate ligands. Among all interactions, SufD showed best Vina score (−14.0) when it interacted with ChEMBL3921511, suggesting SufD protein as a potential drug target. Thus, the SUF system genes identified in this study may serve as promising targets for the development of novel antibacterial therapies.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145136294","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}
引用次数: 0
Novel antimicrobial peptide HFIAP-1 mutant as a β-lactamase inhibitor against extended-spectrum β-lactamases of Escherichia coli: a comprehensive in-silico approach 新型抗菌肽HFIAP-1突变体作为抗大肠杆菌扩展谱β-内酰胺酶的β-内酰胺酶抑制剂:一种综合的计算机方法。
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-24 DOI: 10.1007/s00203-025-04483-0
Elizabeth Annie George, Aniket Naha, Sudha Ramaiah
{"title":"Novel antimicrobial peptide HFIAP-1 mutant as a β-lactamase inhibitor against extended-spectrum β-lactamases of Escherichia coli: a comprehensive in-silico approach","authors":"Elizabeth Annie George,&nbsp;Aniket Naha,&nbsp;Sudha Ramaiah","doi":"10.1007/s00203-025-04483-0","DOIUrl":"10.1007/s00203-025-04483-0","url":null,"abstract":"<div><p>Extended-spectrum β-lactamases in <i>Escherichia coli</i> poses a significant threat for clinicians in tertiary healthcare settings, rendering treatments ineffective with newer β-lactam-β-lactamase inhibitors combinations. To overcome this, the present study was conducted to potential β-lactamase inhibitors, from a library of antimicrobial peptide mutants with enhanced antibacterial potency (~ 7–16%) as compared to their parent peptides. The study screened five peptides and their mutants based on physicochemical, pharmaco-immunogenic properties through comprehensive knowledge-based and machine-learning algorithms. Molecular docking analyses revealed HFIAP-1_M5 (L33K-W7C-N34C) as the potential inhibitor candidate, that predicted to inhibit ~ 82% of all the studied ESβLs (Class A–D) targets as analysed from the intermolecular interaction profiling. HFIAP-1_M5 exhibited enhanced binding affinities (~ 0.2–12.0%) than the parent peptides upon forming hydrogen bonds, van-der Waals interactions and salt bridges with crucial residues concerning the catalytic domains of class A [InterPro ID: IPR045155], class B [InterPro ID: IPR001279], class C [InterPro ID: IPR001466] and class D [InterPro ID: IPR001460] of β-lactamases as defined in the InterPro database. All-atom molecular dynamics simulations, supported by principal component analysis and free energy landscape analysis, confirmed the stability of ESβLs-HFIAP-1_M5 showing stable backbone profiles with minimal residue-level fluctuations throughout the simulation timeframe. Binding free energy calculations along with the energy decomposition analysis further highlighted the key residue contributions to complex stabilization. The study holds promise in developing a combination therapy upon augmenting HFIAP-1_M5 with susceptible β-lactam antibiotics to enhance the therapeutic spectrum of treatment after further experimental validations.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145129852","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}
引用次数: 0
Genomic and structural insights into cazymes & novel AA10 lytic polysaccharide mono-oxygenase from Serratia marcescens CRi_33 for efficient lignocellulosic biomass deconstruction 酶的基因组和结构见解&来自粘质沙雷氏菌CRi_33的新型AA10裂解多糖单加氧酶,用于有效的木质纤维素生物质解构
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-23 DOI: 10.1007/s00203-025-04478-x
Chetana Akhand, Rashi Bamrotwar, Sejal Bhairam, Riddhi Singh, Nishant A. Dafale
{"title":"Genomic and structural insights into cazymes & novel AA10 lytic polysaccharide mono-oxygenase from Serratia marcescens CRi_33 for efficient lignocellulosic biomass deconstruction","authors":"Chetana Akhand,&nbsp;Rashi Bamrotwar,&nbsp;Sejal Bhairam,&nbsp;Riddhi Singh,&nbsp;Nishant A. Dafale","doi":"10.1007/s00203-025-04478-x","DOIUrl":"10.1007/s00203-025-04478-x","url":null,"abstract":"<div><p>Lignocellulosic biomass (LCB) saccharification remains a key challenge for cost-effective value-added products due to structural intricacy. Lytic polysaccharide mono-oxygenase (LPMOs) catalyses the glycosidic bonds cleavage oxidatively in crystalline polysaccharides, facilitating synergistic action with glycoside hydrolases (GHs). While fungal and actinobacterial LPMOs are well studied, bacterial LPMOs, especially in Gram-negative <i>Serratia</i>, are underexplored. The study investigates <i>Serratia marcescens</i> CRi_33 for its LCB deconstruction potential through enzymatic and genomic analyses. The strain exhibited elevated β-glucuronidase activity of 0.54 U/mL, endo-1,4-β-xylanase of 0.41 U/mL, and arabinosidase of 0.48 U/mL, reflecting strong hemicellulolytic potential. CRi_33-derived enzyme concentrate with biotin and cellobiose supplementation, released 152.04 mg/g of reducing sugars from pre-treated wheat straw (WS). FeCl₃ supplementation further enhanced saccharification to 165.04 ± 3.44 mg/g, resulting in an 8.55% increase. Genome analysis revealed 239 CAZymes, including 120 GHs and 11 auxiliary activity enzymes like laccases (AA1), lignin peroxidases (AA2), and benzoquinone reductases (AA6). Notably, a unique AA10 family LPMO, <i>Smr</i>LPMO10A, possessing a GlcNAc-binding domain, was structurally characterized. Structural modeling confirmed a conserved histidine brace, and docking studies showed strong binding affinity of -5.1 kcal/mol to hemicellulosic sugars, particularly galactose and mannose. This suggests dual specificity for chitin and hemicellulose, which is limited and less explored previously in <i>Serratia</i> LPMOs. These findings fill a critical gap in bacterial LPMO knowledge and highlights <i>S. marcescens</i> CRi_33’s efficiency for sustainable waste valorization and biorefinery applications.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145110654","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}
引用次数: 0
Phenotypic, secondary metabolite, and genomic characterization of Bacillus siamensis B03 from brackish water with Anti‑Vibrio potential 具有抗弧菌潜能的苦咸水暹芽孢杆菌B03的表型、次生代谢物和基因组特征
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-23 DOI: 10.1007/s00203-025-04484-z
Co Thi Kim Nguyen, Phuc Giang Hong Lam, Ngoc Thi Thuy Dang, Suong Ngoc Le, Ty Viet Pham, Nam Vo, Hung Tan Dinh, Oanh Viet Kieu Nguyen, Hoang Duc Nguyen
{"title":"Phenotypic, secondary metabolite, and genomic characterization of Bacillus siamensis B03 from brackish water with Anti‑Vibrio potential","authors":"Co Thi Kim Nguyen,&nbsp;Phuc Giang Hong Lam,&nbsp;Ngoc Thi Thuy Dang,&nbsp;Suong Ngoc Le,&nbsp;Ty Viet Pham,&nbsp;Nam Vo,&nbsp;Hung Tan Dinh,&nbsp;Oanh Viet Kieu Nguyen,&nbsp;Hoang Duc Nguyen","doi":"10.1007/s00203-025-04484-z","DOIUrl":"10.1007/s00203-025-04484-z","url":null,"abstract":"<div><p>This study aimed to provide the first genomic, functional, and metabolic characterization of <i>Bacillus siamensis</i> B03 from Lang Co Bay, Vietnam, and to evaluate the hypothesis that it harbors unique metabolic traits and antimicrobial potential against <i>Vibrio</i> spp.. B03 showed no hemolytic activity, moderate biofilm formation, tolerance to 10% NaCl, and broad extracellular enzyme secretion. Ethyl acetate extracts from the cell-free supernatant exhibited in vitro antibacterial activity against five <i>Vibrio</i> species, with inhibition zones of 14.7–22.3 mm. Metabolomic analysis tentatively identified 20 compounds, mainly cyclic dipeptides, some previously reported to possess antimicrobial properties. Draft, plasmid-free genome (3,745,205 bp; 46.4% GC) encodes 3,561 proteins and 72 tRNAs, with genes mainly for amino acid and carbohydrate metabolism, and contains gene clusters for bacillaene, fengycin, difficidin, bacillibactin (100% similarity), and surfactin (78%). Pan-genome analysis of 24 <i>B. siamensis</i> genomes revealed 2,254 core genes, with B03 contributing 31 unique genes, including those encoding NAD-dependent malic enzyme and adenylation domain proteins. These findings suggest <i>B. siamensis</i> B03 as a potential control agent against <i>Vibrio</i> pathogens.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145110451","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}
引用次数: 0
E2 ubiquitin-conjugating enzyme Ubc11 regulates Rst2 protein stability in the fission yeast Schizosaccharomyces pombe E2泛素偶联酶Ubc11调控裂糖酵母Rst2蛋白稳定性
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-22 DOI: 10.1007/s00203-025-04485-y
Ying Huang, Yasir Nawaz
{"title":"E2 ubiquitin-conjugating enzyme Ubc11 regulates Rst2 protein stability in the fission yeast Schizosaccharomyces pombe","authors":"Ying Huang,&nbsp;Yasir Nawaz","doi":"10.1007/s00203-025-04485-y","DOIUrl":"10.1007/s00203-025-04485-y","url":null,"abstract":"<div><p>In <i>Schizosaccharomyces pombe</i>, many transcription factors, including Rst2, remain poorly understood. Rst2 functions downstream of the cAMP-PKA pathway, but its protein stability and potential degradation via the ubiquitin-proteasome system, are not well characterized. This study investigates the -regulation of Rst2 in <i>S. pombe</i>, focusing on expression and degradation via the ubiquitin-proteasome system and E2 enzymes. Protein expression and stability were analyzed by western blotting to assess the impact of E2 mutations on Rst2 regulation. Rst2 transcription remained low at early time points but increased over fourfold by 24 h, remaining elevated through 48 h. Protein stability assays showed rapid Rst2 degradation under cycloheximide (CHX) treatment, while CHX and bortezomib (BZ) treatment preserved Rst2 protein levels, indicating the proteasome-dependent degradation of Rst2. To determine which E2 enzyme(s) are invovled in Rst2 degradation, we individually deleted all non-essential E2 genes and generated two point mutants <i>ubc4-P61S</i> and <i>ubc11-P93L</i> mutant and found that Rst2 is stabilized only in <i>ubc11-P93L</i>. This study shows the role of the ubiquitin-proteasome system and E2 enzyme Ubc11 in regulating Rst2 in <i>S</i>. <i>pombe</i>.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100744","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}
引用次数: 0
The AroC gene is required for pathogenicity and antibiotic sensitivity in Edwardsiella tarda strain ET13 迟发爱德华菌ET13的致病性和抗生素敏感性需要AroC基因
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-22 DOI: 10.1007/s00203-025-04482-1
Huda Ahmed Hassan, Yi Yang, Guoqiang Zhu
{"title":"The AroC gene is required for pathogenicity and antibiotic sensitivity in Edwardsiella tarda strain ET13","authors":"Huda Ahmed Hassan,&nbsp;Yi Yang,&nbsp;Guoqiang Zhu","doi":"10.1007/s00203-025-04482-1","DOIUrl":"10.1007/s00203-025-04482-1","url":null,"abstract":"<div><p><i>Edwardsiella tarda</i> (<i>E. tarda</i>) is a significant enteric pathogen responsible for causing diarrhea, wound infections, and fatal septicemia in humans, as well as various aquatic animals. To investigate the role of the <i>aroC</i> gene in <i>E. tarda’s</i> pathogenicity and antibiotic sensitivity, the <i>ΔaroC</i> mutant and <i>aroC</i><sup><i>+</i></sup> complemented strains of ET13 were constructed. Our in vitro experimental data showed that the ET13<i>ΔaroC</i> mutant failed to grow in Defined Minimal Medium (DMM) broth without aromatic amino acids and exhibited significantly reduced growth compared to the wild-type ET13WT and complemented ET13<i>aroC</i><sup><i>+</i></sup> when aromatic amino acids were supplemented. This indicates that the <i>aroC</i> gene is essential for the growth of <i>E. tarda</i> in the DMM medium. Notably, the ET13<i>ΔaroC</i> mutant displayed significantly reduced adhesion, invasion, and intracellular replication in Caco-2 cells compared to the ET13WT and ET13<i>aroC</i><sup><i>+</i></sup>. Furthermore, the ET13<i>ΔaroC</i> mutant exhibited a reduction in biofilm formation ability and increased sensitivity to antibiotics. The 50% lethal dose (LD<sub>50</sub>) of ET13<i>ΔaroC</i> increased to 4.8 × 10<sup>4</sup> CFU, representing a nearly 5-fold increase compared to ET13WT and ET13<i>aroC</i><sup><i>+</i></sup>. In addition, ET13<i>ΔaroC</i> exhibited reduced colonization in the kidney and spleen of Zebrafish. Notably, the impaired virulence phenotypes of ET13<i>ΔaroC</i> were observed even in nutrient-replete conditions (e.g., LB medium), indicating that these defects are not solely attributed to aromatic amino acid auxotrophy and instead point to a role of <i>aroC</i> beyond supporting bacterial growth. Collectively, our data demonstrate that the <i>aroC</i> gene is required for key virulence-associated phenotypes (adhesion, invasion, intracellular replication, and biofilm formation) and modulates antibiotic sensitivity in <i>E. tarda</i> strain ET13.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100741","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}
引用次数: 0
A predictive model developed to classify Leishmania promastigotes at two distinct life stages using MALDI-TOF mass spectrometry 利用MALDI-TOF质谱法建立了一个预测模型,对利什曼原虫在两个不同的生命阶段进行分类
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-22 DOI: 10.1007/s00203-025-04424-x
Sebastian Cubides-Cely, Betsy Muñoz Serrano, Enrique Mejía-Ospino, Patricia Escobar
{"title":"A predictive model developed to classify Leishmania promastigotes at two distinct life stages using MALDI-TOF mass spectrometry","authors":"Sebastian Cubides-Cely,&nbsp;Betsy Muñoz Serrano,&nbsp;Enrique Mejía-Ospino,&nbsp;Patricia Escobar","doi":"10.1007/s00203-025-04424-x","DOIUrl":"10.1007/s00203-025-04424-x","url":null,"abstract":"<div><p>Investigating the molecular differences between procyclic (non-infective) and metacyclic (infective) promastigotes is essential for understanding the <i>Leishmania</i> life cycle in the sandfly vector and may aid in identifying molecular markers specific to these parasite stages. MALDI-TOF MS, a robust mass spectrometry technique, identifies protein profiles by measuring their mass-to-charge (<i>m/z</i>) ratios. Machine learning (ML) aids in analysing, interpreting, and classifying the complex spectral dataset obtained. This research aims to develop a predictive model to classify procyclic and metacyclic stages based on their protein profiles obtained from MALDI-TOF MS spectra. Promastigotes from the two clones of <i>L. amazonensis</i>, previously typed by molecular approach, were cultured and collected on days 3 and 7 of growth at 27 °C. Our data included at least 10 biological replicates, each in triplicate, for each <i>L. amazonensis</i> clone. They were labelled as Clone1LB3D, Clone1LB7D, Clone2LP3D, and Clone2LP7D. Three supervised classification tools were utilised: support vector machine (SVM), artificial neural networks (ANN), and random forest (RF). The implementation was carried out using Python version 3.12. The predictor variables correspond to the intensities of the spectral signals of the parasites in the <i>m/z</i> ratio range of 600 to 9500. The SVM classifier achieved 100% accuracy, while ANN and RF achieved 95% and 85%, respectively. A confusion matrix confirmed the complete accuracy of SVM across clones and stages. For model robustness, we recommend conducting external validation using independent datasets, including those from different <i>L. amazonensis</i> clones and related <i>Leishmania</i> species, growth phases, and sample preparation methods.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145100743","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}
引用次数: 0
Cloning, expression, purification, and mutant construction of the chitinase PbCHI2 gene from Photobacterium sp. 光杆菌几丁质酶PbCHI2基因的克隆、表达、纯化及突变体的构建
IF 2.6 3区 生物学
Archives of Microbiology Pub Date : 2025-09-20 DOI: 10.1007/s00203-025-04474-1
Zhe Wang, Ziqi Zhao, Lin Pan, Yawen Zhang, Zhuo Guo, Weiye Yang, Liangshan Feng, Xiaohui Wang
{"title":"Cloning, expression, purification, and mutant construction of the chitinase PbCHI2 gene from Photobacterium sp.","authors":"Zhe Wang,&nbsp;Ziqi Zhao,&nbsp;Lin Pan,&nbsp;Yawen Zhang,&nbsp;Zhuo Guo,&nbsp;Weiye Yang,&nbsp;Liangshan Feng,&nbsp;Xiaohui Wang","doi":"10.1007/s00203-025-04474-1","DOIUrl":"10.1007/s00203-025-04474-1","url":null,"abstract":"<div><p>Chitin, the second most abundant biopolymer on Earth, exhibits broad application potential in medicine, cosmetics, and agriculture through its degradation products (chito-oligosaccharides). Here, we characterized a cold-adapted chitinase (PbCHI2) secreted by <i>Photobacterium</i> sp. LG-29 isolated from deep-sea sediments. The <i>PbCHI2</i> gene was cloned into an expression vector and heterologously expressed in <i>Escherichia coli</i> BL21(DE3), followed by protein structure prediction and molecular docking to identify key residues for mutagenesis. The enzyme showed optimal activity at 35 °C while retaining functionality at 4 °C, confirming its cold-adaptation. Notably, it maintained &gt; 60% activity at 60 °C (substrate: 4-MU-GlcNAc3) and &gt; 70% residual activity after 3 h at 45 °C, demonstrating remarkable thermostability. PbCHI2 exhibited pH-dependent activity, with peak performance at pH 8.0 and &gt; 70% activity at pH 11. Metal ion effects revealed Mn<sup>2+</sup>, Ca<sup>2+</sup>, and Mg<sup>2+</sup> as activators, whereas Fe<sup>2+/3+</sup>, Zn<sup>2+</sup>, Cu<sup>2+</sup>, and Cd<sup>2+</sup> acted as inhibitors. Surprisingly, urea, Sodium Dodecyl Sulfate (SDS), and Dithiothreitol (DTT) enhanced activity at specific concentrations. Site-directed mutagenesis within a 5Å radius of the active site yielded mutants with improved catalytic efficiency, validated by HPLC analysis of degradation products (primarily GlcNAc2 and GlcNAc), suggesting exochitinase and β-N-acetylglucosaminidase activities. Structural analysis classified PbCHI2 as a GH18 family chitinase, featuring a ChtBD3 domain and PKD domain(s). To our knowledge, this is the first comprehensive study on a chitinase from <i>Photobacterium</i> sp., providing insights into its cold-adaptation mechanism and laying a foundation for engineering industrially relevant chitinases.</p></div>","PeriodicalId":8279,"journal":{"name":"Archives of Microbiology","volume":"207 11","pages":""},"PeriodicalIF":2.6,"publicationDate":"2025-09-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145090325","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}
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